setup.py

# -*- coding: utf-8 -*-
"""A setuptools based setup module.

For more information, please see:
- https://pypi.python.org/pypi/setuptools
- https://pythonhosted.org/setuptools
- https://python-packaging-user-guide.readthedocs.io/en/latest/distributing/
- https://packaging.python.org/en/latest/distributing.html
- https://github.com/pypa/sampleproject

"""
import glob
import io
import os
from os.path import join

import setuptools

import versioneer


def read(*names, **kwargs):
    r"""Return the contents of a file.

    Default encoding is UTF-8, unless specified otherwise.

    Args:
        - names (list, required): list of strings, parts of the path.
          the path might be relative to the current file.

    Keyword Args:
        **kwargs: Arbitrary keyword arguments.

    Returns:
      String containing the content of the file.

    Examples:
        >>> read('docs/readme.rst')
            u'Overview\n--------\n...'

        >>> read('docs', 'readme.rst')
            u'Overview\n--------\n...'

    """
    fn = os.path.join(os.path.dirname(__file__), *names)
    with io.open(fn, encoding=kwargs.get("encoding", "utf8")) as fd:
        return fd.read()


def read_requirements(fname):
    with open(fname, "r", encoding="utf-8") as file:
        return [line.rstrip() for line in file]


setuptools.setup(
    name="pyscenic",
    version=versioneer.get_version(),
    cmdclass=versioneer.get_cmdclass(),
    description="Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments.",
    long_description=read("README.rst"),
    classifiers=[
        # Get strings from http://pypi.python.org/pypi?%3Aaction=list_classifiers
        "Development Status :: 4 - Beta",
        "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
        "Natural Language :: English",
        "Operating System :: POSIX",
        "Programming Language :: Python",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6",
        "Programming Language :: Python :: Implementation :: CPython",
    ],
    python_requires=">=3.6",
    keywords="single-cell transcriptomics gene-regulatory-network transcription-factors",
    author="Bram Van de Sande",
    url="https://github.com/aertslab/pySCENIC",
    license="GPL-3.0+",
    packages=setuptools.find_packages(where="src"),
    package_dir={"": "src"},
    py_modules=[
        os.path.splitext(os.path.basename(path))[0] for path in glob.glob("src/*.py")
    ],
    include_package_data=True,
    install_requires=read_requirements("requirements.txt"),
    scripts=["src/pyscenic/cli/arboreto_with_multiprocessing.py"],
    entry_points={
        "console_scripts": [
            "pyscenic = pyscenic.cli.pyscenic:main",
            "db2feather = pyscenic.cli.db2feather:main",
            "csv2loom = pyscenic.cli.csv2loom:main",
            "invertdb = pyscenic.cli.invertdb:main",
            "gmt2regions = pyscenic.cli.gmt2regions:main",
        ],
    },
)