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"]},
)