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import os
from setuptools import setup
import seqtyping
def package_files(directory):
paths = []
for (path, directories, filenames) in os.walk(directory):
for filename in filenames:
paths.append(os.path.join('..', path, filename))
return paths
VERSION = seqtyping.__version__
with open('README.md') as fh:
README = fh.read()
setup(
name='seq_typing',
version='{}'.format(VERSION),
packages=['seqtyping',
'seqtyping.modules'],
package_dir={'seqtyping': 'seqtyping'},
package_data={'seqtyping': package_files('.git') +
['reference_sequences/*/*']},
include_package_data=True,
data_files=[('', ['LICENSE'])],
install_requires=[
'ReMatCh', 'biopython'
],
description='Determines which reference sequence is more likely to be present in a given sample',
long_description=README,
long_description_content_type='text/markdown',
keywords=['reference mapping', 'sequence Blast search', 'typing'],
classifiers=[
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Environment :: Console',
'Operating System :: Unix',
'Intended Audience :: Science/Research',
'Programming Language :: Python :: 3',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Medical Science Apps.'
],
url='https://github.com/B-UMMI/seq_typing',
author='Miguel P. Machado',
author_email='mpmachado@medicina.ulisboa.pt',
license='GPL3',
# To use entry_points with .py the first folder cannot have the same name of the script
entry_points={
'console_scripts': [
'seq_typing.py = seqtyping.seq_typing:main',
'ecoli_stx_subtyping.py = seqtyping.ecoli_stx_subtyping:main',
'get_stx_db.py = seqtyping.modules.get_stx_db:main'
]
},
python_requires='>=3.4'
)
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