<commit_before>import os
from setuptools import setup


readme_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                           'README.md')
with open(readme_path, 'r', encoding='utf-8') as fh:
    long_description = fh.read()


def main():
    install_list = ['pysb>=1.3.0,<=1.9.1', 'objectpath',
                    'requests>=2.11', 'lxml', 'ipython', 'future',
                    'networkx>=2', 'pandas<1.3', 'ndex2==2.0.1', 'jinja2',
                    'markupsafe<2.1.0',
                    'protmapper>=0.0.26', 'obonet', 'sympy==1.3',
                    'tqdm', 'pybiopax>=0.0.5']

    extras_require = {
                      # Inputs and outputs
                      'trips_offline': ['pykqml'],
                      'reach_offline': ['cython', 'pyjnius==1.1.4'],
                      'eidos_offline': ['cython', 'pyjnius==1.1.4'],
                      'hypothesis': ['gilda'],
                      'geneways': ['stemming', 'nltk<3.6'],
                      'bel': ['pybel>=0.15.0,<0.16.0'],
                      'sbml': ['python-libsbml'],
                      # Tools and analysis
                      'machine': ['pytz', 'tzlocal', 'tweepy', 'pyyaml>=5.1.0',
                                  'click'],<commit_msg>Bump protmapper version<commit_after>import os
from setuptools import setup


readme_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                           'README.md')
with open(readme_path, 'r', encoding='utf-8') as fh:
    long_description = fh.read()


def main():
    install_list = ['pysb>=1.3.0,<=1.9.1', 'objectpath',
                    'requests>=2.11', 'lxml', 'ipython', 'future',
                    'networkx>=2', 'pandas<1.3', 'ndex2==2.0.1', 'jinja2',
                    'markupsafe<2.1.0',
                    'protmapper>=0.0.27', 'obonet', 'sympy==1.3',
                    'tqdm', 'pybiopax>=0.0.5']

    extras_require = {
                      # Inputs and outputs
                      'trips_offline': ['pykqml'],
                      'reach_offline': ['cython', 'pyjnius==1.1.4'],
                      'eidos_offline': ['cython', 'pyjnius==1.1.4'],
                      'hypothesis': ['gilda'],
                      'geneways': ['stemming', 'nltk<3.6'],
                      'bel': ['pybel>=0.15.0,<0.16.0'],
                      'sbml': ['python-libsbml'],
                      # Tools and analysis
                      'machine': ['pytz', 'tzlocal', 'tweepy', 'pyyaml>=5.1.0',
                                  'click'],
{'fraction_non_alphanumeric': 0.1841070023603462, 'fraction_numerical': 0.03855232100708104, 'mean_word_length': 1.5054187192118227, 'pattern_counts': {'":': 0, '<': 13, '<?xml version=': 0, '>': 17, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6084859', 'n_tokens_mistral': 898, 'n_tokens_neox': 841, 'n_words': 133}