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#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import os
import platform
import re
import ast
import sys
from setuptools import find_packages, setup
from setuptools.extension import Extension
import numpy as np
if sys.version_info.major != 3:
sys.exit("scikit-bio can only be used with Python 3. You are currently "
"running Python %d." % sys.version_info.major)
# version parsing from __init__ pulled from Flask's setup.py
# https://github.com/mitsuhiko/flask/blob/master/setup.py
_version_re = re.compile(r'__version__\s+=\s+(.*)')
with open('skbio/__init__.py', 'rb') as f:
hit = _version_re.search(f.read().decode('utf-8')).group(1)
version = str(ast.literal_eval(hit))
classes = """
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Topic :: Software Development :: Libraries
Topic :: Scientific/Engineering
Topic :: Scientific/Engineering :: Bio-Informatics
Programming Language :: Python :: 3
Programming Language :: Python :: 3 :: Only
Programming Language :: Python :: 3.4
Programming Language :: Python :: 3.5
Operating System :: Unix
Operating System :: POSIX
Operating System :: MacOS :: MacOS X
"""
classifiers = [s.strip() for s in classes.split('\n') if s]
description = ('Data structures, algorithms and educational '
'resources for bioinformatics.')
with open('README.rst') as f:
long_description = f.read()
# Dealing with Cython
USE_CYTHON = os.environ.get('USE_CYTHON', False)
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [
Extension("skbio.metadata._intersection",
["skbio/metadata/_intersection" + ext]),
Extension("skbio.stats.__subsample",
["skbio/stats/__subsample" + ext],
include_dirs=[np.get_include()]),
Extension("skbio.alignment._ssw_wrapper",
["skbio/alignment/_ssw_wrapper" + ext],
include_dirs=[np.get_include()],
libraries=['ssw']),
Extension("skbio.diversity._phylogenetic",
["skbio/diversity/_phylogenetic" + ext],
include_dirs=[np.get_include()])
]
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions)
setup(name='scikit-bio',
version=version,
license='BSD-3-Clause',
description=description,
long_description=long_description,
author="scikit-bio development team",
author_email="gregcaporaso@gmail.com",
maintainer="scikit-bio development team",
maintainer_email="gregcaporaso@gmail.com",
url='http://scikit-bio.org',
packages=find_packages(),
ext_modules=extensions,
include_dirs=[np.get_include()],
install_requires=[
'lockfile >= 0.10.2', # req'd for our usage of CacheControl
'CacheControl >= 0.11.5',
'decorator >= 3.4.2',
'IPython >= 3.2.0',
'matplotlib >= 1.4.3',
'natsort >= 4.0.3',
'numpy >= 1.9.2',
'pandas >= 0.18.0',
'scipy >= 0.15.1',
'nose >= 1.3.7'
],
classifiers=classifiers,
package_data={
'skbio.diversity.alpha.tests': ['data/qiime-191-tt/*'],
'skbio.diversity.beta.tests': ['data/qiime-191-tt/*'],
'skbio.io.tests': ['data/*'],
'skbio.io.format.tests': ['data/*'],
'skbio.stats.tests': ['data/*'],
'skbio.stats.distance.tests': ['data/*'],
'skbio.stats.ordination.tests': ['data/*']
}
)
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