<commit_before>import os

from ez_setup import use_setuptools
use_setuptools()

from setuptools import setup, find_packages

# full path appears to be required for old (0.6.x?) versions of setuptools
root_dir = os.path.dirname(os.path.abspath(__file__))

with open(os.path.join(root_dir, 'doc/description.txt')) as f:
    long_description = f.read()

setup(
    license = 'Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)',
    long_description = long_description,
    use_hg_version = True,
    zip_safe = False,

    author = 'HGVS Contributors',
    author_email = '<EMAIL>',
    description = """HGVS Parser""",
    name = "hgvs",
    package_data = {'hgvs': ['data/*']},
    packages = find_packages(),
    url = 'https://bitbucket.org/invitae/hgvs',

    classifiers = [
        "Development Status :: 3 - Alpha",
        "Intended Audience :: Developers",
        "Intended Audience :: Healthcare Industry",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: Apache Software License",
        "Operating System :: OS Independent",
        "Programming Language :: Python :: 2",
        "Programming Language :: Python",
        "Topic :: Database :: Front-Ends",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Medical Science Apps.",
        ],

    keywords = [
        'bioinformatics',
        'computational biology',
        'genome variants',
        'genome variation',
        'genomic variants',
        'genomic variation',
        'genomics',
        'hgvs',
        ],

    install_requires = [
        'bdi >= 0.1.0',
        'biopython',
        'parsley',
        'recordtype',
        ],

    setup_requires = [
        'hgtools',
        'nose',
        'sphinx',
        ],

    tests_require = [
        'coverage',
        ],
    )

## <LICENSE>
## Copyright 2014 HGVS Contributors (https://bitbucket.org/invitae/hgvs)
## 
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
## 
##     http://www.apache.org/licenses/LICENSE-2.0
## 
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
## </LICENSE><commit_msg>removed accidental tag (!); added sphinxcontrib-fulltoc to setup.py<commit_after>import os

from ez_setup import use_setuptools
use_setuptools()

from setuptools import setup, find_packages

# full path appears to be required for old (0.6.x?) versions of setuptools
root_dir = os.path.dirname(os.path.abspath(__file__))

with open(os.path.join(root_dir, 'doc/description.txt')) as f:
    long_description = f.read()

setup(
    license = 'Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)',
    long_description = long_description,
    use_hg_version = True,
    zip_safe = False,

    author = 'HGVS Contributors',
    author_email = '<EMAIL>',
    description = """HGVS Parser""",
    name = "hgvs",
    package_data = {'hgvs': ['data/*']},
    packages = find_packages(),
    url = 'https://bitbucket.org/invitae/hgvs',

    classifiers = [
        "Development Status :: 3 - Alpha",
        "Intended Audience :: Developers",
        "Intended Audience :: Healthcare Industry",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: Apache Software License",
        "Operating System :: OS Independent",
        "Programming Language :: Python :: 2",
        "Programming Language :: Python",
        "Topic :: Database :: Front-Ends",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Medical Science Apps.",
        ],

    keywords = [
        'bioinformatics',
        'computational biology',
        'genome variants',
        'genome variation',
        'genomic variants',
        'genomic variation',
        'genomics',
        'hgvs',
        ],

    install_requires = [
        'bdi >= 0.1.0',
        'biopython',
        'parsley',
        'recordtype',
        ],

    setup_requires = [
        'hgtools',
        'nose',
        'sphinx',
        'sphinxcontrib-fulltoc',
        ],

    tests_require = [
        'coverage',
        ],
    )

## <LICENSE>
## Copyright 2014 HGVS Contributors (https://bitbucket.org/invitae/hgvs)
## 
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
## 
##     http://www.apache.org/licenses/LICENSE-2.0
## 
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
## </LICENSE>
{'fraction_non_alphanumeric': 0.1261854073930714, 'fraction_numerical': 0.0073543642345655115, 'mean_word_length': 2.755813953488372, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 11, 'https://': 4, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1383762', 'n_tokens_mistral': 1552, 'n_tokens_neox': 1457, 'n_words': 438}