setup.py

#!/usr/bin/env python
# -*- encoding: utf-8 -*-
from __future__ import absolute_import
from __future__ import print_function
import os
import subprocess
import io
import re
from glob import glob
from os.path import basename
from os.path import dirname
from os.path import join
from os.path import splitext

from setuptools import find_packages
from setuptools import setup
from setuptools.command.install import install as DistutilsInstall


class MyInstall(DistutilsInstall):

    def run(self):

        mccortex_dir = os.path.dirname(os.path.realpath(__file__))+"/mccortex"
        if not os.path.exists(mccortex_dir):
            subprocess.call(
                ["git", "clone", "--recursive", "-b", "geno_kmer_count", "https://github.com/phelimb/mccortex", mccortex_dir], cwd=os.path.dirname(os.path.realpath(__file__)))
            subprocess.call(
                ["make", "clean"], cwd=mccortex_dir)
            subprocess.call(
                ["make"], cwd=mccortex_dir)
            subprocess.call(
                ["cp", "bin/mccortex31", "%s/bin/" % os.environ.get('VIRTUAL_ENV', '/usr/local/')], cwd=mccortex_dir)
        DistutilsInstall.run(self)


def read(*names, **kwargs):
    return io.open(
        join(dirname(__file__), *names),
        encoding=kwargs.get('encoding', 'utf8')
    ).read()


setup(
    name='mykrobe',
    version='0.7.0',
    license='MIT',
    description='Antibiotic resistance prediction in minutes',
    # long_description='%s\n%s' % (
    #     re.compile('^.. start-badges.*^.. end-badges',
    #                re.M | re.S).sub('', read('README.md')),
    #     re.sub(':[a-z]+:`~?(.*?)`', r'``\1``', read('CHANGELOG.rst'))
    # ),
    author='Phelim Bradley',
    author_email='wave@phel.im',
    url='https://github.com/Mykrobe-tools/mykrobe',
    packages=find_packages('src'),
    package_dir={'': 'src'},
    py_modules=[splitext(basename(path))[0] for path in glob(
        'src/*.py')]+[splitext(basename(path))[0] for path in glob('src/*/*.py')]+[splitext(basename(path))[0] for path in glob('src/*/*/*.py')],
    include_package_data=True,
    zip_safe=False,
    classifiers=[
        'Intended Audience :: Developers',
        'Operating System :: Unix',
        'Operating System :: POSIX',
        'Programming Language :: Python',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.3',
        'Programming Language :: Python :: 3.4',
        'Programming Language :: Python :: 3.5',
        'Programming Language :: Python :: 3.6',
        'Programming Language :: Python :: Implementation :: CPython',
        'Programming Language :: Python :: Implementation :: PyPy',
        'Topic :: Utilities',
    ],
    keywords=[
        # eg: 'keyword1', 'keyword2', 'keyword3',
    ],
    install_requires=[
        'Biopython',
        "pyvcf",
        'mongoengine',
        # eg: 'aspectlib==1.1.1', 'six>=1.7',
    ],
    extras_require={
        # eg:
        #   'rst': ['docutils>=0.11'],
        #   ':python_version=="2.6"': ['argparse'],
    },
    entry_points={
        'console_scripts': [
            'mykrobe = mykrobe.cli:main',
        ]
    },
    cmdclass={'install': MyInstall}
)