MOOZY/pyproject.toml at a3dfe091c8d219fdbc77641508838dcb0d7b488c · AtlasAnalyticsLab/MOOZY · GitHub

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[build-system]
requires = ["setuptools>=69", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "moozy"
version = "0.1.0"
description = "MOOZY: A Patient-First Foundation Model for Computational Pathology."
requires-python = ">=3.10"
license = {file = "LICENSE"}
readme = "README.md"
authors = [
  {name = "Yousef Kotp", email = "yousefkotp@outlook.com"},
]
keywords = [
  "pathology",
  "computational-pathology",
  "digital-pathology",
  "deep-learning",
  "foundation-model",
  "self-supervised-learning",
  "whole-slide-image",
  "histopathology",
  "medical-imaging",
  "multiple-instance-learning",
  "vision-transformer",
  "slide-level-representation",
]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Healthcare Industry",
  "Intended Audience :: Science/Research",
  "License :: Free for non-commercial use",
  "Operating System :: OS Independent",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Topic :: Scientific/Engineering :: Image Recognition",
  "Topic :: Scientific/Engineering :: Medical Science Apps.",
  "Typing :: Typed",
]
dependencies = [
  "h5py>=3.15,<4",
  "huggingface-hub>=0.20,<2",
  "numpy>=1.26,<3",
  "PyYAML>=6,<7",
  "scikit-survival>=0.25,<1",
  "timm>=1.0,<2",
  "torch>=2.9,<3",
  "typer>=0.20,<1",
  "wandb>=0.22,<1",
]

[project.optional-dependencies]
dev = [
  "mypy==1.19.1",
  "pre-commit==4.5.1",
  "ruff==0.15.8",
]

[project.scripts]
moozy = "moozy.cli.main:main"

[project.urls]
Homepage = "https://github.com/AtlasAnalyticsLab/MOOZY"
Repository = "https://github.com/AtlasAnalyticsLab/MOOZY"
Documentation = "https://github.com/AtlasAnalyticsLab/MOOZY/tree/main/docs"
"Model Weights" = "https://huggingface.co/AtlasAnalyticsLab/MOOZY"
"Bug Tracker" = "https://github.com/AtlasAnalyticsLab/MOOZY/issues"

[tool.setuptools.packages.find]
include = [
  "moozy*",
]
exclude = [
  "huggingface*",
]

[tool.ruff]
target-version = "py310"
line-length = 120
extend-exclude = [
  "huggingface",
]

[tool.ruff.lint]
select = ["E9", "F", "I"]

[tool.mypy]
python_version = "3.10"
files = [
  "moozy/config/__init__.py",
  "moozy/config/data.py",
  "moozy/config/model.py",
  "moozy/config/stage1.py",
  "moozy/config/stage2.py",
  "moozy/config/tasks.py",
  "moozy/config/training.py",
  "moozy/data/stage1/types.py",
  "moozy/data/stage2/types.py",
  "moozy/models/factory.py",
  "moozy/models/variants.py",
  "moozy/training/callbacks/__init__.py",
  "moozy/training/callbacks/checkpoint.py",
  "moozy/training/callbacks/logging.py",
  "moozy/training/engine/__init__.py",
  "moozy/training/engine/base.py",
  "moozy/training/engine/stage1.py",
  "moozy/training/engine/stage2.py",
  "moozy/training/runners/__init__.py",
  "moozy/training/runners/stage1.py",
  "moozy/training/runners/stage2.py",
]
follow_imports = "skip"
ignore_missing_imports = true
pretty = true
show_error_codes = true
warn_redundant_casts = true
warn_unused_ignores = true