Add py-sncosmo package

6 files changed, 234 insertions, 22 deletions

diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py
index 86875bbcae..09d1688f4b 100644
--- a/var/spack/repos/builtin/packages/py-astropy/package.py
+++ b/var/spack/repos/builtin/packages/py-astropy/package.py
@@ -24,29 +24,40 @@
 ##############################################################################
 from spack import *
 
+
 class PyAstropy(Package):
-    """
-    The Astropy Project is a community effort to develop a single core
+    """The Astropy Project is a community effort to develop a single core
     package for Astronomy in Python and foster interoperability between
-    Python astronomy packages.
-    """
+    Python astronomy packages."""
+
     homepage = 'http://www.astropy.org/'
+    url = 'https://pypi.python.org/packages/source/a/astropy/astropy-1.1.2.tar.gz'
 
+    version('1.1.2',     'cbe32023b5b1177d1e2498a0d00cda51')
     version('1.1.post1', 'b52919f657a37d45cc45f5cb0f58c44d')
 
-    def url_for_version(self, version):
-        return 'https://pypi.python.org/packages/source/a/astropy/astropy-{0}.tar.gz'.format(version)
-
-    extends('python')
+    # Required dependencies
+    extends('python@2.6.5:2.7,3.3:')
+    depends_on('py-numpy@1.6.0:')
 
+    # Optional dependencies
     depends_on('cfitsio')
     depends_on('expat')
     depends_on('py-h5py')
-    depends_on('py-numpy')
+    depends_on('py-pyyaml')
     depends_on('py-scipy')
+    depends_on('py-matplotlib')
+    depends_on('py-pytz')
+    depends_on('py-scikit-image')
+    depends_on('py-pandas')
+
+    # TODO: Add packages
+    # depends_on('py-beautiful-soup')
+    # depends_on('py-xmllint')
+    # depends_on('py-wcsaxes')
+    # depends_on('py-objgraph')
 
     def install(self, spec, prefix):
         python('setup.py', 'build', '--use-system-cfitsio',
-                                    '--use-system-expat')
-        python('setup.py', 'install', '--prefix=' + prefix)
-
+               '--use-system-expat')
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py
new file mode 100644
index 0000000000..d57ef4bd76
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-emcee/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# 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 PyEmcee(Package):
+    """emcee is an MIT licensed pure-Python implementation of Goodman & Weare's
+    Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler."""
+
+    homepage = "http://dan.iel.fm/emcee/current/"
+    url = "https://pypi.python.org/packages/source/e/emcee/emcee-2.1.0.tar.gz"
+
+    version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7')
+
+    extends('python')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index a8eb027ba5..a92fc3c9c7 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -23,23 +23,34 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import re
+
 
 class PyH5py(Package):
-    """The h5py package provides both a high- and low-level interface to the HDF5 library from Python."""
+    """The h5py package provides both a high- and low-level interface to the
+    HDF5 library from Python."""
+
     homepage = "https://pypi.python.org/pypi/h5py"
     url      = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
 
-    version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+    version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4')
     version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74')
+    version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
 
-    extends('python', ignore=lambda f: re.match(r'bin/cy*', f))
-    depends_on('hdf5')
-    depends_on('py-numpy')
+    variant('mpi', default=False, description='Build with MPI support')
+
+    extends('python', ignore=r'bin/cy.*')
+    depends_on('hdf5@1.8.4:+mpi', when='+mpi')
+    depends_on('hdf5@1.8.4:~mpi', when='~mpi')
+    depends_on('py-numpy@1.6.1:')
     depends_on('py-cython')
-    depends_on('py-six')
-    depends_on('py-pkgconfig')
+    depends_on('mpi', when='+mpi')
 
     def install(self, spec, prefix):
-        python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix)
-        python('setup.py', 'install', '--prefix=%s' % prefix)
+        python('setup.py', 'configure',
+               '--hdf5={0}'.format(spec['hdf5'].prefix))
+
+        if '+mpi' in spec:
+            env['CC'] = spec['mpi'].mpicc
+            python('setup.py', 'configure', '--mpi')
+
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py
new file mode 100644
index 0000000000..5a42268a73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-iminuit/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# 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 PyIminuit(Package):
+    """Interactive IPython-Friendly Minimizer based on SEAL Minuit2."""
+
+    homepage = "https://pypi.python.org/pypi/iminuit"
+    url      = "https://pypi.python.org/packages/source/i/iminuit/iminuit-1.2.tar.gz"
+
+    version('1.2', '4701ec472cae42015e26251703e6e984')
+
+    # Required dependencies
+    extends('python@2.7:2.8,3.4:')
+    depends_on('py-setuptools')
+
+    # Optional dependencies
+    depends_on('py-numpy')
+    depends_on('py-matplotlib')
+
+    def install(self, spec, prefix):
+        site_packages = '{0}/lib/python{1}/site-packages'.format(
+            prefix, spec['python'].version.up_to(2))
+
+        # site-packages directory must already exist
+        mkdirp(site_packages)
+
+        # PYTHONPATH must include site-packages directory
+        env['PYTHONPATH'] += ':{0}'.format(site_packages)
+
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py
new file mode 100644
index 0000000000..38fa0561db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nestle/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 PyNestle(Package):
+    """Nested sampling algorithms for evaluating Bayesian evidence."""
+
+    homepage = "http://kbarbary.github.io/nestle/"
+    url = "https://pypi.python.org/packages/source/n/nestle/nestle-0.1.1.tar.gz"
+
+    version('0.1.1', '4875c0f9a0a8e263c1d7f5fa6ce604c5')
+
+    # Required dependencies
+    extends('python')
+    depends_on('py-numpy@1.6:')
+
+    # Optional dependencies
+    depends_on('py-scipy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py
new file mode 100644
index 0000000000..d40623ffa1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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 PySncosmo(Package):
+    """SNCosmo is a Python library for high-level supernova cosmology
+    analysis."""
+
+    homepage = "http://sncosmo.readthedocs.io/"
+    url = "https://pypi.python.org/packages/source/s/sncosmo/sncosmo-1.2.0.tar.gz"
+
+    version('1.2.0', '028e6d1dc84ab1c17d2f3b6378b2cb1e')
+
+    # Required dependencies
+    # py-sncosmo binaries are duplicates of those from py-astropy
+    extends('python@2.6:2.7,3.3:', ignore=r'bin/*')
+    depends_on('py-numpy')
+    depends_on('py-scipy')
+    depends_on('py-astropy')
+
+    # Recommended dependencies
+    depends_on('py-matplotlib')
+    depends_on('py-iminuit')
+    depends_on('py-emcee')
+    depends_on('py-nestle')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))