setup.py

from setuptools import setup, find_packages
import os


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

setup(
    name='pathogen-embed',
    version='3.1.0',
    description='Reduced dimension embeddings for pathogen sequences',
    url='https://github.com/blab/pathogen-embed/',
    author='Sravani Nanduri <nandsra@cs.washington.edu> , John Huddleston <huddlej@gmail.com>',
    author_email='nandsra@cs.washington.edu',
    long_description=long_description,
    long_description_content_type="text/markdown",
    license='MIT License',
    project_urls = {
        "Documentation": "https://blab.github.io/pathogen-embed/",
        "Bug Reports": "https://github.com/blab/pathogen-embed/issues",
        "Source Code": "https://github.com/blab/pathogen-embed/tree/main",
        "Change Log": "https://github.com/blab/pathogen-embed/tree/main/CHANGES.md",
    },
    package_dir={"": "src"},
    packages=find_packages(where="src", exclude=['test']),
    install_requires=['numpy',
                      'pandas',
                      "biopython",
                      'scikit-learn >=1.3,<1.5',
                      'umap-learn ==0.5.*',
                      # Pin Numba at maximum supported version for the pinned umap-learn version.
                      # For more details see:
                      # https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
                      'numba <0.59.0',
                      'matplotlib',
                      'hdbscan'
                      ],
    extras_require = {
        'dev': [
            "cram >=0.7",
        ]
    },
    classifiers=[
        "Operating System :: OS Independent",
        'Intended Audience :: Science/Research',
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.8',
        'Programming Language :: Python :: 3.9',
        'Programming Language :: Python :: 3.10',
        'Programming Language :: Python :: 3.11',
    ],
    entry_points = {
        "console_scripts": [
            "pathogen-embed = pathogen_embed.__main__:run_embed",
            "pathogen-distance = pathogen_embed.__main__:run_distance",
            "pathogen-cluster = pathogen_embed.__main__:run_cluster",
            "pathogen-cluster-mutations = pathogen_embed.__main__:run_cluster_mutations",
        ]
    }
)