setup.py

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

"""Setup module for the gene_prioritization package."""

import codecs  # To use a consistent encoding
import os
import re

import setuptools

#################################################################

PACKAGES = setuptools.find_packages(where='src')
META_PATH = os.path.join('src', '__init__.py')
KEYWORDS = ['Gene Prioritization', 'Networks Biology',
            'Drug Target Prioritization']
CLASSIFIERS = [
    'Development Status :: 4 - Beta',
    'Environment :: Console',
    'Intended Audience :: Developers',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: MIT Software License',
    'Operating System :: OS Independent',
    'Programming Language :: Python',
    'Programming Language :: Python :: 3.4',
    'Programming Language :: Python :: 3.5',
    'Programming Language :: Python :: 3.6',
    'Topic :: Scientific/Engineering :: Bio-Informatics'
]
INSTALL_REQUIRES = [
    'numpy',
    'pandas',
    'scipy',
    'py2cytoscape',
    'rpy2',
    'scikit-learn',
    'xlrd',
    'openpyxl',
    'python-igraph',
    'click',
    'jinja2',
]

EXTRAS_REQUIRE = {

}
TESTS_REQUIRE = [

]
ENTRY_POINTS = {
    'console_scripts': [
        'gene_prioritization = gene_prioritization.cli:main',
    ]
}
DEPENDENCY_LINKS = [

]

PACKAGE_DATA = {
    '': [
        '*.r',
        '*.R'
    ]
}

#################################################################

HERE = os.path.abspath(os.path.dirname(__file__))


def read(*parts):
    """Build an absolute path from *parts* and return the contents of the resulting file. Assume UTF-8 encoding."""
    with codecs.open(os.path.join(HERE, *parts), 'rb', 'utf-8') as f:
        return f.read()


META_FILE = read(META_PATH)


def find_meta(meta):
    """Extract __*meta*__ from META_FILE"""
    meta_match = re.search(
        r'^__{meta}__ = ["\']([^"\']*)["\']'.format(meta=meta),
        META_FILE, re.M
    )
    if meta_match:
        return meta_match.group(1)
    raise RuntimeError('Unable to find __{meta}__ string'.format(meta=meta))


def get_long_description():
    """Get the long_description from the README.rst file. Assume UTF-8 encoding."""
    with codecs.open(os.path.join(HERE, 'README.rst'), encoding='utf-8') as f:
        long_description = f.read()
    return long_description


if __name__ == '__main__':
    setuptools.setup(
        name=find_meta('title'),
        version=find_meta('version'),
        description=find_meta('description'),
        long_description=get_long_description(),
        url=find_meta('url'),
        author=find_meta('author'),
        author_email=find_meta('email'),
        maintainer=find_meta('author'),
        maintainer_email=find_meta('email'),
        license=find_meta('license'),
        classifiers=CLASSIFIERS,
        keywords=KEYWORDS,
        packages=PACKAGES,
        package_dir={'': 'src'},
        install_requires=INSTALL_REQUIRES,
        extras_require=EXTRAS_REQUIRE,
        tests_require=TESTS_REQUIRE,
        entry_points=ENTRY_POINTS,
        dependency_links=DEPENDENCY_LINKS,
        package_data=PACKAGE_DATA,
        include_package_data=True,
    )