autoprognosis/setup.cfg at main · hertera1/autoprognosis · GitHub

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[metadata]
name = autoprognosis
description = A system for automating the design of predictive modeling pipelines tailored for clinical prognosis.
author = vanderschaarlab
author_email =
license =  Apache-2.0 license
long_description = file: README.md
long_description_content_type = text/markdown; charset=UTF-8
url = https://www.vanderschaar-lab.com/

# Change if running only on Windows, Mac or Linux (comma-separated)
platforms = any

classifiers =
    Programming Language :: Python :: 3
    Topic :: Scientific/Engineering :: Artificial Intelligence
    Intended Audience :: Healthcare Industry
    License :: OSI Approved :: BSD License
    Operating System :: OS Independent


[options]
zip_safe = False
packages = find_namespace:
include_package_data = True
package_dir =
    =src

# Require a min/specific Python version (comma-separated conditions)
python_requires = >=3.9

depends =
    cloudpickle
    hyperimpute>=0.1.16
    joblib
    lifelines
    loguru
    matplotlib
    numpy>=1.20
    optuna>=3.1.0
    pandas
    pydantic
    pyod
    redis
    scikit-learn>=1.0
    scipy>=1.3.2
    seaborn
    shap>=0.40.0
    statsmodels
    torch>=1.10

install_requires =
    importlib-metadata; python_version<"3.8"
    %(depends)s


[options.packages.find]
where = src
exclude =
    tests

[options.extras_require]
# Add here additional requirements for extra features, to install with:
# `pip install autoprognosis[PDF]` like:
# PDF = ReportLab; RXP

# Various extras:
# Additional dependencies for certain explainers:
explainers =
    lime
    symbolic_pursuit

# Additional dependencies for boosting methods:
boosting =
    catboost
    lightgbm
    xgboost

# Additional dependencies for tabnet:
tabnet =
    pytorch_tabnet

# Additional dependencies for survival:
survival =
    pycox
    torchtuples
    xgbse

# Additional dependencies for dashboard:
dashboard =
    plotly
    psutil
    pydantic
    streamlit

# All extras:
all =
    %(explainers)s
    %(boosting)s
    %(tabnet)s
    %(survival)s
    %(dashboard)s

# Docs requirements:
docs =
    docutils<0.21
    lxml[html_clean]
    m2r2
    mistune
    nbconvert
    nbsphinx
    sphinx
    sphinx_rtd_theme
    sphinxemoji

# Development requirements:
dev =
    %(all)s
    %(docs)s
    bandit
    click
    nbformat
    pre-commit
    pycox
    pytest
    pytest-benchmark
    pytest-cov
    pytest-xdist[psutil]
    pytest-xprocess
    ruff
    setuptools
    tabulate

[tool:pytest]
# Specify command line options as you would do when invoking pytest directly.
# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
# in order to write a coverage file that can be read by Jenkins.
# CAUTION: --cov flags may prohibit setting breakpoints while debugging.
#          Comment those flags to avoid this py.test issue.
norecursedirs =
    dist
    build
    .tox
testpaths = tests
# Use pytest markers to select/deselect specific tests
# markers =
#     slow: mark tests as slow (deselect with '-m "not slow"')
#     system: mark end-to-end system tests

[bdist_wheel]
# Use this option if your package is pure-python
universal = 1

[devpi:upload]
# Options for the devpi: PyPI server and packaging tool
# VCS export must be deactivated since we are using setuptools-scm
no_vcs = 1
formats = bdist_wheel