setup.py

import codecs
import os.path

from setuptools import find_packages
from setuptools import setup

with open("README.md", encoding="UTF-8") as fh:
    long_description = fh.read()


def read(rel_path):
    here = os.path.abspath(os.path.dirname(__file__))
    with codecs.open(os.path.join(str(here), rel_path), "r") as fp:
        return fp.read()


def get_version(rel_path):
    for line in read(rel_path).splitlines():
        if line.startswith("__version__"):
            delim = '"' if '"' in line else "'"
            return line.split(delim)[1]
    raise RuntimeError("Unable to find version string.")


setup(
    name="xi-mzidentml-converter",
    version="0.3.6",
    description="xi-mzidentml-converter uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to "
                "parse mzIdentML files (v1.2.0) and extract crosslink information. Results are written to a "
                "relational database (PostgreSQL or SQLite) using sqlalchemy.",
    long_description_content_type="text/markdown",
    long_description=long_description,
    author="Colin Combe, Lars Kolbowski, Suresh Hewapathirana",
    license="'Apache 2.0",
    url="https://github.com/PRIDE-Archive/xi-mzidentml-converter",
    packages=find_packages(),
    include_package_data=True,
    package_data={'config': ['logging.ini'], 'schema': ['*.xsd']},
    install_requires=[
        'lxml>=4.9.1',
        'numpy>=1.14.3',
        'pandas>=0.21.0',
        'pymzml>=0.7.8',
        'pyteomics>=4.7.3',
        'requests>=2.31.0',
        'urllib3>=1.24.2',
        'pytest',
        'psycopg2-binary',
        'sqlalchemy==2.0.21',
        'sqlalchemy-utils',
        'obonet',
        'python-multipart',
        'python-jose',
        'passlib',
        'jose',
        'orjson'
    ],
    entry_points={"console_scripts": ["process_dataset = parser.process_dataset:main"]},
    platforms=["any"],
    classifiers=[
        "Programming Language :: Python :: 3",
        "License :: OSI Approved :: Apache Software License",
        "Operating System :: OS Independent",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
    keywords="crosslinking python proteomics",
    python_requires=">=3.10",
)