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setup.py
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setup.py
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import os
import io
from setuptools import setup, find_packages, Command
from os import path
root = 'MrY'
name = 'MrY'
exec(open("MrY/version.py").read())
here = path.abspath(path.dirname(__file__))
description = ('Mr.Y -- Management of references at YanaiLab')
install_requires = [
'snakemake>=4.0.0, <6',
'pyyaml>=3.12',
'tabulate>=0.7',
]
# do not require installation if built by ReadTheDocs
# (we mock these modules in docs/source/conf.py)
if 'READTHEDOCS' not in os.environ or \
os.environ['READTHEDOCS'] != 'True':
install_requires.extend([
])
else:
install_requires.extend([
#'pandas>=0.13, <1',
])
# get long description from file
long_description = ''
with io.open(path.join(here, 'README.md'), encoding='UTF-8') as fh:
long_description = fh.read()
class CleanCommand(Command):
"""Removes files generated by setuptools.
"""
# see https://github.com/trigger/trigger/blob/develop/setup.py
user_options = []
def initialize_options(self):
pass
def finalize_options(self):
pass
def run(self):
error_msg = 'You must run this command in the package root!'
if not os.getcwd() == here:
raise OSError(error_msg)
else:
os.system('rm -rf ./dist ./build ./*.egg-info ')
setup(
name=name,
version=__version__,
description=description,
long_description=long_description,
# homepage
url='https://github.com/Puriney/Mr.Y',
author='Yun Yan',
author_email='[email protected]',
license='GPLv3',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
'Development Status :: 1 - Planning',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Utilities',
'License :: Other/Proprietary License',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3 :: Only',
],
keywords='GENCODE Ensemble NCBI genome transcriptome reference management',
# packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
packages=find_packages(exclude=['docs', 'tests*']),
# packages=find_packages(root),
# libraries = [],
install_requires=install_requires,
# tests_require=[],
extras_require={
'docs': [
'sphinx',
'sphinx-rtd-theme',
'sphinx-argparse',
'mock',
],
'tests': [
'pytest>=3, <4',
'pytest-cov>=2.2.1, <3',
],
},
# data
package_data={
'MrY': [
'template/*', # config.yaml, etc
'workflow/*' # snakemake workflow
]
},
# data outside the package
# data_files=[('my_data', ['data/data_file'])],
entry_points={
'console_scripts': [
('yun = '
'MrY.__init__:main'),
],
},
cmdclass={
'clean': CleanCommand,
},
)