old_contents: import os
  from setuptools import setup, find_packages
  from Cython.Build import cythonize
  from Cython.Distutils import build_ext
  
  try:
      import numpy
      np_install = True
  except ImportError:
      np_install = False
  
  # allow setup.py to be run from any path
  os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))
  
  setup(
      name='pyquant',
      version='0.1.0',
      packages=find_packages(),
      scripts=['scripts/pyQuant'],
      entry_points={'console_scripts': ['pyQuant = pyquant.command_line:run_pyquant',]},
      install_requires = ['pythomics', 'pandas', 'scipy', 'cython', 'lxml', 'scikit-learn', 'patsy', 'numpy'],
      include_package_data=True,
      description='A framework for the analysis of quantitative mass spectrometry data',
      url='http://www.github.com/pandeylab/pyquant',
      author='Chris Mitchell <chris.mit7@gmail.com>',
      classifiers=[
          'License :: OSI Approved :: MIT License',
          'Operating System :: OS Independent',
          'Programming Language :: Python',
      ],
      ext_modules = cythonize("pyquant/*.pyx"),
      include_dirs=[numpy.get_include()] if np_install else None,
  )
  
new_contents: import os
  from setuptools import setup, find_packages
  try:
      from Cython.Build import cythonize
      from Cython.Distutils import build_ext
      CYTHON=True
  except ImportError:
      CYTHON=False
  
  try:
      import numpy
      np_install = True
  except ImportError:
      np_install = False
  
  # allow setup.py to be run from any path
  os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))
  
  setup(
      name='pyquant',
      version='0.1.0',
      packages=find_packages(),
      scripts=['scripts/pyQuant'],
      entry_points={'console_scripts': ['pyQuant = pyquant.command_line:run_pyquant',]},
      install_requires = ['pythomics', 'pandas', 'scipy', 'cython', 'lxml', 'scikit-learn', 'patsy', 'numpy'],
      include_package_data=True,
      description='A framework for the analysis of quantitative mass spectrometry data',
      url='http://www.github.com/pandeylab/pyquant',
      author='Chris Mitchell <chris.mit7@gmail.com>',
      classifiers=[
          'License :: OSI Approved :: MIT License',
          'Operating System :: OS Independent',
          'Programming Language :: Python',
      ],
      ext_modules = cythonize("pyquant/*.pyx") if CYTHON else None,
      include_dirs=[numpy.get_include()] if np_install else None,
  )
  
subject: install options