setup.py

from setuptools import setup, Extension, find_packages
import sys

if ("install" in sys.argv) and sys.version_info < (2, 7, 0):
		print "SMALR requires Python 2.7"
		sys.exit(-1)

globals = {}
execfile("smalr/__init__.py", globals)
__version__ = globals["__version__"]
__author__ = globals["__author__"]
__email__ = globals["__email__"]

with open('README.rst') as readme_file:
    readme = readme_file.read()

requirements = [
	'pbcore >= 0.9.4',
	'h5py >= 2.0.1',
	'numpy >= 1.7.1, < 1.14',
	'cython >= 0.17',
	'pysam >= 0.14.0',
	'unittest2'
	]

setup_requirements = [
	# TODO(jbeaulaurier): put setup requirements (distutils extensions, etc.) here
	"nose",
]

test_requirements = [
    # TODO: put package test requirements here
]

setup(
	name = 'smalr',
	version=__version__,
	author=__author__,
	author_email=__email__,
	description='A pipeline for single molecule-level modification analysis of SMRT reads',
	long_description=readme,
	url='https://github.com/jbeaulaurier/SMALR',
	
	packages=find_packages(include=['smalr']),
	include_package_data=True,
	package_data= {'smalr': ['R/*.r']},
	zip_safe= False,
	keywords='smalr methylation single-molecule bacteria SMRT pacbio',

	entry_points={"console_scripts" : ["smalr = smalr.smalr_multicontig:main"]},
	install_requires=requirements,

	classifiers=[
	'Development Status :: 5 - Production/Stable',
	'Intended Audience :: Developers',
	'License :: OSI Approved :: BSD License',
	'Natural Language :: English',
	'Programming Language :: Python :: 2',
	'Programming Language :: Python :: 2.7',
	],
	test_suite='nose.collector',
	tests_require=test_requirements,
	setup_requires=setup_requirements,
)