import os

from setuptools.extension import Extension

from setuptools import setup, find_packages

def read(fname):

    return open(os.path.join(os.path.dirname(__file__), fname)).read()

setup(

    name="genomelake",

    version="0.1.5",

    description="Simple and efficient random access to genomic data for deep learning models.",

    long_description=read("README.md"),

    url="https://github.com/kundajelab/genomelake",

    author="Chuan-Sheng Foo",

    author_email="csfoo@cs.stanford.edu",

    license="BSD-3",

    classifiers=[

        "Development Status :: 3 - Alpha",

        "Intended Audience :: Science/Research",

        "Intended Audience :: Developers",

        "Topic :: Scientific/Engineering",

        "License :: OSI Approved :: BSD License",

        "Programming Language :: Python :: 2.7",

        "Programming Language :: Python :: 3.5",

        "Programming Language :: Python :: 3.6",

        "Operating System :: POSIX :: Linux",

    ],

    keywords="deeplearning neuralnets genomics",

    packages=find_packages(exclude=["contrib", "docs", "tests*"]),

    setup_requires=["cython"],

    ext_modules=[Extension("genomelake.util", ["genomelake/util.pyx"])],

    install_requires=[

        "bcolz>=1.1",

        "numpy",

        "pybedtools",

        "pyBigWig",

        "pysam",

        "six>=1.9.0",

        "tiledb>=0.2.0",

    ],

    extras_require={"develop": ["coveralls", "pytest>=3.3.1", "pytest-cov"]},

)