mhcflurry/setup.py at master · openvax/mhcflurry · GitHub

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# 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 find_packages, setup


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

try:
    with open(readme_filename, "r") as f:
        readme = f.read()
except:
    logging.warning("Failed to load %s" % readme_filename)
    readme = ""


def readme_for_pypi(text):
    # PyPI's Markdown renderer (cmark-gfm) does not support GitHub's
    # "> [!IMPORTANT]" alert syntax and would display the literal "[!IMPORTANT]"
    # token. Convert each alert marker line to a bold label so the PyPI
    # long_description renders as a clean blockquote. GitHub keeps the colored
    # callout because README.md on disk is unchanged.
    import re
    labels = {
        "NOTE": "Note",
        "TIP": "Tip",
        "IMPORTANT": "Important",
        "WARNING": "Warning",
        "CAUTION": "Caution",
    }
    return re.sub(
        r"(?m)^(\s*>\s*)\[!(NOTE|TIP|IMPORTANT|WARNING|CAUTION)\][ \t]*$",
        lambda m: "%s**%s**" % (m.group(1), labels[m.group(2)]),
        text,
    )


with open("mhcflurry/version.py", "r") as f:
    version = re.search(
        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]', f.read(), re.MULTILINE
    ).group(1)

if __name__ == "__main__":
    required_packages = [
        "pandas>=2.0",
        "appdirs",
        "ahocorasick-rs",
        "scikit-learn",
        "mhcgnomes>=3.0.1",
        "numpy>=1.22.4",
        "pyyaml",
        "tqdm",
        "torch>=2.0.0",
    ]

    setup(
        name="mhcflurry",
        version=version,
        description="MHC Binding Predictor",
        author="Tim O'Donnell and Alex Rubinsteyn",
        author_email="timodonnell@gmail.com",
        url="https://github.com/openvax/mhcflurry",
        license="Apache-2.0",
        entry_points={
            "console_scripts": [
                "mhcflurry = mhcflurry.cli.main:main",
                "mhcflurry-downloads = mhcflurry.cli.downloads_command:run",
                "mhcflurry-pseudosequences = mhcflurry.pseudosequences:main",
                "mhcflurry-predict = mhcflurry.cli.predict_command:run",
                "mhcflurry-predict-scan = mhcflurry.cli.predict_scan_command:run",
                "mhcflurry-class1-train-allele-specific-models = "
                "mhcflurry.cli.train_allele_specific_models_command:run",
                "mhcflurry-class1-train-pan-allele-models = "
                "mhcflurry.cli.train_pan_allele_models_command:run",
                "mhcflurry-class1-train-processing-models = "
                "mhcflurry.cli.train_processing_models_command:run",
                "mhcflurry-class1-select-allele-specific-models = "
                "mhcflurry.cli.select_allele_specific_models_command:run",
                "mhcflurry-class1-select-pan-allele-models = "
                "mhcflurry.cli.select_pan_allele_models_command:run",
                "mhcflurry-class1-select-processing-models = "
                "mhcflurry.cli.select_processing_models_command:run",
                "mhcflurry-calibrate-percentile-ranks = "
                "mhcflurry.cli.calibrate_percentile_ranks_command:run",
                "mhcflurry-class1-train-presentation-models = "
                "mhcflurry.cli.train_presentation_models_command:run",
                "_mhcflurry-cluster-worker-entry-point = "
                "mhcflurry.cluster_parallelism:worker_entry_point",
            ]
        },
        python_requires=">=3.10",
        classifiers=[
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Operating System :: OS Independent",
            "Intended Audience :: Science/Research",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.10",
            "Programming Language :: Python :: 3.11",
            "Programming Language :: Python :: 3.12",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
        ],
        package_data={
            "mhcflurry": ["downloads.yml"],
        },
        install_requires=required_packages,
        long_description=readme_for_pypi(readme),
        long_description_content_type="text/markdown",
        packages=find_packages(include=["mhcflurry", "mhcflurry.*"]),
    )