setup.py

#!/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
import sys

# Always prefer setuptools over distutils
from setuptools import find_packages, setup
from setuptools.command.test import test as TestCommand

# 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="4.7.2",
    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="https://clinical-genomics.github.io/chanjo/",
    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",
    ],
)