#!/usr/bin/env python

# -*- encoding: utf-8 -*-

"""Setup script"""

from __future__ import absolute_import

from __future__ import print_function

import io

import re

from glob import glob

from os.path import basename

from os.path import dirname

from os.path import join

from os.path import splitext

from setuptools import find_packages

from setuptools import setup

def _read(*names, **kwargs):

    return io.open(

        join(dirname(__file__), *names),

        encoding=kwargs.get('encoding', 'utf8')

    ).read()

setup(

    name='janggu',

    version='0.10.2',

    license='GPL-3.0',

    description='Utilities and datasets for deep learning in genomics',

    long_description='%s\n%s' % (

        re.compile('^.. start-badges.*^.. end-badges',

                   re.M | re.S).sub('', _read('README.rst')),

        re.sub(':[a-z]+:`~?(.*?)`', r'``\1``', _read('CHANGELOG.rst'))

    ),

    long_description_content_type='text/x-rst',

    author='Wolfgang Kopp',

    author_email='wolfgang.kopp@mdc-berlin.de',

    url='https://github.com/BIMSBbioinfo/janggu',

    packages=find_packages('src'),

    package_dir={'': 'src'},

    package_data={'janggu': ['resources/*.fa',

                             'resources/*.bed',

                             'resources/*.csv']},

    py_modules=[splitext(basename(path))[0] for path in glob('src/*.py')],

    include_package_data=True,

    zip_safe=False,

    classifiers=[

        # complete list: http://pypi.python.org/pypi?%3Aaction=list_classifiers

        'Development Status :: 5 - Production/Stable',

        'Intended Audience :: Developers',

        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',

        'Operating System :: Unix',

        'Operating System :: POSIX',

        'Programming Language :: Python',

        'Programming Language :: Python :: 3.5',

        'Programming Language :: Python :: 3.6',

        'Programming Language :: Python :: 3.7',

        'Topic :: Utilities',

    ],

    keywords=[

        'genomics', 'epigenomics', 'bioinformatics',

        'deep learning', 'machine learning'

    ],

    install_requires=[

        'numpy',

        'pandas',

        'Biopython==1.77',

        'h5py',

        'pybedtools',

        'pydot',

        'pysam<0.16,!=0.15.3',

        'pyBigWig',

        'progress',

        'matplotlib',

        'seaborn',

        'scikit-learn',

        'scipy',

    ],

    extras_require={

        "tf": ['tensorflow==1.14', 'keras<2.3'],

        "tf_gpu": ['tensorflow-gpu==1.14', 'keras<2.3'],

        "tf2": ['tensorflow==2.2', 'keras==2.4.3'],

        "tf2_gpu": ['tensorflow-gpu==2.2', 'keras==2.4.3'],

    },

    entry_points={

        'console_scripts': [

            'janggu = janggu.cli:main',

            'janggu-trim = janggu.janggutrim:main',

        ]

    }

)