import os
import re
import subprocess

import setuptools

directory = os.path.dirname(os.path.abspath(__file__))

# version
init_path = os.path.join(directory, 'ontobio', '__init__.py')
with open(init_path) as read_file:
    text = read_file.read()
version = '0.1.2'

# long_description
readme_path = os.path.join(directory, 'README.md')
try:
    # copied from dhimmel/obonet:
    # Try to create an reStructuredText long_description from README.md
    args = 'pandoc', '--from', 'markdown', '--to', 'rst', readme_path
    long_description = subprocess.check_output(args)
    long_description = long_description.decode()
except Exception as error:
    # Fallback to markdown (unformatted on PyPI) long_description
    print('README.md conversion to reStructuredText failed. Error:')
    print(error)
    with open(readme_path) as read_file:
        long_description = read_file.read()

setuptools.setup(
    name='ontobio',
    version=version,
    author='Chris Mungall',
    author_email='cmungall@gmail.com',
    url='https://github.com/biolink-api/ontobio',
    description='Library for working with OBO Library Ontologies and associations',
    long_description=long_description,
    license='BSD',
    #packages=['ontobio'],
    packages=setuptools.find_packages(),

    keywords='ontology graph obo owl sparql networkx network',
    classifiers=[
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Topic :: Scientific/Engineering :: Information Analysis',
        'License :: OSI Approved :: BSD License',
        'Programming Language :: Python :: 3',
        'Topic :: Scientific/Engineering :: Visualization'
    ],

    # Dependencies
    install_requires=[
        'networkx',
        'pyyaml',
        'pysolr',
        'requests',
        'sparqlwrapper',
        'cachier',
        'prefixcommons',
        'scipy'
    ],

    # 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': ['plotly'],
        'test': ['pytest'],
    },
    scripts=['bin/ogr.py', 'bin/ogr-assoc.py']
    # 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.
    #entry_points={
    #    'console_scripts': [
    #        'sample=sample:main',
    #    ],
    #},
)

import os
import re
import subprocess

import setuptools

directory = os.path.dirname(os.path.abspath(__file__))

# version
init_path = os.path.join(directory, 'ontobio', '__init__.py')
with open(init_path) as read_file:
    text = read_file.read()
version = '0.1.2'

# long_description
readme_path = os.path.join(directory, 'README.md')
try:
    # copied from dhimmel/obonet:
    # Try to create an reStructuredText long_description from README.md
    args = 'pandoc', '--from', 'markdown', '--to', 'rst', readme_path
    long_description = subprocess.check_output(args)
    long_description = long_description.decode()
except Exception as error:
    # Fallback to markdown (unformatted on PyPI) long_description
    print('README.md conversion to reStructuredText failed. Error:')
    print(error)
    with open(readme_path) as read_file:
        long_description = read_file.read()

setuptools.setup(
    name='ontobio',
    version=version,
    author='Chris Mungall',
    author_email='cmungall@gmail.com',
    url='https://github.com/biolink/ontobio',
    description='Library for working with OBO Library Ontologies and associations',
    long_description=long_description,
    license='BSD',
    #packages=['ontobio'],
    packages=setuptools.find_packages(),

    keywords='ontology graph obo owl sparql networkx network',
    classifiers=[
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Topic :: Scientific/Engineering :: Information Analysis',
        'License :: OSI Approved :: BSD License',
        'Programming Language :: Python :: 3',
        'Topic :: Scientific/Engineering :: Visualization'
    ],

    # Dependencies
    install_requires=[
        'networkx',
        'pyyaml',
        'pysolr',
        'requests',
        'sparqlwrapper',
        'cachier',
        'prefixcommons',
        'scipy'
    ],

    # 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': ['plotly'],
        'test': ['pytest'],
    },
    scripts=['bin/ogr.py', 'bin/ogr-assoc.py']
    # 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.
    #entry_points={
    #    'console_scripts': [
    #        'sample=sample:main',
    #    ],
    #},
)

fix url