old_contents: from __future__ import print_function
  
  import os
  from distutils.core import setup
  from setuptools import find_packages
  try:
      from Cython.Build import cythonize
      import Cython.Distutils
      CYTHON=True
  except ImportError:
      CYTHON=False
      print('CYTHON UNAVAILABLE')
  try:
      import numpy
      NUMPY = True
  except ImportError:
      NUMPY = False
      print('NUMPY NOT INSTALLED')
  
  # 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-ms',
      version='0.1.43rc1',
      packages=find_packages(),
      scripts=['scripts/pyQuant'],
      entry_points={'console_scripts': ['pyQuant = pyquant.command_line:run_pyquant',]},
      install_requires = ['cython', 'numpy', 'scipy', 'patsy', 'pythomics', 'pandas', 'lxml', 'scikit-learn', 'simplejson'],
      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',
      ],
      cmdclass={'build_ext': Cython.Distutils.build_ext} if CYTHON else {},
      ext_modules = cythonize("pyquant/*.pyx") if CYTHON else [],
      include_dirs = [numpy.get_include()] if NUMPY else [],
  )
  
new_contents: from __future__ import print_function
  
  import os
  from distutils.core import setup
  from setuptools import find_packages
  try:
      from Cython.Build import cythonize
      import Cython.Distutils
      CYTHON=True
  except ImportError:
      CYTHON=False
      print('CYTHON UNAVAILABLE')
  try:
      import numpy
      NUMPY = True
  except ImportError:
      NUMPY = False
      print('NUMPY NOT INSTALLED')
  
  # 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-ms',
      version='0.1.43rc2',
      packages=find_packages(),
      scripts=['scripts/pyQuant'],
      entry_points={'console_scripts': ['pyQuant = pyquant.command_line:run_pyquant',]},
      install_requires = ['cython', 'numpy', 'scipy >= 0.18.*', 'patsy', 'pythomics >= 0.3.41', 'pandas', 'lxml', 'scikit-learn', 'simplejson'],
      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',
      ],
      cmdclass={'build_ext': Cython.Distutils.build_ext} if CYTHON else {},
      ext_modules = cythonize("pyquant/*.pyx") if CYTHON else [],
      include_dirs = [numpy.get_include()] if NUMPY else [],
  )
  
subject: Fix versions of scipy and pythomics