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setup.py
executable file
·126 lines (105 loc) · 4.09 KB
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setup.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Based on https://github.com/pypa/sampleproject/blob/master/setup.py."""
# To use a consistent encoding
import codecs
import os
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
import sys
# Shortcut for building/publishing to Pypi
if sys.argv[-1] == 'publish':
os.system('python setup.py sdist bdist_wheel upload')
sys.exit()
def parse_reqs(req_path='./requirements.txt'):
"""Recursively parse requirements from nested pip files."""
install_requires = []
with codecs.open(req_path, 'r') as handle:
# remove comments and empty lines
lines = (line.strip() for line in handle
if line.strip() and not line.startswith('#'))
for line in lines:
# check for nested requirements files
if line.startswith('-r'):
# recursively call this function
install_requires += parse_reqs(req_path=line[3:])
else:
# add the line as a new requirement
install_requires.append(line)
return install_requires
# This is a plug-in for setuptools that will invoke py.test
# when you run python setup.py test
class PyTest(TestCommand):
"""Set up the py.test test runner."""
def finalize_options(self):
"""Set options for the command line."""
TestCommand.finalize_options(self)
self.test_args = []
self.test_suite = True
def run_tests(self):
"""Execute the test runner command."""
# Import here, because outside the required eggs aren't loaded yet
import pytest
sys.exit(pytest.main(self.test_args))
setup(
name='chanjo',
# Versions should comply with PEP440. For a discussion on
# single-sourcing the version across setup.py and the project code,
# see http://packaging.python.org/en/latest/tutorial.html#version
version='4.7',
description='Coverage analysis tool for clinical sequencing',
# What does your project relate to? Separate with spaces.
keywords='coverage sequencing clinical exome completeness diagnostics',
author='Robin Andeer',
author_email='robin.andeer@gmail.com',
license='MIT',
# The project's main homepage
url='http://www.chanjo.co/',
packages=find_packages(exclude=('tests*', 'docs', 'examples')),
# If there are data files included in your packages that need to be
# installed, specify them here.
include_package_data=True,
package_data=dict(chanjo=['demo/files/*']),
zip_safe=False,
# Install requirements loaded from ``requirements.txt``
install_requires=parse_reqs(),
tests_require=[
'pytest',
],
cmdclass=dict(test=PyTest),
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and
# allow pip to create the appropriate form of executable for the
# target platform.
entry_points={
'console_scripts': [
'chanjo = chanjo.cli:root',
],
'chanjo.subcommands.4': [
'init = chanjo.cli:init',
'sex = chanjo.cli:sex',
'sambamba = chanjo.cli:sambamba',
'db = chanjo.cli:db_cmd',
'load = chanjo.cli:load',
'link = chanjo.cli:link',
'calculate = chanjo.cli:calculate',
]
},
# See: http://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
# How mature is this project? Common values are:
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 5 - Production/Stable',
# Indicate who your project is intended for
'Intended Audience :: Science/Research',
'Topic :: Software Development',
'Topic :: Scientific/Engineering :: Bio-Informatics',
# Pick your license as you wish (should match "license" above)
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 3',
'Environment :: Console',
],
)