pheweb/setup.py at master · FINNGEN/pheweb · GitHub

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# to install: `pip install -e .` or `pip install .`
# to upload to pypi:
#     0. have a good `~/.pypirc`
#     1. set a new version in `pheweb/version.py`
#     2. `rm -r dist && python3 setup.py sdist bdist_wheel && twine upload dist/*`
# to upgrade: `pip3 install --upgrade --upgrade-strategy only-if-needed --no-cache-dir pheweb`
# to test: `python3 setup.py test`


from setuptools import setup
import os.path
from pheweb.load_source.load_source import load_source

version = load_source('pheweb.version', os.path.join('pheweb', 'version.py')).version

setup(
    name='PheWeb',
    version=version,
    description="A tool for building PheWAS websites from association files",
    long_description='Please see the README `on github <https://github.com/statgen/pheweb>`__',
    author="Peter VandeHaar",
    author_email="pjvh@umich.edu",
    url="https://github.com/statgen/pheweb",
    license="MIT",
    classifiers=[
        'Programming Language :: Python :: 3 :: Only',
        'Operating System :: Unix',
        'License :: OSI Approved :: MIT License',
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Visualization',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Topic :: Internet :: WWW/HTTP :: WSGI :: Application',
    ],

    packages=['pheweb'],
    entry_points={'console_scripts': [
        'pheweb=pheweb.command_line:main',
        'detect-ref=pheweb.load.detect_ref:main',
    ]},
    # TODO: add test_suite (ie, make a single file that runs tests, figure out how to access input_data, make a data_dir in /tmp)
    include_package_data=True,
    zip_safe=False,
    cffi_modules=['pheweb/load/cffi/ffibuilder.py:ffibuilder'],
    setup_requires=[
        'cffi~=1.11',
        'pytest-runner~=4.0',
    ],
    install_requires=[
        'Jinja2~=3.1.2',
        'Flask~=3.0.0',
        'Flask-Compress~=1.15',
        'Flask-Cors~=5.0.1',
        'Flask-Login~=0.6.3',
        'Werkzeug~=3.0.0',
        'pyasn1~=0.6.1',
        'google-api-python-client~=2.167.0',
        'google-auth~=2.34.0',
        'google-auth-httplib2~=0.2.0',
        'google-compute-engine~=2.8.13',
        'rauth~=0.7',
        'pysam~=0.23.0',
        'marisa-trie~=1.2.1',
        'intervaltree==3.2.1',
        'tqdm~=4.67.0',
        'openpyxl~=3.1.5',
        'scipy~=1.15.2',
        'numpy~=2.2.5',
        'requests[security]~=2.32.3',
        'cryptography~=44.0.2',
        'idna~=3.10',
        'gunicorn~=23.0.0',
        'boltons~=25.0.0',
        'cffi~=1.17.1',
        'wget~=3.2',
        'elasticsearch~=9.0.0',
        'latex~=0.7.0',
        'attrs',
        'pandas~=2.2.3',
        'SQLAlchemy~=1.4.54',
        'PyMySQL>=0.10.1',
        'mysqlclient>=2.0.1',
        'smart_open[gcs]~=7.1.0',
        'prometheus-flask-exporter~=0.23.2',
        'tiledb~=0.33.6',
    ],
    dependency_links=[],
    tests_require=[
        'pytest~=3.4',
        'selenium~=4.6.1',
        'testcontainers~=3.7.1'
    ],
)