setup.py

#! /usr/bin/env python

import os
import sys

extra = {}

try:
    from setuptools import setup
except ImportError:
    from distutils.core import setup


def read_reqs_file(reqs_name):
    """Read requirements file for given requirements group."""
    path_reqs_file = os.path.join(
        "requirements", "requirements-{}.txt".format(reqs_name)
    )
    with open(path_reqs_file, "r") as reqs_file:
        return [
            pkg.rstrip() for pkg in reqs_file.readlines() if not pkg.startswith("#")
        ]


with open(os.path.join("pypiper", "_version.py"), "r") as versionfile:
    version = versionfile.readline().split()[-1].strip("\"'\n")


basic_reqs = read_reqs_file("pypiper")

# Requirements for tests
test_reqs = read_reqs_file("test")

# Allow specification of desired features, which implies dependencies.
addl_reqs = {
    bundle_name: read_reqs_file(bundle_name) for bundle_name in ["ngstk", "plot"]
}

# Complete collection of user requirements.
addl_reqs["all"] = list({pkg for bundle in addl_reqs.values() for pkg in bundle})

# Dev installation is full user + test.
addl_reqs["dev"] = list(set(test_reqs + addl_reqs["all"]))

with open("README.md") as f:
    long_description = f.read()

setup(
    name="piper",
    packages=["pypiper"],
    install_requires=basic_reqs,
    version=version,
    description="A lightweight python toolkit for gluing together restartable, robust command line pipelines",
    long_description=long_description,
    long_description_content_type="text/markdown",
    classifiers=[
        "Development Status :: 4 - Beta",
        "License :: OSI Approved :: BSD License",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
    author="Nathan Sheffield, Johanna Klughammer, Andre Rendeiro",
    author_email="nathan@code.databio.org, jklughammer@cemm.oeaw.ac.at, arendeiro@cemm.oeaw.ac.at",
    url="https://github.com/databio/pypiper/",
    license="BSD2",
    test_suite="tests",  # python setup.py test
    tests_require=test_reqs,  # Test-specific package dependencies
    # Extra package if doing `python setup.py test`
    setup_requires=(
        ["pytest-runner"] if {"test", "pytest", "ptr"} & set(sys.argv) else []
    ),
    extras_require=addl_reqs,
    # Version-specific items
    **extra
)