a b/setup.py 

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#!/usr/bin/env python





  
  

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





  
  

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"""Setup script"""





  
  

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from __future__ import absolute_import





  
  

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from __future__ import print_function





  
  

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import io





  
  

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import re





  
  

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from glob import glob





  
  

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from os.path import basename





  
  

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from os.path import dirname





  
  

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from os.path import join





  
  

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from os.path import splitext





  
  

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from setuptools import find_packages





  
  

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from setuptools import setup





  
  

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def _read(*names, **kwargs):





  
  

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    return io.open(





  
  

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        join(dirname(__file__), *names),





  
  

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





  
  

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    ).read()





  
  

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setup(





  
  

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    name='janggu',





  
  

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    version='0.10.2',





  
  

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    license='GPL-3.0',





  
  

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





  
  

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





  
  

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





  
  

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





  
  

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





  
  

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    ),





  
  

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    long_description_content_type='text/x-rst',





  
  

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    author='Wolfgang Kopp',





  
  

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





  
  

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





  
  

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    packages=find_packages('src'),





  
  

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    package_dir={'': 'src'},





  
  

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





  
  

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                             'resources/*.bed',





  
  

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                             'resources/*.csv']},





  
  

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





  
  

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    include_package_data=True,





  
  

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    zip_safe=False,





  
  

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    classifiers=[





  
  

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





  
  

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





  
  

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        'Intended Audience :: Developers',





  
  

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





  
  

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        'Operating System :: Unix',





  
  

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        'Operating System :: POSIX',





  
  

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        'Programming Language :: Python',





  
  

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        'Programming Language :: Python :: 3.5',





  
  

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        'Programming Language :: Python :: 3.6',





  
  

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        'Programming Language :: Python :: 3.7',





  
  

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        'Topic :: Utilities',





  
  

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    ],





  
  

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    keywords=[





  
  

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





  
  

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        'deep learning', 'machine learning'





  
  

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    ],





  
  

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    install_requires=[





  
  

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        'numpy',





  
  

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        'pandas',





  
  

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        'Biopython==1.77',





  
  

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        'h5py',





  
  

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        'pybedtools',





  
  

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        'pydot',





  
  

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        'pysam<0.16,!=0.15.3',





  
  

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        'pyBigWig',





  
  

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        'progress',





  
  

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        'matplotlib',





  
  

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        'seaborn',





  
  

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        'scikit-learn',





  
  

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        'scipy',





  
  

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    ],





  
  

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    extras_require={





  
  

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





  
  

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





  
  

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





  
  

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





  
  

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    },





  
  

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    entry_points={





  
  

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        'console_scripts': [





  
  

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            'janggu = janggu.cli:main',





  
  

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





  
  

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        ]





  
  

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    }





  
  

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)