setup.py

from setuptools import setup
from os import path


# this is ugly, but appears to be standard practice:
# https://stackoverflow.com/questions/17583443/what-is-the-correct-way-to-share-package-version-with-setup-py-and-the-package/17626524#17626524
def extract_version(filename: str):
    with open(filename) as f:
        lines = f.readlines()
    version_comment = (
        "# version line; WARNING: do not remove or change this line or comment"
    )
    for line in lines:
        if version_comment in line:
            idx = line.index(version_comment)
            line_prefix = line[:idx]
            parts = line_prefix.split("=")
            parts = [part.strip() for part in parts]
            version_str = parts[-1]
            version_str = version_str.replace('"', "")
            version_str = version_str.replace("'", "")
            version_str = version_str.strip()
            return version_str
    raise AssertionError(f"could not find version in {filename}")


version = extract_version("nuad/__version__.py")
print(f"nuad version = {version}")


with open("requirements.txt") as fp:
    install_requires = fp.read().strip().split("\n")

# read the contents of your README file
this_directory = path.abspath(path.dirname(__file__))
with open(path.join(this_directory, "README.md"), encoding="utf-8") as f:
    long_description = f.read()

setup(
    name="nuad",
    packages=["nuad"],
    version=version,
    license="MIT",
    description='nuad stands for "NUcleic Acid Designer". Enables one to specify constraints on a DNA (or RNA) nanostructure made from synthetic DNA/RNA and then attempts to find concrete DNA sequences that satisfy the constraints.',
    author="David Doty",
    author_email="doty@ucdavis.edu",
    url="https://github.com/UC-Davis-molecular-computing/nuad",
    long_description=long_description,
    long_description_content_type="text/markdown; variant=GFM",
    python_requires=">=3.10",
    install_requires=install_requires,
    include_package_data=True,
)