#
# This file is part of the AffBio package for clustering of
# biomolecular structures.
#
# Copyright (c) 2015-2016, by Arthur Zalevsky <aozalevsky@fbb.msu.ru>
#
# AffBio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# AffBio 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 GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public
# License along with AffBio; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
#

# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path

from setuptools.extension import Extension
from Cython.Build import cythonize

here = path.abspath(path.dirname(__file__))

# Get the long description from the README file

with open('README.rst', 'r') as f:
    long_description = f.read()

extensions = [
    Extension(
        "affbio/lvc",
        ["affbio/lvc.pyx"])
]


setup(
    name='affbio',

    # Versions should comply with PEP440.  For a discussion on single-sourcing
    # the version across setup.py and the project code, see
    # https://packaging.python.org/en/latest/single_source_version.html
    version='0.0.4.1',

    description='Affinity Propagation for biostructures',
    long_description=long_description,

    # The project's main homepage.
    url='http://vsb.fbb.msu.ru/rhodecode/software/aff_cluster',

    # Author details
    author='Arthur Zalevsky',
    author_email='aozalevsky@fbb.msu.ru',

    # Choose your license
    license='GPLv3',

    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
    classifiers=[
        # How mature is this project? Common values are
        #   3 - Alpha
        #   4 - Beta
        #   5 - Production/Stable
        'Development Status :: 4 - Beta',

        # Indicate who your project is intended for
        'Intended Audience :: Developers',
        'Topic :: Scientific/Engineering :: Bio-Informatics',

        # Pick your license as you wish (should match "license" above)
        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',

        # Specify the Python versions you support here. In particular, ensure
        # that you indicate whether you support Python 2, Python 3 or both.
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 2.7',
    ],

    # What does your project relate to?
    keywords='clustering bioinformatics',

    # You can just specify the packages manually here if your project is
    # simple. Or you can use find_packages().
    packages=find_packages(exclude=['data', 'old', 'supplement']),

    # Alternatively, if you want to distribute just a my_module.py, uncomment
    # this:
    #   py_modules=["my_module"],

    # List run-time dependencies here.  These will be installed by pip when
    # your project is installed. For an analysis of "install_requires" vs pip's
    # requirements files see:
    # https://packaging.python.org/en/latest/requirements.html
    setup_requires=[
        'setuptools>=25.0',
        'Cython>=0.19.0',
        ],

    install_requires=[
        'numpy>=1.6,<1.11',
        'mpi4py',
        'h5py',
        'psutil',
        'natsort',
        'prody',
        'pyRMSD',
        'bottleneck',
        ],

    ext_modules=cythonize(extensions),

    # List additional groups of dependencies here (e.g. development
    # dependencies). You can install these using the following syntax,
    # for example:
    # $ pip install -e .[dev,test]
    # extras_require={
    #    'dev': ['check-manifest'],
    #    'test': ['coverage'],
    # },

    # If there are data files included in your packages that need to be
    # installed, specify them here.  If using Python 2.6 or less, then these
    # have to be included in MANIFEST.in as well.
    # package_data={
    #    'sample': ['package_data.dat'],
    # },

    # Although 'package_data' is the preferred approach, in some case you may
    # need to place data files outside of your packages. See:
    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
    # data_files=[('my_data', ['data/data_file'])],

    # To provide executable scripts, use entry points in preference to the
    # "scripts" keyword. Entry points provide cross-platform support and allow
    # pip to create the appropriate form of executable for the target platform.
    entry_points={
        'console_scripts': [
            'affbio=affbio.cli:run',
        ],
    },
    # scripts=['bin/affbio.py'],
)
