"""A setuptools based setup module.

See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""

# Always prefer setuptools over distutils
from codecs import open
from os import path
from setuptools import setup

here = path.abspath(path.dirname(__file__))

# Get the long description from the relevant file
with open(path.join(here, 'README.rst')) as f:
    long_description = f.read()


setup(
    name='FUCHS',

    # Versions should comply with PEP440.  For a discussion on single-sourcing
    # the version across setup.py and the project code, see
    # https://packaging.python.org/en/latest/single_source_version.html
    version='0.3.1',

    description='FUll circular RNA CHaracterization from RNA-Seq',
    long_description=long_description,

    # The project's main homepage.
    url='https://github.com/dieterich-lab/FUCHS',

    # Author details

    author='Franzi Metge',
    author_email='franziska.metge@age.mpg.de',

    maintainer='Tobias Jakobi',
    maintainer_email='Tobias.Jakobi@med.Uni-Heidelberg.DE',

    # Choose your license
    license='License :: OSI Approved :: GNU General Public License (GPL)',

    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
    classifiers=[
        # How mature is this project? Common values are

        # Development Status :: 1 - Planning
        # Development Status :: 2 - Pre-Alpha
        # Development Status :: 3 - Alpha
        # Development Status :: 4 - Beta
        # Development Status :: 5 - Production/Stable
        # Development Status :: 6 - Mature
        # Development Status :: 7 - Inactive

        'Development Status :: 4 - Beta',

        # Indicate who your project is intended for
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',

        # Pick your license as you wish (should match "license" above)
        'License :: OSI Approved :: GNU General Public License (GPL)',

        # Specify the Python versions you support here. In particular, ensure
        # that you indicate whether you support Python 2, Python 3 or both.
        # 'Programming Language :: Python :: 2',
        # 'Programming Language :: Python :: 2.6',
        # 'Programming Language :: Python :: 2.7',
        # 'Programming Language :: Python :: 3',
        # 'Programming Language :: Python :: 3.2',
        # 'Programming Language :: Python :: 3.3',
        # 'Programming Language :: Python :: 3.4',
        'Programming Language :: Python :: 3.5',
        'Programming Language :: Python :: 3.6',
        'Programming Language :: Python :: 3.7',
        'Programming Language :: Python :: 3.8',

    ],

    # What does your project relate to?
    keywords='circular RNA characterization',

    # You can just specify the packages manually here if your project is
    # simple. Or you can use find_packages().
    packages=['FUCHS'],

    # List run-time dependencies here.  These will be installed by pip when
    # your project is installed. For an analysis of "install_requires" vs pip's
    # requirements files see:
    # https://packaging.python.org/en/latest/requirements.html
    install_requires=[
        'pysam>=0.9.0',
        'pybedtools>=0.7.8',
        'pathos>=0.2.1',
        'numpy>=1.17.0'
    ],

    # List additional groups of dependencies here (e.g. development
    # dependencies). You can install these using the following syntax,
    # for example:
    # $ pip install -e .[dev,test]
    # extras_require={
    #     'dev': ['check-manifest'],
    #     'test': ['coverage'],
    # },

    # If there are data files included in your packages that need to be
    # installed, specify them here.  If using Python 2.6 or less, then these
    # have to be included in MANIFEST.in as well.
    package_data={
        'FUCHS': ['data/*'],
        'FUCHS': ['scripts/*.R'],
    },

    # Although 'package_data' is the preferred approach, in some case you may
    # need to place data files outside of your packages. See:
    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
    # data_files=[('my_data', ['data/data_file'])],

    # To provide executable scripts, use entry points in preference to the
    # "scripts" keyword. Entry points provide cross-platform support and allow
    # pip to create the appropriate form of executable for the target platform.

    zip_safe=False,

    entry_points={
        'console_scripts': [
            'FUCHS=FUCHS:main'
        ],
    },

    scripts=[
        'scripts/FUCHS',
        'scripts/summarized_coverage_profiles.R',
        'scripts/make_coverage_picture.R',
        'scripts/guided_denovo_circle_structure_parallel'
    ],
    project_urls={  # Optional
        'Bug Reports': 'https://github.com/dieterich-lab/FUCHS/issues',
        'Dieterich Lab': 'https://dieterichlab.org',
        'Source': 'https://github.com/dieterich-lab/FUCHS',
        'Documentation': 'http://docs.circ.tools'
},
)
