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

* 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.

4 files changed, 103 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/elemental/package.py b/var/spack/repos/builtin/packages/elemental/package.py
index f1cc77c33c..24b5bf8d15 100644
--- a/var/spack/repos/builtin/packages/elemental/package.py
+++ b/var/spack/repos/builtin/packages/elemental/package.py
@@ -68,6 +68,7 @@ class Elemental(CMakePackage):
     # Hack to forward variant to openblas package
     # Allow Elemental to build internally when using 8-byte ints
     depends_on('openblas +openmp', when='+openmp_blas ~int64_blas')
+
     # Note that this forces us to use OpenBLAS until #1712 is fixed
     depends_on('lapack', when='~openmp_blas')
     depends_on('metis')
diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py
index f0355fb96d..38839c9bf0 100644
--- a/var/spack/repos/builtin/packages/lbann/package.py
+++ b/var/spack/repos/builtin/packages/lbann/package.py
@@ -46,7 +46,7 @@ class Lbann(CMakePackage):
     depends_on('cuda', when='+gpu')
     depends_on('mpi')
     depends_on('opencv@3.2.0', when='+opencv')
-    depends_on('protobuf@3.0.2')
+    depends_on('protobuf@3.0.2:')
 
     def build_type(self):
         if '+debug' in self.spec:
diff --git a/var/spack/repos/builtin/packages/py-griddataformats/package.py b/var/spack/repos/builtin/packages/py-griddataformats/package.py
new file mode 100644
index 0000000000..ee77959e96
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-griddataformats/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# 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 PyGriddataformats(PythonPackage):
+    """The gridDataFormats package provides classes to unify reading
+    and writing n-dimensional datasets. One can read grid data from
+    files, make them available as a Grid object, and write out the
+    data again."""
+
+    homepage = "http://www.mdanalysis.org/GridDataFormats"
+    url      = "https://pypi.io/packages/source/G/GridDataFormats/GridDataFormats-0.3.3.tar.gz"
+
+    version('0.3.3', '5c83d3bdd421eebcee10111942c5a21f')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.0.3:', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py
new file mode 100644
index 0000000000..9f96b04836
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# 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'))