<commit_before>from ez_setup import use_setuptools
use_setuptools()
from setuptools import setup
import sys

def main():
    # Only install functools32 if we're in Python 2 (it's not available
    # for Python 3)
    install_list = ['pysb>=1.3.0', 'objectpath', 'rdflib==4.2.1',
                    'requests>=2.11', 'lxml', 'ipython', 'future',
                    'networkx==1.11', 'pandas']
    # We implicitly require numpy since pandas depends on numpy
    if sys.version_info[0] == 2:
        install_list.append('functools32')

    extras_require = {'machine': ['pytz', 'tzlocal', 'tweepy', 'ndex2',
                                  'pyyaml', 'click'],
                       
                      # Assemblers
                      'pybel_assembler': ['pybel'],

                      # Databases
                      'chembl_client': ['sympy'],
                      'ndex_client': ['ndex2'],

                      # db
                      'db': ['sqlalchemy', 'boto3'],

                      # explanation
                      'explanation': ['kappy==4.0.0rc1'],

                      # literature
                      's3_client': ['boto3', 'botocore'],

                      # sources
                      'bel': ['pybel'],
                      'biopax': ['pyjnius'],
                      'eidos': ['yaml', 'objectpath', 'pyjnius'],
                      'geneways': ['stemming', 'nltk'],
                      'index_cards': ['objectpath'],
                      'ndex_cx': ['objectpath'],
                      'reach': ['objectpath'],
                      'sofia': ['openpyxl'],
                      'bbn': ['rdflib-jsonld'],

                      # util
                      'kappa_util': ['pygraphviz'],
                      'plot_formatting': ['matplotlib'],
                      'aws': ['boto3'],
                      }
    extras_require['all'] = list({dep for deps in extras_require.values()
                                  for dep in deps})

    setup(name='indra',
          version='1.7.0',
          description='Integrated Network and Dynamical Reasoning Assembler',
          long_description='INDRA is a framework '
              'for assembling rule-based mathematical models and '
              'mechanistic networks of biochemical systems from natural '
              'language and pathway databases.',
          author='<NAME>',
          author_email='<EMAIL>',
          url='http://github.com/sorgerlab/indra',
          packages=['indra', 'indra.assemblers', 'indra.belief',
                    'indra.benchmarks', 'indra.databases', 'indra.db',
                    'indra.explanation', 'indra.explanation.paths_graph',
                    'indra.literature', 'indra.mechlinker',
                    'indra.preassembler', 'indra.sources',
                    'indra.sources.bbn', 'indra.sources.bel',
                    'indra.sources.biopax', 'indra.sources.cwms',
                    'indra.sources.eidos',
                    'indra.sources.geneways', 'indra.sources.index_cards',<commit_msg>In setup.py's extras_require section: * Removed dependencies already covered as standard dependencies * Consolidated bel and ndex dependency categories * Depend on jnius-indra instead of pyjnius<commit_after>from ez_setup import use_setuptools
use_setuptools()
from setuptools import setup
import sys

def main():
    # Only install functools32 if we're in Python 2 (it's not available
    # for Python 3)
    install_list = ['pysb>=1.3.0', 'objectpath', 'rdflib==4.2.1',
                    'requests>=2.11', 'lxml', 'ipython', 'future',
                    'networkx==1.11', 'pandas']
    # We implicitly require numpy since pandas depends on numpy
    if sys.version_info[0] == 2:
        install_list.append('functools32')

    extras_require = {'machine': ['pytz', 'tzlocal', 'tweepy', 'ndex2',
                                  'pyyaml', 'click'],
                       
                      'ndex': ['ndex2'],
                      'bel': ['pybel'],

                      # db
                      'db': ['sqlalchemy', 'boto3'],

                      # explanation
                      'explanation': ['kappy==4.0.0rc1'],

                      # literature
                      's3_client': ['boto3', 'botocore'],

                      # sources
                      'biopax': ['jnius-indra'],
                      'eidos': ['yaml', 'jnius-indra'],
                      'geneways': ['stemming', 'nltk'],
                      'sofia': ['openpyxl'],
                      'bbn': ['rdflib-jsonld'],

                      # util
                      'kappa_util': ['pygraphviz'],
                      'plot_formatting': ['matplotlib'],
                      'aws': ['boto3'],
                      }
    extras_require['all'] = list({dep for deps in extras_require.values()
                                  for dep in deps})

    setup(name='indra',
          version='1.7.0',
          description='Integrated Network and Dynamical Reasoning Assembler',
          long_description='INDRA is a framework '
              'for assembling rule-based mathematical models and '
              'mechanistic networks of biochemical systems from natural '
              'language and pathway databases.',
          author='<NAME>',
          author_email='<EMAIL>',
          url='http://github.com/sorgerlab/indra',
          packages=['indra', 'indra.assemblers', 'indra.belief',
                    'indra.benchmarks', 'indra.databases', 'indra.db',
                    'indra.explanation', 'indra.explanation.paths_graph',
                    'indra.literature', 'indra.mechlinker',
                    'indra.preassembler', 'indra.sources',
                    'indra.sources.bbn', 'indra.sources.bel',
                    'indra.sources.biopax', 'indra.sources.cwms',
                    'indra.sources.eidos',
                    'indra.sources.geneways', 'indra.sources.index_cards',
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