Add abipy package and dependencies (#3352)

* Add abipy package and dependencies

* Add first official release of py-abipy

* Ignore files from dependencies during activation

var/spack/repos/builtin/packages/py-abipy/package.py

+##############################################################################
+# 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 PyAbipy(PythonPackage):
+    """Python package to automate ABINIT calculations and analyze
+    the results."""
+
+    homepage = "https://github.com/abinit/abipy"
+    url      = "https://pypi.io/packages/source/a/abipy/abipy-0.2.0.tar.gz"
+
+    version('0.2.0', 'af9bc5cf7d5ca1a56ff73e2a65c5bcbd')
+
+    variant('gui',     default=False, description='Build the GUI')
+    variant('ipython', default=False, description='Build IPython support')
+
+    extends('python', ignore='bin/(feff_.*|gaussian_analyzer|get_environment|html2text|nc3tonc4|nc4tonc3|ncinfo|pmg|pydii|tabulate|tqdm)')
+
+    depends_on('python@2.7:')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython',     type='build')
+
+    depends_on('py-six',                 type=('build', 'run'))
+    depends_on('py-prettytable',         type=('build', 'run'))
+    depends_on('py-tabulate',            type=('build', 'run'))
+    depends_on('py-apscheduler@2.1.0',   type=('build', 'run'))
+    depends_on('py-pydispatcher@2.0.5:', type=('build', 'run'))
+    depends_on('py-tqdm',                type=('build', 'run'))
+    depends_on('py-html2text',           type=('build', 'run'))
+    depends_on('py-pyyaml@3.11:',        type=('build', 'run'))
+    depends_on('py-pandas',              type=('build', 'run'))
+    depends_on('py-numpy@1.9:',          type=('build', 'run'))
+    depends_on('py-scipy@0.14:',         type=('build', 'run'))
+    depends_on('py-spglib',              type=('build', 'run'))
+    depends_on('py-pymatgen@4.7.2:',     type=('build', 'run'))
+    depends_on('py-netcdf4',             type=('build', 'run'))
+    depends_on('py-matplotlib@1.5:',     type=('build', 'run'))
+    depends_on('py-seaborn',             type=('build', 'run'))
+
+    depends_on('py-wxpython', type=('build', 'run'), when='+gui')
+    depends_on('py-wxmplot',  type=('build', 'run'), when='+gui')
+
+    depends_on('py-ipython',  type=('build', 'run'), when='+ipython')
+    depends_on('py-jupyter',  type=('build', 'run'), when='+ipython')
+    depends_on('py-nbformat', type=('build', 'run'), when='+ipython')
+
+    def build_args(self, spec, prefix):
+        args = []
+
+        if '+ipython' in spec:
+            args.append('--with-ipython')
+
+        return args

var/spack/repos/builtin/packages/py-apscheduler/package.py

+##############################################################################
+# 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 PyApscheduler(PythonPackage):
+    """In-process task scheduler with Cron-like capabilities."""
+
+    homepage = "https://github.com/agronholm/apscheduler"
+    url      = "https://pypi.io/packages/source/A/APScheduler/APScheduler-3.3.1.tar.gz"
+
+    version('3.3.1', '6342b3b78b41920a8aa54fd3cd4a299d')
+    version('2.1.0', 'b837d23822fc46651862dd2186ec361a')
+
+    depends_on('py-setuptools@0.7:', type='build')
+
+    depends_on('py-six@1.4.0:',   type=('build', 'run'))
+    depends_on('py-pytz',         type=('build', 'run'))
+    depends_on('py-tzlocal@1.2:', type=('build', 'run'))

var/spack/repos/builtin/packages/py-cdo/package.py

@@ -39,4 +39,4 @@ class PyCdo(PythonPackage):
 
     depends_on('py-setuptools', type='build')
     depends_on('py-scipy', type=('build', 'run'))
-    depends_on('py-netcdf', type=('build', 'run'))
+    depends_on('py-netcdf4', type=('build', 'run'))

var/spack/repos/builtin/packages/py-html2text/package.py

+##############################################################################
+# 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 PyHtml2text(PythonPackage):
+    """Turn HTML into equivalent Markdown-structured text."""
+
+    homepage = "https://github.com/Alir3z4/html2text/"
+    url      = "https://pypi.io/packages/source/h/html2text/html2text-2016.9.19.tar.gz"
+
+    version('2016.9.19', 'd6b07e32ed21f186496f012691e02dd5')
+
+    depends_on('py-setuptools', type='build')

var/spack/repos/builtin/packages/py-monty/package.py

+##############################################################################
+# 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 PyMonty(PythonPackage):
+    """Monty is the missing complement to Python."""
+
+    homepage = "https://github.com/materialsvirtuallab/monty"
+    url      = "https://pypi.io/packages/source/m/monty/monty-0.9.6.tar.gz"
+
+    version('0.9.6', '406ea69fdd112feacfdf208624d56903')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six',        type=('build', 'run'))

var/spack/repos/builtin/packages/py-netcdf4/package.py

+##############################################################################
+# 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 PyNetcdf4(PythonPackage):
+    """Python interface to the netCDF Library."""
+
+    homepage = "https://github.com/Unidata/netcdf4-python"
+    url      = "https://pypi.io/packages/source/n/netCDF4/netCDF4-1.2.7.tar.gz"
+
+    version('1.2.7',   '77b357d78f9658dd973dee901f6d86f8')
+    version('1.2.3.1', '24fc0101c7c441709c230e76af611d53')
+
+    depends_on('py-setuptools',   type='build')
+    depends_on('py-cython@0.19:', type='build')
+
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
+
+    depends_on('netcdf')
+    depends_on('hdf5@1.8.0:')

var/spack/repos/builtin/packages/py-palettable/package.py

+##############################################################################
+# 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 PyPalettable(PythonPackage):
+    """Color palettes for Python."""
+
+    homepage = "https://jiffyclub.github.io/palettable/"
+    url      = "https://pypi.io/packages/source/p/palettable/palettable-3.0.0.tar.gz"
+
+    version('3.0.0', '6e430319fe01386c81dbbc62534e3cc4')
+
+    depends_on('py-setuptools', type='build')

var/spack/repos/builtin/packages/py-pydispatcher/package.py

+##############################################################################
+# 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 PyPydispatcher(PythonPackage):
+    """Multi-producer-multi-consumer signal dispatching mechanism."""
+
+    homepage = "http://pydispatcher.sourceforge.net/"
+    url      = "https://pypi.io/packages/source/P/PyDispatcher/PyDispatcher-2.0.5.tar.gz"
+
+    version('2.0.5', '1b9c2ca33580c2770577add7130b0b28')
+
+    depends_on('py-setuptools', type='build')

var/spack/repos/builtin/packages/py-pymatgen/package.py

+##############################################################################
+# 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 PyPymatgen(PythonPackage):
+    """Python Materials Genomics is a robust materials analysis code that
+    defines core object representations for structures and molecules with
+    support for many electronic structure codes. It is currently the core
+    analysis code powering the Materials Project."""
+
+    homepage = "http://www.pymatgen.org/"
+    url      = "https://pypi.io/packages/source/p/pymatgen/pymatgen-4.7.2.tar.gz"
+
+    version('4.7.2', '9c3a6e8608671c216e4ef89778646fd6')
+    version('4.6.2', '508f77fdc3e783587348e93e4dfed1b8')
+
+    extends('python', ignore='bin/tabulate')
+
+    depends_on('py-setuptools@18.0:', type='build')
+
+    depends_on('py-numpy@1.9:',          type=('build', 'run'))
+    depends_on('py-six',                 type=('build', 'run'))
+    depends_on('py-requests',            type=('build', 'run'))
+    depends_on('py-pyyaml@3.11:',        type=('build', 'run'))
+    depends_on('py-monty@0.9.6:',        type=('build', 'run'))
+    depends_on('py-scipy@0.14:',         type=('build', 'run'))
+    depends_on('py-pydispatcher@2.0.5:', type=('build', 'run'))
+    depends_on('py-tabulate',            type=('build', 'run'))
+    depends_on('py-spglib@1.9.8.7:',     type=('build', 'run'))
+    depends_on('py-matplotlib@1.5:',     type=('build', 'run'))
+    depends_on('py-palettable@2.1.1:',   type=('build', 'run'))

var/spack/repos/builtin/packages/py-pytz/package.py

@@ -29,12 +29,12 @@ class PyPytz(PythonPackage):
     """World timezone definitions, modern and historical."""
 
     homepage = "https://pypi.python.org/pypi/pytz"
-    url      = "https://pypi.python.org/packages/source/p/pytz/pytz-2014.10.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pytz/pytz-2016.10.tar.gz"
 
-    version('2016.6.1', 'b6c28a3b968bc1d8badfb61b93874e03',
-            url="https://pypi.python.org/packages/5d/8e/6635d8f3f9f48c03bb925fab543383089858271f9cfd1216b83247e8df94/pytz-2016.6.1.tar.gz")
-    version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
-    version('2015.4', '417a47b1c432d90333e42084a605d3d8')
-    version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29')
+    version('2016.10',  'cc9f16ba436efabdcef3c4d32ae4919c')
+    version('2016.6.1', 'b6c28a3b968bc1d8badfb61b93874e03')
+    version('2014.10',  'eb1cb941a20c5b751352c52486aa1dd7')
+    version('2015.4',   '417a47b1c432d90333e42084a605d3d8')
+    version('2016.3',   'abae92c3301b27bd8a9f56b14f52cb29')
 
     depends_on('py-setuptools', type='build')

var/spack/repos/builtin/packages/py-seaborn/package.py

+##############################################################################
+# 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 PySeaborn(PythonPackage):
+    """Seaborn: statistical data visualization.
+
+    Seaborn is a library for making attractive and informative statistical
+    graphics in Python. It is built on top of matplotlib and tightly
+    integrated with the PyData stack, including support for numpy and pandas
+    data structures and statistical routines from scipy and statsmodels."""
+
+    homepage = "http://seaborn.pydata.org/"
+    url      = "https://pypi.io/packages/source/s/seaborn/seaborn-0.7.1.tar.gz"
+
+    version('0.7.1', 'ef07e29e0f8a1f2726abe506c1a36e93')
+
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-numpy',      type=('build', 'run'))
+    depends_on('py-scipy',      type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-pandas',     type=('build', 'run'))

var/spack/repos/builtin/packages/py-netcdf/package.py → var/spack/repos/builtin/packages/py-spglib/package.py

@@ -25,14 +25,14 @@
 from spack import *
 
 
-class PyNetcdf(PythonPackage):
-    """Python interface to the netCDF Library."""
-    homepage = "http://unidata.github.io/netcdf4-python"
-    url      = "https://github.com/Unidata/netcdf4-python/tarball/v1.2.3.1rel"
+class PySpglib(PythonPackage):
+    """Python bindings for C library for finding and handling
+    crystal symmetries."""
 
-    version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af')
+    homepage = "http://atztogo.github.io/spglib/"
+    url      = "https://pypi.io/packages/source/s/spglib/spglib-1.9.9.18.tar.gz"
 
+    version('1.9.9.18', 'b8b46268d3aeada7b9b201b11882548f')
+
+    depends_on('py-setuptools@18.0:', type='build')
     depends_on('py-numpy', type=('build', 'run'))
-    depends_on('py-cython', type=('build', 'run'))
-    depends_on('py-setuptools', type=('build', 'run'))
-    depends_on('netcdf')

var/spack/repos/builtin/packages/py-tzlocal/package.py

+##############################################################################
+# 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 PyTzlocal(PythonPackage):
+    """tzinfo object for the local timezone."""
+
+    homepage = "https://github.com/regebro/tzlocal"
+    url      = "https://pypi.io/packages/source/t/tzlocal/tzlocal-1.3.tar.gz"
+
+    version('1.3', '3cb544b3975b59f91a793850a072d4a8')
+
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-pytz', type=('build', 'run'))