old_contents: 
  from setuptools import setup, find_packages
  # To use a consistent encoding
  from codecs import open
  from os import path
  
  here = path.abspath(path.dirname(__file__))
  PACKAGES = [
      'lib',
      'lib.scripts',
      'lib.scripts.biosql',
      'lib.scripts.blast',
      'lib.scripts.ftp',
      'lib.scripts.genbank',
      'lib.scripts.manager',
      'lib.scripts.multiprocessing',
      'lib.scripts.phylogenetic_analyses'
  ]
  # Get the long description from the README file
  with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
      long_description = f.read()
  
  setup(
      name='orthologs',
      description="A project that will help to analyze orthologous gense.",
      version='0.1.0',
      long_description=long_description,
      url='https://github.com/robear22890/Orthologs-Project',
      license='?',
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Science/Research',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Visualization',
          'Programming Language :: Python :: 3',
          'Operating System :: Unix',
          'Natural Language :: English'
      ],
      packages=
  )
  
new_contents: # Used:
  # https://github.com/pypa/sampleproject/blob/master/setup.py
  # https://github.com/biopython/biopython/blob/master/setup.py
  
  from setuptools import setup, find_packages
  # To use a consistent encoding
  from codecs import open
  from os import path
  
  here = path.abspath(path.dirname(__file__))
  
  PACKAGES = [
      'lib',
      'lib.scripts',
      'lib.scripts.biosql',
      'lib.scripts.blast',
      'lib.scripts.ftp',
      'lib.scripts.genbank',
      'lib.scripts.manager',
      'lib.scripts.multiprocessing',
      'lib.scripts.phylogenetic_analyses'
  ]
  
  # Get the long description from the README file
  with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
      long_description = f.read()
  
  setup(
      name='orthologs',
      description="A project that will help to analyze orthologous gense.",
      version='0.1.0',
      long_description=long_description,
      url='https://github.com/robear22890/Orthologs-Project',
      license='?',
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Science/Research',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Scientific/Engineering :: Visualization',
          'Programming Language :: Python :: 3',
          'Operating System :: Unix',
          'Natural Language :: English'
      ],
      packages=PACKAGES,
      install_requires=[],
  )
  
subject: Develop here. Belongs in top level Orthologs Project.