setup.py

from setuptools import setup, find_packages
def readme():
    with open('README.md') as f:
        return f.read()
long_description='NGSphy is a Python open-source tool for the genome-wide simulation of NGS data (read counts or Illumina reads) obtained from thousands of gene families evolving under a common species tree, with multiple haploid and/or diploid individuals per species, where sequencing coverage (depth) heterogeneity can vary among species, individuals and loci, including off-target or uncaptured loci.'

setup(name='ngsphy',\
    version='1.0.13',\
    description='phylogenomic simulation of NGS data ',\
    long_description=long_description,\
    url='https://github.com/merlyescalona/ngsphy',\
    download_url='https://github.com/merlyescalona/ngsphy/blob/master/dist/ngsphy-1.0.13.tar.gz',\
    author='Merly Escalona',\
    author_email='merlyescalona@uvigo.es',\
    license='GNU/GPL v3',\
    packages=['ngsphy'],\
    package_dir={'ngsphy': 'ngsphy'},\
    py_modules = [\
        'ngsphy.coverage', \
        'ngsphy.individual', \
        'ngsphy.loggingformatter', \
        'ngsphy.msatools', \
        'ngsphy.ngsphyexceptions', \
        'ngsphy.readcounts', \
        'ngsphy.reads', \
        'ngsphy.rerooter', \
        'ngsphy.sequence', \
        'ngsphy.settings'
    ],\
    install_requires=[\
        'argparse',\
        'ConfigParser',\
        'datetime',\
        'dendropy',\
        'logging',\
        'multiprocessing',\
        'numpy',\
        'setuptools',\
        'scipy'\
    ],
    package_data={
        'data':['data/*'],\
        'doc':['doc/*'],\
    },\
    classifiers=[\
        'Development Status :: 4 - Beta',\
        'Intended Audience :: Education',\
        'Intended Audience :: Science/Research',\
        'Intended Audience :: Developers',\
        'Topic :: Scientific/Engineering :: Bio-Informatics',\
        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',\
        'Programming Language :: Python :: 2.7'\
    ],\
    keywords='biology phylogenomics next-generation sequencing coverage targeted-sequencing',\
    python_requires='~=2.7',\
    scripts=['scripts/ngsphy'],\
    entry_points={
        'console_scripts':[\
            'ngsphy = ngsphy.__main__:main'\
        ]\
    },\
    zip_safe=False\
  )