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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 @ git+https://github.com/pysb/pysb.git', 'objectpath',
'requests>=2.11', 'lxml', 'ipython', 'future',
'networkx>=3', 'pandas>=2', 'ndex2', 'jinja2',
'protmapper>=0.0.29', 'obonet',
'tqdm', 'pybiopax>=0.0.5']
extras_require = {
# Inputs and outputs
'trips_offline': ['pykqml'],
'reach_offline': ['cython<3', 'pyjnius==1.1.4'],
'eidos_offline': ['cython<3', 'pyjnius==1.1.4'],
'hypothesis': ['gilda>1.0.0'],
'geneways': ['stemming', 'nltk<3.6'],
'bel': ['pybel>=0.15.0,<0.16.0'],
'tkg': ['pybel>=0.15.0,<0.16.0',
'texttoknowledgegraph; python_version >= "3.9"'],
'sbml': ['python-libsbml'],
# Tools and analysis
'machine': ['pytz', 'tzlocal', 'tweepy', 'pyyaml>=5.1.0',
'click'],
'explanation': ['kappy==4.1.2', 'paths-graph'],
'grounding': ['adeft', 'gilda>1.0.0'],
# AWS interface and database
'aws': ['boto3', 'reportlab'],
# Utilities
'graph': ['pygraphviz'],
'plot': ['matplotlib'],
'isi': ['nltk<3.6', 'unidecode'],
'api': ['flask>=3.0,<4.0',
'flask_restx>=1.3.0',
'flask_cors',
'docstring-parser',
'gunicorn'],
# scikit-learn 1.5.0 breaks DisambManager.run_adeft_disambiguation
# see: https://github.com/gyorilab/adeft/issues/80
'sklearn_belief': ['scikit-learn<1.5.0'],
'owl': ['pronto'],
'tests':
['pytest',
'pytest-cov',
'pynose' # This is needed for PySB with_model in
# some tests
],
}
extras_require['all'] = list({dep for deps in extras_require.values()
for dep in deps})
setup(name='indra',
version='1.24.0',
description='Integrated Network and Dynamical Reasoning Assembler',
long_description=long_description,
long_description_content_type='text/markdown',
author='Benjamin Gyori',
author_email='b.gyori@northeastern.edu',
url='http://github.com/gyorilab/indra',
packages=['indra', 'indra.assemblers',
'indra.assemblers.cx', 'indra.assemblers.cyjs',
'indra.assemblers.english',
'indra.assemblers.graph', 'indra.assemblers.html',
'indra.assemblers.index_card',
'indra.assemblers.indranet',
'indra.assemblers.kami', 'indra.assemblers.pybel',
'indra.assemblers.pysb', 'indra.assemblers.sbgn',
'indra.assemblers.sif', 'indra.assemblers.tsv',
'indra.belief',
'indra.benchmarks', 'indra.databases',
'indra.explanation', 'indra.explanation.model_checker',
'indra.explanation.pathfinding',
'indra.literature', 'indra.mechlinker',
'indra.ontology', 'indra.ontology.bio',
'indra.ontology.virtual',
'indra.ontology.app', 'indra.pipeline',
'indra.preassembler',
'indra.preassembler.grounding_mapper', 'indra.sources',
'indra.sources.acsn',
'indra.sources.bel', 'indra.sources.biofactoid',
'indra.sources.biopax', 'indra.sources.creeds',
'indra.sources.crog', 'indra.sources.ctd',
'indra.sources.dgi',
'indra.sources.drugbank', 'indra.sources.eidos',
'indra.sources.geneways', 'indra.sources.gnbr',
'indra.sources.hprd', 'indra.sources.hypothesis',
'indra.sources.index_cards',
'indra.sources.indra_db_rest', 'indra.sources.isi',
'indra.sources.minerva', 'indra.sources.ndex_cx',
'indra.sources.reach', 'indra.sources.omnipath',
'indra.sources.phosphoelm',
'indra.sources.rlimsp', 'indra.sources.semrep',
'indra.sources.signor',
'indra.sources.sparser', 'indra.sources.tas',
'indra.sources.tees', 'indra.sources.tkg',
'indra.sources.trips', 'indra.sources.trrust',
'indra.sources.ubibrowser',
'indra.sources.virhostnet',
'indra.sources.wormbase',
'indra.resources', 'indra.statements',
'indra.tests', 'indra.tests.test_obo_clients',
'indra.tools',
'indra.tools.machine', 'indra.util'],
install_requires=install_list,
extras_require=extras_require,
include_package_data=True,
keywords=[
'systems', 'biology', 'model', 'pathway', 'assembler',
'nlp', 'mechanism', 'biochemistry', 'network',
'big mechanism', 'bigmech',
'world modelers',
'communicating with computers', 'cwc',
'automated scientific discovery framework', 'asdf',
'automating scientific knowledge extraction', 'aske',
'panacea',
],
classifiers=[
'Development Status :: 4 - Beta',
'Environment :: Console',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
'Programming Language :: Python :: 3.12',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Chemistry',
'Topic :: Scientific/Engineering :: Mathematics',
],
entry_points={'console_scripts':
['indra-machine = indra.tools.machine.cli:main']}
)
if __name__ == '__main__':
main()