setup.py

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import os
import logging
import re

from setuptools import setup, find_packages

readme_dir = os.path.dirname(__file__)
readme_path = os.path.join(readme_dir, "README.md")

try:
    with open(readme_path, "r") as f:
        readme_markdown = f.read()
except:
    logging.warn("Failed to load %s" % readme_path)
    readme_markdown = ""

with open("vaxrank/version.py", "r") as f:
    match = re.search(r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]', f.read(), re.MULTILINE)
    if not match:
        raise RuntimeError("Cannot find version information")
    else:
        version = match.group(1)

if not version:
    raise RuntimeError("Cannot find version information")


with open("requirements.txt") as f:
    requirements = [req.strip() for req in f.read().splitlines() if req.strip()]


if __name__ == "__main__":
    setup(
        name="vaxrank",
        version=version,
        description="Mutant peptide ranking for personalized cancer vaccines",
        author="Alex Rubinsteyn, Julia Kodysh",
        author_email="alex@openvax.org, julia@openvax.org",
        url="https://github.com/openvax/vaxrank",
        license="http://www.apache.org/licenses/LICENSE-2.0.html",
        classifiers=[
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Operating System :: OS Independent",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
        ],
        # 3.10+ for PEP 604 union syntax (``str | None``) and dataclass
        # slots=True used in the LENS multi-predictor loader. CI already
        # tests only 3.10-3.13 so this matches tested reality.
        python_requires=">=3.10",
        install_requires=requirements,
        long_description=readme_markdown,
        long_description_content_type="text/markdown",
        packages=find_packages(exclude=["tests", "tests.*"]),
        package_data={"vaxrank": [
            "templates/*", "data/*", "logging.conf", "config/*.yaml"]},
        entry_points={"console_scripts": ["vaxrank = vaxrank.cli.entry_point:main"]},
    )