From 06e848379bd1d77a4bae55bd9a10d7b9e6550b74 Mon Sep 17 00:00:00 2001 From: Werner Van Geit Date: Thu, 25 Oct 2018 20:19:25 +0200 Subject: [PATCH] First versions packages for bluepyopt/bluepymm/efel (#120) * Add first version of bluepymm/bluepyopt/efel packages and dependencies --- .../builtin/packages/py-bluepymm/package.py | 46 ++++++++++++++++++ .../builtin/packages/py-bluepyopt/package.py | 47 +++++++++++++++++++ .../repos/builtin/packages/py-deap/package.py | 36 ++++++++++++++ .../repos/builtin/packages/py-efel/package.py | 44 +++++++++++++++++ .../packages/py-ipyparallel/package.py | 43 +++++++++++++++++ 5 files changed, 216 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-bluepymm/package.py create mode 100644 var/spack/repos/builtin/packages/py-bluepyopt/package.py create mode 100644 var/spack/repos/builtin/packages/py-deap/package.py create mode 100644 var/spack/repos/builtin/packages/py-efel/package.py create mode 100644 var/spack/repos/builtin/packages/py-ipyparallel/package.py diff --git a/var/spack/repos/builtin/packages/py-bluepymm/package.py b/var/spack/repos/builtin/packages/py-bluepymm/package.py new file mode 100644 index 0000000000000..49f48bd64fffb --- /dev/null +++ b/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') diff --git a/var/spack/repos/builtin/packages/py-bluepyopt/package.py b/var/spack/repos/builtin/packages/py-bluepyopt/package.py new file mode 100644 index 0000000000000..de7f859b87c1d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-bluepyopt/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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') diff --git a/var/spack/repos/builtin/packages/py-deap/package.py b/var/spack/repos/builtin/packages/py-deap/package.py new file mode 100644 index 0000000000000..12075b5bd9a91 --- /dev/null +++ b/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') diff --git a/var/spack/repos/builtin/packages/py-efel/package.py b/var/spack/repos/builtin/packages/py-efel/package.py new file mode 100644 index 0000000000000..6d898e8e663e4 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-efel/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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') diff --git a/var/spack/repos/builtin/packages/py-ipyparallel/package.py b/var/spack/repos/builtin/packages/py-ipyparallel/package.py new file mode 100644 index 0000000000000..b4c7986c0eabe --- /dev/null +++ b/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') +