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import os
from glob import glob
from setuptools import setup, find_packages
import subprocess
import imp
DISTNAME = 'nimfa'
MAINTAINER = 'Marinka Zitnik'
MAINTAINER_EMAIL = 'marinka@cs.stanford.edu'
DESCRIPTION = 'A Python module for nonnegative matrix factorization'
LONG_DESCRIPTION = open('README.md').read()
URL = 'http://nimfa.biolab.si'
DOWNLOAD_URL = 'http://github.com/marinkaz/nimfa'
KEYWORDS = ['matrix factorization', 'nonnegative matrix factorization',
'bioinformatics', 'data mining', 'machine learning']
LICENSE = 'BSD'
VERSION = '1.3.2'
ISRELEASED = True
INSTALL_REQUIRES = (
'numpy>=1.7.0',
'scipy>=0.12.0',
)
def get_package_data(topdir, excluded=set()):
retval = []
for dirname, subdirs, files in os.walk(os.path.join(DISTNAME, topdir)):
for x in excluded:
if x in subdirs:
subdirs.remove(x)
retval.append(os.path.join(dirname[len(DISTNAME)+1:], '*.*'))
return retval
def get_data_files(dest, source):
retval = []
for dirname, subdirs, files in os.walk(source):
retval.append(
(os.path.join(dest, dirname[len(source)+1:]), glob(os.pathjoin(dirname, '*.*')))
)
return retval
# Return the git revision as a string
def git_version():
"""Return the git revision as a string.
Copied from numpy setup.py
"""
def _minimal_ext_cmd(cmd):
# construct minimal environment
env = {}
for k in ['SYSTEMROOT', 'PATH']:
v = os.environ.get(k)
if v is not None:
env[k] = v
# LANGUAGE is used on win32
env['LANGUAGE'] = 'C'
env['LANG'] = 'C'
env['LC_ALL'] = 'C'
out = subprocess.Popen(cmd, stdout = subprocess.PIPE, env=env).communicate()[0]
return out
try:
out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
GIT_REVISION = out.strip().decode('ascii')
except OSError:
GIT_REVISION = "Unknown"
return GIT_REVISION
def write_version_py(filename='nimfa/version.py'):
# Copied from numpy setup.py
cnt = """
# THIS FILE IS GENERATED FROM NIMFA SETUP.PY
short_version = '%(version)s'
version = '%(version)s'
full_version = '%(full_version)s'
git_revision = '%(git_revision)s'
release = %(isrelease)s
if not release:
version = full_version
short_version += ".dev"
"""
FULLVERSION = VERSION
if os.path.exists('.git'):
GIT_REVISION = git_version()
elif os.path.exists('nimfa/version.py'):
# must be a source distribution, use existing version file
version = imp.load_source('nimfa.version', 'nimfa/version.py')
GIT_REVISION = version.git_revision
else:
GIT_REVISION = 'Unknown'
if not ISRELEASED:
FULLVERSION += '.dev0+' + GIT_REVISION[:7]
a = open(filename, 'w')
try:
a.write(cnt % {'version': VERSION,
'full_version': FULLVERSION,
'git_revision': GIT_REVISION,
'isrelease': str(ISRELEASED)})
finally:
a.close()
def setup_package():
write_version_py()
setup(
name=DISTNAME,
version=VERSION,
author=MAINTAINER,
author_email=MAINTAINER_EMAIL,
maintainer=MAINTAINER,
maintainer_email=MAINTAINER_EMAIL,
description=DESCRIPTION,
url=URL,
download_url=DOWNLOAD_URL,
keywords=KEYWORDS,
install_requires=INSTALL_REQUIRES,
packages=find_packages(),
package_dir={DISTNAME: './nimfa'},
package_data={DISTNAME: get_package_data('datasets')},
license=LICENSE,
long_description=LONG_DESCRIPTION,
classifiers=['Intended Audience :: Science/Research',
'Intended Audience :: Developers',
'License :: OSI Approved',
'Programming Language :: Python',
'Topic :: Software Development',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 3',],
)
if __name__ == "__main__":
setup_package()