setup.py

#!/bin/env python
"""
@author: Edwin Tye (Edwin.Tye@phe.gov.uk)
"""
import re
import subprocess
from setuptools import setup
from setuptools.extension import Extension

try:
    import numpy
except ImportError:
    raise ImportError('numpy needs to be installed before PyGOM can be '
                      'installed. Try installing with "pip install numpy" '
                      'before installing PyGOM.')

## For the cython parts ###
try:
    from Cython.Distutils import build_ext
except ImportError:
    use_cython = False
else:
    use_cython = True

cmdclass = { }
ext_modules = [ ]

#For this to work the .c files are not include in GIT except in the release
#release branch (the c files would be created using python setup.py sdist)
if use_cython:
    ext_modules += [
        Extension("pygom.model._tau_leap",
                  ["pygom/model/_tau_leap.pyx"],
                  include_dirs=[numpy.get_include()],
#                  extra_compile_args=['-fopenmp'],
#                  extra_link_args=['-fopenmp']),
)
    ]
    cmdclass.update({'build_ext': build_ext})
else:
#    raise ImportError('You will need Cython installed to create'
#                      'the c extensions. Try installing with'
#                      '"pip install cython" before installing PyGOM.')
    ext_modules += [
        Extension("pygom.model._tau_leap",
                  ["pygom/model/_tau_leap.c"],
                  include_dirs=[numpy.get_include()],
#                  extra_compile_args=['-fopenmp'],
#                  extra_link_args=['-fopenmp']),
)
    ]
package_data = {
   'pygom.data': ['eg1.json'],# An example epijson file
   }

# read the requirements file and have use that to populate install_requires
requires = open("requirements.txt").read().strip().split("\n")
install_requires = []
extras_require = {}
for r in requires:
    if ";" in r:
        # requirements.txt conditional dependencies need to be reformatted for wheels
        # to the form: `'[extra_name]:condition' : ['requirements']`
        req, cond = r.split(";", 1)
        cond = ":" + cond
        cond_reqs = extras_require.setdefault(cond, [])
        cond_reqs.append(req)
    else:
        install_requires.append(r)

with open('README.rst', 'r') as f:
    readme = f.read()

setup_requires = [
    'setuptools-scm>=3.2.0',
    'setuptools_scm_git_archive',
    'numpy>=1.12.0'
    ]

setup(
    name='pygom',
    use_scm_version=True,
    description='ODE modeling in Python',
    long_description=readme,
    long_description_content_type='text/x-rst',
    license="GPL2",
    url='https://github.com/PublicHealthEngland/pygom',
    author="Thomas Finnie",
    author_email="Thomas.Finnie@phe.gov.uk",
    packages=[
        'pygom',
        'pygom.model',
        'pygom.model.ode_utils',
        'pygom.loss',
        'pygom.utilR'
    ],
    package_data=package_data,
    include_package_data=True,
    cmdclass=cmdclass,
    ext_modules=ext_modules,
    install_requires=install_requires,
    extras_require=extras_require,
    setup_requires=setup_requires,
    test_suite='tests',
    scripts=[]
    )