setup.py

#!/usr/bin/env python

"""Package setup
"""

import os.path as op
import sys

import numpy as np

from setuptools import setup, find_packages, Extension
from setuptools.command.test import test as testCommand
from setup_helper import SetupHelper

import versioneer


class PyTest(testCommand):
    """Allow testing to be run from setuptools."""

    def initialize_options(self):
        testCommand.initialize_options(self)
        self.test_args = []

    def finalize_options(self):
        testCommand.finalize_options(self)
        self.test_args += ["--cov", "jcvi", "tests"]

    def run_tests(self):
        # pylint:disable=import-outside-toplevel
        import pytest

        errno = pytest.main(self.test_args)
        sys.exit(errno)


NAME = "jcvi"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

# Use the helper
h = SetupHelper(initfile="jcvi/__init__.py", readmefile="README.md")
h.check_version(NAME, majorv=3, minorv=6)
cmdclass = versioneer.get_cmdclass()
include_dirs = []
setup_dir = op.abspath(op.dirname(__file__))
requirements = [x.strip() for x in open(op.join(setup_dir, "requirements.txt"))]
h.install_requirements(requires=["cython", "numpy"])

# Build the ext
try:
    from Cython.Distutils import build_ext

    cmdclass.update({"build_ext": build_ext})
except ImportError:
    print("Cython not installed. Skip compiling Cython extensions.")

include_dirs.append(np.get_include())

ext_modules = [
    Extension(
        "jcvi.assembly.chic",
        ["jcvi/assembly/chic.pyx"],
        include_dirs=include_dirs,
        extra_compile_args=["-O3"],
    ),
    Extension(
        "jcvi.formats.cblast", ["jcvi/formats/cblast.pyx"], extra_compile_args=["-O3"]
    ),
]

packages = [NAME] + [
    ".".join((NAME, x)) for x in find_packages("jcvi", exclude=["test*.py"])
]

cmdclass.update({"test": PyTest})

setup(
    name=NAME,
    author=h.author,
    author_email=h.email,
    version=versioneer.get_version(),
    license=h.license,
    long_description=h.long_description,
    long_description_content_type="text/markdown",
    cmdclass=cmdclass,
    packages=packages,
    include_package_data=True,
    package_data={"jcvi.utils.data": ["*.*"]},
    ext_modules=ext_modules,
    classifiers=classifiers,
    zip_safe=False,
    url="http://github.com/tanghaibao/jcvi",
    description="Python utility libraries on genome assembly, annotation and comparative genomics",
    setup_requires=["setuptools>=18.0", "cython"],
    install_requires=requirements,
    tests_require=["pytest", "pytest-cov", "pytest-benchmark"],
)