setup.py

#!/usr/bin/env python

"""Copy number variation toolkit for targeted DNA sequencing."""

from os.path import dirname, join
from glob import glob

setup_args = {}

try:
    from setuptools import setup
    # Dependencies for easy_install and pip:
    setup_args.update(
        install_requires=[
            'numpy >= 1.6',
            'scipy >= 0.9',
            'matplotlib >= 1.1',
            'pandas >= 0.17.1',
            'pysam >= 0.8',
            'pyvcf >= 0.5',
            'reportlab >= 3.0',
            'biopython >= 1.62',
            'pyfaidx >= 0.4.7',
            'future >= 0.15.2'
        ])
except ImportError:
    from distutils.core import setup

DIR = (dirname(__file__) or '.')
with open(join(DIR, 'cnvlib', '_version.py')) as handle:
    VERSION = handle.readline().split('=')[-1].strip().replace('"','')

setup_args.update(
    name='CNVkit',
    version=VERSION,
    description=__doc__,
    author='Eric Talevich',
    author_email='eric.talevich@ucsf.edu',
    url='http://github.com/etal/cnvkit',
    packages=[
        'cnvlib',
        'cnvlib.ngfrills',
        'cnvlib.segmentation',
    ],
    scripts=[join(DIR, 'cnvkit.py')] + glob(join(DIR, 'scripts/*.py')),
    classifiers=[
        "Development Status :: 4 - Beta",
        "Environment :: Console",
        "Intended Audience :: Science/Research",
        "Intended Audience :: Healthcare Industry",
        "License :: OSI Approved :: Apache Software License",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: POSIX",
        "Operating System :: POSIX :: Linux",
        "Operating System :: Unix",
        "Programming Language :: Python",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.4",
        "Programming Language :: Python :: 2",
        "Programming Language :: Python :: 2.7",
        "Topic :: Scientific/Engineering",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Medical Science Apps.",
        "Topic :: Scientific/Engineering :: Visualization",
    ],
)

setup(**setup_args)