text: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  
  """The setup script."""
  
  from setuptools import setup, find_packages
  
  with open('README.rst') as readme_file:
      readme = readme_file.read()
  
  requirements = [
      "reframed>=1.2",
      "pandas>=0.20.0",
      "requests>=2.18"
  ]
  
  included_files = {
      'carveme': [
          'config.cfg',
          'data/input/bigg_models.csv',
          'data/input/biomass_db.tsv',
          'data/input/manually_curated.csv',
          'data/input/media_db.tsv',
          'data/input/metabolomics_park2016.csv',
          'data/input/unbalanced_metabolites.csv',
          'data/input/bigg_proteins.faa',
          'data/input/equilibrator_compounds.tsv.gz',
          'data/input/refseq_release_201.tsv.gz',
          'data/generated/bigg_gibbs.csv',
          'data/generated/bigg_gprs.csv.gz',
          'data/generated/model_specific_data.csv.gz',
          'data/generated/universe_draft.xml.gz',
          'data/generated/universe_bacteria.xml.gz',
          'data/generated/universe_grampos.xml.gz',
          'data/generated/universe_gramneg.xml.gz',
          'data/generated/universe_archaea.xml.gz',
          'data/benchmark/media_db.tsv',
          'data/benchmark/biolog/bsub/biolog_carbon.tsv',
          'data/benchmark/biolog/bsub/biolog_phosphorus.tsv',
          'data/benchmark/biolog/bsub/biolog_nitrogen.tsv',
          'data/benchmark/biolog/bsub/biolog_sulfur.tsv',
          'data/benchmark/biolog/ecol/biolog_carbon.tsv',
          'data/benchmark/biolog/ecol/biolog_phosphorus.tsv',
          'data/benchmark/biolog/ecol/biolog_nitrogen.tsv',
          'data/benchmark/biolog/ecol/biolog_sulfur.tsv',
          'data/benchmark/biolog/paer/biolog_carbon.tsv',
          'data/benchmark/biolog/rsol/biolog_carbon.tsv',
          'data/benchmark/biolog/rsol/biolog_phosphorus.tsv',
          'data/benchmark/biolog/rsol/biolog_nitrogen.tsv',
          'data/benchmark/biolog/rsol/biolog_sulfur.tsv',
          'data/benchmark/biolog/sone/biolog_carbon.tsv',
          'data/benchmark/biolog/sone/biolog_nitrogen.tsv',
          'data/benchmark/essentiality/bsub.tsv',
          'data/benchmark/essentiality/ecol.tsv',
          'data/benchmark/essentiality/mgen.tsv',
          'data/benchmark/essentiality/paer.tsv',
          'data/benchmark/essentiality/sone.tsv',
          'data/benchmark/fasta/Bsubtilis_168.faa',
          'data/benchmark/fasta/Paeruginosa_PAO1.faa',
          'data/benchmark/fasta/Ecoli_K12_MG1655.faa',
          'data/benchmark/fasta/M_genitalium_G37.faa',
          'data/benchmark/fasta/Rsolanacearum_GMI1000.faa',
          'data/benchmark/fasta/Soneidensis_MR1.faa',
          'data/benchmark/models/bsub.xml',
          'data/benchmark/models/rsol.xml',
          'data/benchmark/models/ecol.xml',
          'data/benchmark/models/paer.xml',
          'data/benchmark/models/sone.xml',
          'data/benchmark/models/mgen.xml',
          'data/benchmark/results/biolog.tsv',
          'data/benchmark/results/essentiality.tsv',
      ]
  }
  
  
  setup(
      name='carveme',
      version='1.4.1',
      description="CarveMe: automated metabolic model reconstruction",
      long_description=readme,
      author="Daniel Machado",
      author_email='cdanielmachado@gmail.com',
      url='https://github.com/cdanielmachado/carveme',
      entry_points={
          'console_scripts': [
              'build_universe=carveme.cli.build_universe:main',
              'carve=carveme.cli.carve:main',
              'gapfill=carveme.cli.gapfill:main',
              'merge_community=carveme.cli.merge_community:main',
              'benchmark=carveme.cli.benchmark:main',
          ],
      },
      #   package_dir={'':'src'},
      packages=find_packages(),
      include_package_data=True,
      package_data=included_files,
      install_requires=requirements,
      license="Apache Software License 2.0",
      zip_safe=False,
      keywords='carveme',
      classifiers=[
          'Development Status :: 5 - Production/Stable',
          'Environment :: Console', 
          'Intended Audience :: Science/Research',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Programming Language :: Python :: 3.6',
          'Programming Language :: Python :: 3.7',
          'License :: OSI Approved :: Apache Software License',
      ],
      setup_requires=['setuptools_scm']
      #    test_suite='tests',
      #    tests_require=test_requirements,
  )
  