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setup.py
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setup.py
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# -*- coding: utf-8 -*-
# Copyright 2013 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import absolute_import, print_function
from itertools import chain
from setuptools import setup, find_packages
import versioneer
requirements = ['numpy>=1.9.1',
'scipy>=0.14.0',
'blessings>=1.5.1',
'pandas>=1.1.3',
'ordered-set>=1.2',
'cobra>=0.11.1',
'future>=0.15.2',
'optlang>=1.4.2',
'numexpr>=2.4',
'requests>=2.10.0',
'networkx>=2.4',
'escher>=1.1.2',
'IProgress>=0.4',
'inspyred>=1.0',
'lazy-object-proxy>=1.2.0',
'palettable>=2.1.1',
'gnomic==1.0.1',
'openpyxl>=2.4.5',
'click>=6.7']
extra_requirements = {
'docs': ['Sphinx>=1.3.5', 'numpydoc>=0.5'],
'plotly': ['plotly>=4.12.0'],
'bokeh': ['bokeh<=0.12.1'],
'jupyter': ['jupyter>=1.0.0', 'ipywidgets>=4.1.1'],
'test': ['pytest', 'pytest-cov', 'pytest-benchmark'],
'parallel': ['redis>=2.10.5', 'ipyparallel>=5.0.1'],
'sbml': ['python-libsbml>=5.13.0', 'lxml>=3.6.0']
}
extra_requirements['all'] = list(set(chain(*extra_requirements.values())))
# Run
# pandoc --from=markdown --to=rst README.md -o README.rst
# from time to time, to keep README.rst updated
try:
with open('README.rst', 'r') as f:
description = f.read()
except:
description = ''
setup(
name='cameo',
version=versioneer.get_version(),
cmdclass=versioneer.get_cmdclass(),
packages=find_packages(),
install_requires=requirements,
extras_require=extra_requirements,
include_package_data=True,
entry_points='''
[console_scripts]
cameo=cli:main
''',
author='Nikolaus Sonnenschein, Joao Cardoso, Emre Özdemir, Kristian Jensen',
author_email='[email protected]',
description='cameo - computer aided metabolic engineering & optimization',
license='Apache License Version 2.0',
keywords='biology metabolism bioinformatics',
url='http://cameo.bio',
long_description=description,
classifiers=[
'Development Status :: 3 - Alpha',
'Topic :: Utilities',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'License :: OSI Approved :: Apache Software License'
],
)