setup.py

#! /usr/bin/env python
# -*- encoding:utf-8 -*-
import os
import sys
sys.path.append('CIRI_long')
import codecs
from pathlib import Path
from subprocess import getstatusoutput
from setuptools import setup, Extension, find_packages
from setuptools.command.build_ext import build_ext
from setuptools.command.install import install

from CIRI_long.version import __version__


class CustomInstall(install):
    def run(self):
        # Build library
        lib_dir = Path(os.path.abspath(__file__)).parent / 'libs' / 'striped_smith_waterman'
        status, ret = getstatusoutput('cd {} && make libssw.so'.format(lib_dir))
        if status != 0:
            sys.exit('Build Error: {}'.format(ret))
        else:
            print(ret)
        # Install
        install.run(self)


def read(infile):
    return codecs.open(os.path.join(os.path.dirname(__file__), infile)).read()

setup(
    name='CIRI-long',
    python_requires='>3.7.0',
    version=__version__,
    url='https://github.com/bioinfo-biols/CIRI-long',
    description='circular RNA identification from Nanopore',
    long_description=read('README.md'),
    long_description_content_type='text/markdown',
    author='Jinyang Zhang',
    author_email='zhangjinyang@biols.ac.cn',
    maintainer='Jinyang Zhang',
    maintainer_email='zhangjinyang@biols.ac.cn',
    license='MIT',
    keywords='circRNA',
    packages=find_packages(exclude=['doc', 'tests']),
    entry_points={
        'console_scripts': [
            'CIRI-long=CIRI_long.main:main',
        ]
    },
    include_package_data=True,
    zip_safe=False,
    install_requires=[
        'argparse>=1.2.1', 'Cython>=0.29.13', 'mappy>=2.17', 'numpy>=1.17.0', 'pandas>=0.25.0',
        'pysam>=0.15.3', 'python-Levenshtein>=0.12.1', 'scikit-learn>=0.21.3', 'scipy>=1.3.1',
        'biopython>=1.76', 'pyspoa>=0.0.5', 'bwapy>=0.1.4', 'edlib>=1.3.9', 'pyccs>=1.1.0',
    ],
    test_suite="nose.collector",
    tests_require=['nose==1.3.7'],
    classifiers=[
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python',
        'Intended Audience :: Developers',
        'Operating System :: OS Independent',
    ],
    cmdclass={
        'build_ext': build_ext,
        'install': CustomInstall,
    }
)