old_contents: from setuptools import setup
  from setuptools import Extension
  from setuptools import find_packages
  
  from distutils.command.build_ext import build_ext as _build_ext
  
  import os
  import subprocess
  import glob
  
  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()
  
  fake_ext = Extension(
  	"prophyle.fake_extension",
  	["prophyle/fake_extension.c"],
  )
  
  class build_ext(_build_ext):
  	def run(self):
  		subprocess.call('make -C prophyle', shell=True)
  		_build_ext.run(self)
  
  setup(
  	name='prophyle',
  
  	version='0.1.0.11',
  
  
  	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 = find_packages(),
  
  	install_requires=['ete3', 'numpy', 'wheel', 'six', 'scipy', 'bitarray'],
  
  	package_data={
  		'prophyle': [
  			'README.rst',
  			'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',
  		]
  	},
  
  	ext_modules=[fake_ext],
  
  	entry_points={
  			'console_scripts': [
  			'prophyle = prophyle.prophyle:main',
  			'newick2makefile.py = prophyle.newick2makefile:main',
  			'create_final_fasta.py = prophyle.create_final_fasta:main',
  			'assignment.py = prophyle.assignment:main',
  		]
  	},
  
  	cmdclass={'build_ext': build_ext},
  )
  
new_contents: from setuptools import setup
  from setuptools import Extension
  from setuptools import find_packages
  
  from distutils.command.build_ext import build_ext as _build_ext
  
  import os
  import subprocess
  import glob
  
  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()
  
  fake_ext = Extension(
  	"prophyle.fake_extension",
  	["prophyle/fake_extension.c"],
  )
  
  class build_ext(_build_ext):
  	def run(self):
  		subprocess.call('make -C prophyle', shell=True)
  		_build_ext.run(self)
  
  setup(
  	name='prophyle',
  
  	version='0.1.0.12',
  
  
  	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 = find_packages(),
  
  	install_requires=['ete3', 'numpy', 'wheel', 'six', 'scipy', 'bitarray'],
  
  	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',
  		]
  	},
  
  	ext_modules=[fake_ext],
  
  	entry_points={
  			'console_scripts': [
  			'prophyle = prophyle.prophyle:main',
  			'newick2makefile.py = prophyle.newick2makefile:main',
  			'create_final_fasta.py = prophyle.create_final_fasta:main',
  			'assignment.py = prophyle.assignment:main',
  		]
  	},
  
  	cmdclass={'build_ext': build_ext},
  )
  
subject: Fix list of included files