setup.py

# -*- coding: utf-8 -*-

from __future__ import absolute_import

from warnings import warn
from sys import argv, version_info

from setuptools import setup, find_packages

if version_info[:2] == (3, 4):
    warn("Support for Python 3.4 was dropped by pandas. Since cobrapy is a "
         "pure Python package you can still install it but will have to "
         "carefully manage your own pandas and numpy versions. We no longer "
         "include it in our automatic testing.")

setup_kwargs = dict()
setup_requirements = []
# prevent pytest-runner from being installed on every invocation
if {'pytest', 'test', 'ptr'}.intersection(argv):
    setup_requirements.append("pytest-runner")

extras = {
    'array': ["scipy"],
    'sbml': ["python-libsbml", "lxml"]
}
extras["all"] = sorted(list(extras))

try:
    with open('README.rst') as handle:
        readme = handle.read()
    with open('INSTALL.rst') as handle:
        install = handle.read()
    setup_kwargs["long_description"] = readme + "\n\n" + install
except IOError:
    setup_kwargs["long_description"] = ''

setup(
    name="cobra",
    version="0.10.1",
    packages=find_packages(),
    setup_requires=setup_requirements,
    install_requires=[
        "six",
        "future",
        "swiglpk",
        "ruamel.yaml<0.15",
        "numpy>=1.6",
        "pandas>=0.17.0",
        "optlang>=1.2.5",
        "tabulate"
    ],
    tests_require=[
        "jsonschema > 2.5",
        "pytest",
        "pytest-benchmark"
    ],
    extras_require=extras,
    package_data={
         '': [
             'test/data/*',
             'mlab/matlab_scripts/*m'
         ]
    },
    author="The cobrapy core team",
    author_email="cobra-pie@googlegroups.com",
    description="COBRApy is a package for constraints-based modeling of "
    "biological networks",
    license="LGPL/GPL v2+",
    keywords=("metabolism biology linear programming optimization flux"
              " balance analysis fba"),
    url="https://opencobra.github.io/cobrapy",
    test_suite="cobra.test.suite",
    download_url='https://pypi.python.org/pypi/cobra',
    classifiers=[
        'Development Status :: 5 - Production/Stable',
        'Environment :: Console',
        'Intended Audience :: Science/Research',
        'License :: OSI Approved :: GNU Lesser General Public License v2'
            ' or later (LGPLv2+)',
        'License :: OSI Approved :: GNU General Public License v2'
            ' or later (GPLv2+)',
        'Operating System :: OS Independent',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3.4',
        'Programming Language :: Python :: 3.5',
        'Programming Language :: Python :: 3.6',
        'Programming Language :: Python :: Implementation :: CPython',
        'Topic :: Scientific/Engineering',
        'Topic :: Scientific/Engineering :: Bio-Informatics'
    ],
    platforms="GNU/Linux, Mac OS X >= 10.7, Microsoft Windows >= 7",
    **setup_kwargs
)