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setup.py
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setup.py
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"""
Module computing Resource Balance Analysis.
This file is adapted from
https://github.com/pypa/sampleproject/
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
long_description = f.read()
with open(path.join(here, 'rba', '_version.py'), 'r') as f:
version = f.readline().split("'")[1]
with open(path.join(here, 'rba', '_authors.py'), 'r') as f:
authors = f.readline().split("'")[1]
setup(
name='rbapy',
# 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=version,
description='Package for automated generation of bacterial Resource Balance Analysis (RBA) models and simulation of RBA models',
long_description=long_description,
# The project's main homepage.
url='https://sysbioinra.github.io/RBApy/',
# Author details
author=authors,
author_email='[email protected]',
# 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 :: 3 - Alpha',
# Indicate who your project is intended for
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering',
'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',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.5',
],
# What does your project relate to?
keywords=[
'metabolism',
'Resource Balance Analysis',
'molecular biology',
'cell biology',
'biochemistry',
'systems biology',
'computational biology',
'mathematical modeling',
'numerical simulation',
],
# You can just specify the packages manually here if your project is
# simple. Or you can use find_packages().
packages=find_packages(exclude=['contrib', 'docs', 'tests']),
# 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
install_requires=[
'biopython',
'lxml',
'numpy',
'pandas',
'python-libsbml',
'scipy',
'requests'
],
# 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={
'cplex': ['cplex'],
'cplex_conv_opt': ['conv_opt[cplex]'],
'cplex_optlang': ['optlang', 'cplex'],
'glpk': ['glpk'],
'swiglpk': ['swiglpk'],
'glpk_conv_opt': ['conv_opt'],
'glpk_optlang': ['optlang'],
'gurobi': ['gurobipy'],
'gurobi_conv_opt': ['conv_opt[gurobi]'],
'gurobi_optlang': ['optlang', 'gurobipy'],
'dev': ['check-manifest'],
'test': ['pytest', 'pytest-cov', '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': [
'generate-rba-model=rba.cli.generate_rba_model:main',
'solve-rba-model=rba.cli.solve_rba_model:main',
],
},
)