setup.py

# 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


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 = ""


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 = [
        "six",
        "pandas>=0.20.3",
        "appdirs",
        "scikit-learn",
        "mhcgnomes>=0.8.4",
        "numpy<2.0",
        "pyyaml",
        "tqdm",
        "tensorflow>=2.15.0",
        "tf-keras"
    ]

    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="http://www.apache.org/licenses/LICENSE-2.0.html",
        entry_points={
            "console_scripts": [
                "mhcflurry-downloads = mhcflurry.downloads_command:run",
                "mhcflurry-predict = mhcflurry.predict_command:run",
                "mhcflurry-predict-scan = mhcflurry.predict_scan_command:run",
                "mhcflurry-class1-train-allele-specific-models = "
                "mhcflurry.train_allele_specific_models_command:run",
                "mhcflurry-class1-train-pan-allele-models = "
                "mhcflurry.train_pan_allele_models_command:run",
                "mhcflurry-class1-train-processing-models = "
                "mhcflurry.train_processing_models_command:run",
                "mhcflurry-class1-select-allele-specific-models = "
                "mhcflurry.select_allele_specific_models_command:run",
                "mhcflurry-class1-select-pan-allele-models = "
                "mhcflurry.select_pan_allele_models_command:run",
                "mhcflurry-class1-select-processing-models = "
                "mhcflurry.select_processing_models_command:run",
                "mhcflurry-calibrate-percentile-ranks = "
                "mhcflurry.calibrate_percentile_ranks_command:run",
                "mhcflurry-class1-train-presentation-models = "
                "mhcflurry.train_presentation_models_command:run",
                "_mhcflurry-cluster-worker-entry-point = "
                "mhcflurry.cluster_parallelism:worker_entry_point",
            ]
        },
        classifiers=[
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Operating System :: OS Independent",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
        ],
        package_data={
            "mhcflurry": ["downloads.yml"],
        },
        install_requires=required_packages,
        long_description=readme,
        long_description_content_type="text/markdown",
        packages=[
            "mhcflurry",
        ],
    )