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Added a package for the MDAnalysis toolkit. (#3576)

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* Added a package for the MDAnalysis toolkit.

* Added the dependency on setuptools.

* Added the rest of the dependencies to the py-mdanalysis package.  Also
added the griddataformats and seaborn packages to satisfy requirements.

* Removed seaborn package since it has been recently added.

* Fixed flake8 error

* Removed inadvertent commits.

* Cleaned up reviewers feedback.
This commit is contained in:
Brian Van Essen
2017-04-10 19:02:32 -07:00
committed by Adam J. Stewart
parent 4627655704
commit 808e9b4649
4 changed files with 103 additions and 1 deletions
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var/spack/repos/builtin/packages/py-mdanalysis/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PyMdanalysis(PythonPackage):
"""MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation
packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and
Gromacs. (See the lists of supported trajectory formats and
topology formats.)"""
homepage = "http://www.mdanalysis.org"
url = "https://pypi.io/packages/source/M/MDAnalysis/MDAnalysis-0.15.0.tar.gz"
version('0.15.0', '19e5a8e6c2bfe85f6209d1d7a36e4f20')
variant('analysis', default=True,
description='Enable analysis packages: matplotlib, scipy, seaborn')
variant('amber', default=False,
description='Support AMBER netcdf format.')
depends_on('python@2.7:')
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.16:', type='build')
depends_on('py-numpy@1.5.0:', type=('build', 'run'))
depends_on('py-six@1.4.0:', type=('build', 'run'))
depends_on('py-biopython@1.59:', type=('build', 'run'))
depends_on('py-networkx@1.0:', type=('build', 'run'))
depends_on('py-griddataformats@0.3.2:', type=('build', 'run'))
depends_on('py-matplotlib', when='+analysis', type=('build', 'run'))
depends_on('py-scipy', when='+analysis', type=('build', 'run'))
depends_on('py-seaborn', when='+analysis', type=('build', 'run'))
depends_on('py-netcdf4@1.0:', when='+amber', type=('build', 'run'))
depends_on('hdf5', when='+amber', type=('run'))