old_contents: import setuptools
  
  import os
  import subprocess
  import sys
  
  if sys.version_info < (3,2):
  	sys.exit('Minimum supported Python version is 3.2')
  
  here = os.path.abspath(os.path.dirname(__file__))
  
  # Get the long description from the README file
  with open(os.path.join(here, 'README.rst'), encoding='utf-8') as f:
  	long_description = f.read()
  
  
  # Get the current version
  exec(open("prophyle/version.py").read())
  
  setuptools.setup(
  	name='prophyle',
  
  	version=VERSION,
  
  	description='ProPhyle metagenomic classifier',
  
  	long_description=long_description,
  
  	url='https://github.com/karel-brinda/prophyle',
  
  	author='Karel Brinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov',
  	author_email='kbrinda@hsph.harvard.edu, salikhov.kamil@gmail.com, pignottisimone@gmail.com, gregory.kucherov@univ-mlv.fr',
  
  	license='MIT',
  
  	classifiers=[
  		'Development Status :: 4 - Beta',
  		'Topic :: Scientific/Engineering :: Bio-Informatics',
  		'Programming Language :: Python :: 3 :: Only',
  		'License :: OSI Approved :: MIT License',
  	],
  
  	keywords='metagenomics classification NGS',
  
  	packages = ["prophyle"],
  
  	install_requires=['ete3', 'wheel', 'bitarray', 'psutil'],
  
  	package_data={
  		'prophyle': [
  			'Makefile',
  			'*.py',
  			'prophyle_assembler/*.cpp',
  			'prophyle_assembler/*.h',
  			'prophyle_assembler/Makefile',
  			'prophyle_index/*.c',
  			'prophyle_index/*.h',
  			'prophyle_index/Makefile',
  			'prophyle_index/bwa/*.c',
  			'prophyle_index/bwa/*.h',
  			'prophyle_index/bwa/Makefile',
  			'trees/*.nw',
  		],
  	},
  
  	entry_points={
  			'console_scripts': [
  				'prophyle = prophyle.prophyle:main',
  				'prophyle_propagation_makefile.py = prophyle.prophyle_propagation_makefile:main',
  				'prophyle_merge_fa.py = prophyle.prophyle_merge_fa:main',
  				'prophyle_test_tree.py = prophyle.prophyle_test_tree:main',
  				'prophyle_assignment.py = prophyle.prophyle_assignment:main',
  				'prophyle_merge_trees.py = prophyle.prophyle_merge_trees:main',
  			]
  	},
  )
  
new_contents: import setuptools
  
  import os
  import sys
  
  if sys.version_info < (3,2):
  	sys.exit('Minimum supported Python version is 3.2')
  
  here = os.path.abspath(os.path.dirname(__file__))
  
  # Get the long description from the README file
  with open(os.path.join(here, 'README.rst'), encoding='utf-8') as f:
  	long_description = f.read()
  
  
  # Get the current version
  exec(open("prophyle/version.py").read())
  
  setuptools.setup(
  	name='prophyle',
  
  	version=VERSION,
  
  	description='ProPhyle metagenomic classifier',
  
  	long_description=long_description,
  
  	url='https://github.com/karel-brinda/prophyle',
  
  	author='Karel Brinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov',
  	author_email='kbrinda@hsph.harvard.edu, salikhov.kamil@gmail.com, pignottisimone@gmail.com, gregory.kucherov@univ-mlv.fr',
  
  	license='MIT',
  
  	classifiers=[
  		'Development Status :: 4 - Beta',
  		'Topic :: Scientific/Engineering :: Bio-Informatics',
  		'Programming Language :: Python :: 3 :: Only',
  		'License :: OSI Approved :: MIT License',
  	],
  
  	keywords='metagenomics classification NGS',
  
  	packages = ["prophyle"],
  
  	install_requires=['ete3', 'wheel', 'bitarray', 'psutil'],
  
  	package_data={
  		'prophyle': [
  			'Makefile',
  			'*.py',
  			'prophyle_assembler/*.cpp',
  			'prophyle_assembler/*.h',
  			'prophyle_assembler/Makefile',
  			'prophyle_index/*.c',
  			'prophyle_index/*.h',
  			'prophyle_index/Makefile',
  			'prophyle_index/bwa/*.c',
  			'prophyle_index/bwa/*.h',
  			'prophyle_index/bwa/Makefile',
  			'trees/*.nw',
  		],
  	},
  
  	entry_points={
  			'console_scripts': [
  				'prophyle = prophyle.prophyle:main',
  				'prophyle_propagation_makefile.py = prophyle.prophyle_propagation_makefile:main',
  				'prophyle_merge_fa.py = prophyle.prophyle_merge_fa:main',
  				'prophyle_test_tree.py = prophyle.prophyle_test_tree:main',
  				'prophyle_assignment.py = prophyle.prophyle_assignment:main',
  				'prophyle_merge_trees.py = prophyle.prophyle_merge_trees:main',
  			]
  	},
  )
  
subject: Update setup.py