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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# ----------------------------------------------------------------------------
# Copyright (c) 2011-2015, The BIOM Format 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 sys
from setuptools import setup, find_packages
from setuptools.extension import Extension
try:
import numpy as np
except ImportError:
raise ImportError("numpy must be installed prior to installing biom")
# Hack to prevent stupid "TypeError: 'NoneType' object is not callable" error
# in multiprocessing/util.py _exit_function when running `python
# setup.py test` (see
# http://www.eby-sarna.com/pipermail/peak/2010-May/003357.html),
# borrowed from https://github.com/getsentry/sentry/blob/master/setup.py
for m in ('multiprocessing', 'logging'):
try:
__import__(m)
except ImportError:
pass
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Jose Clemente",
"Jai Ram Rideout", "Jorge Cañardo Alastuey", "Michael Hall"]
__license__ = "BSD"
__version__ = "2.1.5"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt@colorado.edu"
long_description = """BIOM: Biological Observation Matrix
http://www.biom-format.org
The Biological Observation Matrix (BIOM) format or: how I learned to stop
worrying and love the ome-ome
Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout,
Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle,
Folker Meyer, Rob Knight, J Gregory Caporaso
GigaScience 2012, 1:7.
"""
classes = """
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Software Development :: Libraries :: Application Frameworks
Topic :: Software Development :: Libraries :: Python Modules
Programming Language :: Python
Programming Language :: Python :: 2.7
Programming Language :: Python :: Implementation :: CPython
Operating System :: OS Independent
Operating System :: POSIX :: Linux
Operating System :: MacOS :: MacOS X
"""
classifiers = [s.strip() for s in classes.split('\n') if s]
# Dealing with Cython
USE_CYTHON = os.environ.get('USE_CYTHON', False)
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [Extension("biom._filter",
["biom/_filter" + ext]),
Extension("biom._transform",
["biom/_transform" + ext]),
Extension("biom._subsample",
["biom/_subsample" + ext])]
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions)
install_requires = ["click", "numpy >= 1.3.0", "future >= 0.14.3",
"scipy >= 0.13.0"]
# HACK: for backward-compatibility with QIIME 1.9.x, pyqi must be installed.
# pyqi is not used anymore in this project.
if sys.version_info[0] < 3:
install_requires.append("pyqi")
setup(name='biom-format',
version=__version__,
description='Biological Observation Matrix (BIOM) format',
long_description=long_description,
license=__license__,
author=__maintainer__,
author_email=__email__,
maintainer=__maintainer__,
maintainer_email=__email__,
url='http://www.biom-format.org',
test_suite='nose.collector',
packages=find_packages(),
include_package_data=True,
ext_modules=extensions,
include_dirs=[np.get_include()],
install_requires=install_requires,
extras_require={'test': ["nose >= 0.10.1", "flake8"],
'hdf5': ["h5py >= 2.2.0"]
},
classifiers=classifiers,
entry_points='''
[console_scripts]
biom=biom.cli:cli
''')
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