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#!/usr/bin/env python3
"""
Presto setup
"""
# Imports
import os
import sys
# Check setup requirements
if sys.version_info < (3,7,0):
sys.exit('At least Python 3.7.0 is required.')
try:
from setuptools import setup
except ImportError:
sys.exit('Please install setuptools before installing presto.')
# Get version, author and license information
info_file = os.path.join('presto', 'Version.py')
__version__, __author__, __license__ = None, None, None
try:
exec(open(info_file).read())
except:
sys.exit('Failed to load package information from %s.\n' % info_file)
if __version__ is None:
sys.exit('Missing version information in %s\n.' % info_file)
if __author__ is None:
sys.exit('Missing author information in %s\n.' % info_file)
if __license__ is None:
sys.exit('Missing license information in %s\n.' % info_file)
# Load long package description
#desc_files = ['README.rst', 'INSTALL.rst', 'NEWS.rst']
desc_files = ['README.rst']
long_description = '\n\n'.join([open(f, 'r').read() for f in desc_files])
# Define installation path for commandline tools
scripts = ['AlignSets.py',
'AssemblePairs.py',
'BuildConsensus.py',
'ClusterSets.py',
'CollapseSeq.py',
'ConvertHeaders.py',
'EstimateError.py',
'FilterSeq.py',
'MaskPrimers.py',
'PairSeq.py',
'ParseHeaders.py',
'ParseLog.py',
'SplitSeq.py',
'UnifyHeaders.py']
install_scripts = [os.path.join('bin', s) for s in scripts]
# Parse requirements
if os.environ.get('READTHEDOCS', None) == 'True':
# Set empty install_requires to get install to work on readthedocs
install_requires = []
else:
with open('requirements.txt') as req:
install_requires = req.read().splitlines()
# Setup
setup(name='presto',
version=__version__,
author=__author__,
author_email='immcantation@googlegroups.com',
description='A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.',
long_description=long_description,
zip_safe=False,
license=__license__,
url='http://presto.readthedocs.io',
download_url='https://github.com/immcantation/presto/tags',
keywords=['bioinformatics', 'sequencing', 'immunology', 'adaptive immunity',
'immunoglobulin', 'AIRR-seq', 'Rep-Seq',
'B cell repertoire analysis', 'adaptive immune receptor repertoires'],
install_requires=install_requires,
packages=['presto'],
package_dir={'presto': 'presto'},
scripts=install_scripts,
classifiers=['Development Status :: 4 - Beta',
'Environment :: Console',
'Intended Audience :: Science/Research',
'Natural Language :: English',
'Operating System :: OS Independent',
'Programming Language :: Python :: 3.7',
'Topic :: Scientific/Engineering :: Bio-Informatics'])
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