old_contents: from setuptools import setup
  
  setup_requires = [
      'numpy',
  ]
  
  install_requires = [
      'numpy',
      'negspy',
      'pysam',
      'dask',
      'requests',
      'h5py',
      'pandas',
      'slugid',
      'sortedcontainers',
      'nose',
      'cooler>=0.8.5',
      'pybbi>=0.2.0',
      'Click>=7'
  ]
  
  setup(
      name='clodius',
      version='0.10.11',
      description='Tile generation for big data',
      author='Peter Kerpedjiev',
      author_email='pkerpedjiev@gmail.com',
      url='',
      packages=['clodius', 'clodius.cli', 'clodius.tiles'],
      setup_requires=setup_requires,
      install_requires=install_requires,
      scripts=[
          'scripts/tsv_to_mrmatrix.py'
      ],
      entry_points={
          'console_scripts': [
              'clodius = clodius.cli.aggregate:cli'
          ]
      }
  )
  
new_contents: from setuptools import setup
  import os
  import io
  
  
  def read(*parts, **kwargs):
      filepath = os.path.join(HERE, *parts)
      encoding = kwargs.pop('encoding', 'utf-8')
      with io.open(filepath, encoding=encoding) as fh:
          text = fh.read()
      return text
  
  
  def get_requirements(path):
      content = read(path)
      return [
          req
          for req in content.split("\n")
          if req != '' and not req.startswith('#')
      ]
  
  
  setup_requires = [
      'numpy',
  ]
  
  install_requires = get_requirements('requirements.txt')
  
  setup(
      name='clodius',
      version='0.10.11',
      description='Tile generation for big data',
      author='Peter Kerpedjiev',
      author_email='pkerpedjiev@gmail.com',
      url='',
      packages=['clodius', 'clodius.cli', 'clodius.tiles'],
      setup_requires=setup_requires,
      install_requires=install_requires,
      scripts=[
          'scripts/tsv_to_mrmatrix.py'
      ],
      entry_points={
          'console_scripts': [
              'clodius = clodius.cli.aggregate:cli'
          ]
      }
  )
  
subject: Read install_requires from requirements.txt