First versions packages for bluepyopt/bluepymm/efel (spack#120)

* Add first version of bluepymm/bluepyopt/efel packages and dependencies

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

@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 PyBluepymm(PythonPackage):
+    """Blue Brain Model Management Python Library"""
+
+    homepage = "https://github.com/BlueBrain/BluePyMM"
+    url = "https://pypi.io/packages/source/b/bluepymm/bluepymm-0.6.35.tar.gz"
+
+    version('0.6.35', sha256='8455e4543057e2a4889cce46bfe841a4041eaa039d6aece1ac2ccfdb755c1ccf')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-bluepyopt', type='run')
+    depends_on('py-matplotlib', type='run')
+    # The below dependency should disappear once the matplotlib package is fixed
+    depends_on('py-backports-functools-lru-cache', type='run')
+    depends_on('py-pandas', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('py-ipyparallel', type='run')
+    depends_on('py-lxml', type='run')
+    depends_on('py-sh', type='run')
+    depends_on('neuron', type='run')

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

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+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 PyBluepyopt(PythonPackage):
+    """Bluebrain Python Optimisation Library"""
+
+    homepage = "https://github.com/BlueBrain/BluePyOpt"
+    url = "https://pypi.io/packages/source/b/bluepyopt/bluepyopt-1.6.56.tar.gz"
+
+    version('1.6.56', sha256='1c57c91465ca4b947fe157692e7004a3e6df02e4151e3dc77a8831382a8f1ab9')
+
+    variant('neuron', default=True, description="Use BluePyOpt together with NEURON")
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pandas', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('py-efel', type='run')
+    depends_on('py-deap', type='run')
+    depends_on('py-ipyparallel', type='run')
+    depends_on('py-pickleshare', type='run')
+    depends_on('py-future', type='run')
+    depends_on('py-jinja2', type='run')
+    depends_on('neuron', type='run', when='+neuron')

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

@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 PyDeap(PythonPackage):
+    """Distributed Evolutionary Algorithms in Python"""
+
+    homepage = "https://github.com/deap/deap"
+    url = "https://pypi.io/packages/source/d/deap/deap-1.2.2.tar.gz"
+
+    version('1.2.2', sha256='95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf')
+
+    depends_on('py-setuptools', type='build')

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

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+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 PyEfel(PythonPackage):
+    """The Electrophys Feature Extract Library (eFEL) allows 
+    neuroscientists to automatically extract features from time series data 
+    recorded from neurons (both in vitro and in silico).
+    Examples are the action potential width and amplitude in 
+    voltage traces recorded during whole-cell patch clamp experiments.
+    The user of the library provides a set of traces and selects the 
+    features to be calculated. The library will then extract the requested 
+    features and return the values to the user."""
+    homepage = "https://github.com/BlueBrain/eFEL"
+    url = "https://pypi.io/packages/source/e/efel/efel-3.0.22.tar.gz"
+
+    version('3.0.22', sha256='97b2c1a0425b12cd419e8539bb1e936ce64c4e93f5d0dd7f81f38554490064a2')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy', type='run')
+    depends_on('py-six', type='run')

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

@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 PyIpyparallel(PythonPackage):
+    """Use multiple instances of IPython in parallel, interactively."""
+
+    homepage = "http://ipython.org"
+    url = "https://pypi.io/packages/source/i/ipyparallel/ipyparallel-6.2.2.tar.gz"
+
+    version('6.2.2', sha256='02b225966d5c20f12b1fba0b6b10aa5d352a6b492e075f137ff0ff6e95b9358e')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-tornado', type='run')
+    depends_on('py-traitlets', type='run')
+    depends_on('py-zmq', type='run')
+    depends_on('py-ipython', type='run')
+    depends_on('py-ipykernel', type='run')
+    depends_on('py-futures', type='run')
+