import sys

from setuptools import setup, find_packages

from setuptools.command.test import test as TestCommand

from medacy import __version__, __authors__

packages = find_packages()

def readme():

    with open('README.md') as f:

        return f.read()

class PyTest(TestCommand):

    """

    Custom Test Configuration Class

    Read here for details: https://docs.pytest.org/en/latest/goodpractices.html

    """

    user_options = [("pytest-args=", "a", "Arguments to pass to pytest")]

    def initialize_options(self):

        TestCommand.initialize_options(self)

        self.pytest_args = "--cov-config .coveragerc --cov-report html --cov-report term --cov=medacy"

    def run_tests(self):

        import shlex

        # import here, cause outside the eggs aren't loaded

        import pytest

        errno = pytest.main(shlex.split(self.pytest_args))

        sys.exit(errno)

setup(

    name='medacy',

    version=__version__,

    python_requires='>=3.6',

    license='GNU GENERAL PUBLIC LICENSE',

    description='Medical Natural Language Processing (NLP) with spaCy',

    long_description=readme(),

    packages=packages,

    url='https://github.com/NLPatVCU/medaCy',

    author=__authors__,

    keywords='natural-language-processing medical-natural-language-processing machine-learning nlp-library metamap clinical-text-processing',

    classifiers=[

        'Status :: 4 - Beta',

        'License :: OSI Approved :: GNU General Public License (GPL)',

        'Programming Language :: Python :: 3.7',

        'Natural Language :: English',

        'Topic :: Text Processing :: Linguistic',

        'Intended Audience :: Science/Research'

    ],

    dependency_links=[

        'https://github.com/explosion/spacy-models/releases//tag/en_core_web_sm-2.2.5'

    ],

    install_requires=[

        'spacy==2.2.2',

        'scispacy==0.2.2',

        'scikit-learn>=0.20.0',

        'torch>=1.2.0',

        'pytorch-crf==0.7.2',

        'numpy>=1.16.1',

        'transformers==2.3.0',

        'sklearn-crfsuite',

        'xmltodict>=0.11.0',

        'joblib>=0.12.5',

        'tabulate>=0.8.2',

        'pathos>=0.2.2.1',

        'msgpack>=0.3.0,<0.6',

        'msgpack-numpy<0.4.4.0',

        'gensim==3.8.0',

        'en_core_web_sm @ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.2.5/en_core_web_sm-2.2.5.tar.gz'

    ],

    extras_require={

        ':python_version == "3.6"': [

            'dataclasses',

        ],

    },

    tests_require=[

        "pytest",

        "pytest-cov",

    ],

    cmdclass={"pytest": PyTest},

    include_package_data=True,

    zip_safe=False

)