pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "wsi-toolbox"
version = "0.4.2"
description = "A comprehensive toolkit for Whole Slide Image processing, feature extraction, and clustering analysis"
readme = "README.md"
requires-python = "==3.12.*"
license = {file = "LICENSE"}
authors = [
    {name = "Ken Enda", email = "ken@endaaman.com"},
]
keywords = ["wsi", "pathology", "deep-learning", "clustering", "histopathology"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
]
dependencies = [
    "h5py>=3.13.0",
    "imagecodecs>=2024.12.30",
    "joblib>=1.4.2",
    "leidenalg>=0.10.2",
    "matplotlib>=3.9.4",
    "networkx>=3.3",
    "numpy<2",
    "opencv-python-headless>=4.11.0.86",
    "openpyxl>=3.1.5",
    "openslide-python>=1.4.1",
    "pandas>=2.2.3",
    "pillow>=11.0.0",
    "pyqt6>=6.8.1",
    "python-igraph>=0.11.8",
    "rich>=14.0.0",
    "scikit-learn>=1.6.1",
    "seaborn>=0.13.2",
    "streamlit>=1.43.2",
    "streamlit-antd-components>=0.3.2",
    "streamlit-aggrid>=0.3.4.post3",
    "taskipy>=1.14.1",
    "tifffile>=2025.2.18",
    "timm>=0.9.16",
    "torch>=2.5.1",
    "torchvision>=0.20.1",
    "transformers>=4.40.0",
    "umap-learn>=0.5.7",
    "zarr>=3",
    "pydantic-autocli>=0.2.0",
    "einops>=0.8.1",
]

[project.scripts]
wsi-toolbox = "wsi_toolbox.cli:main"
wt = "wsi_toolbox.cli:main"

[project.urls]
Homepage = "https://github.com/technoplasm/wsi-toolbox"
Repository = "https://github.com/technoplasm/wsi-toolbox"
Documentation = "https://github.com/technoplasm/wsi-toolbox/blob/master/README.md"

# [[tool.uv.index]]
# name = "pytorch"
# url = "https://download.pytorch.org/whl/cu121"
# explicit = true

[project.optional-dependencies]
build = ["torch", "packaging", "wheel", "setuptools"]
compile = ["flash-attn"]

[tool.uv]
no-build-isolation-package = ["flash-attn"]
preview = true

# [tool.uv.sources]
# # x86_64 Linux: use CUDA 12.1 wheels, otherwise: use default PyPI (CPU)
# torch = [
#     { index = "pytorch", marker = "sys_platform == 'linux' and platform_machine == 'x86_64'" },
# ]
# torchvision = [
#     { index = "pytorch", marker = "sys_platform == 'linux' and platform_machine == 'x86_64'" },
# ]

[[tool.uv.index]]
name = "pytorch-cu128"
url = "https://download.pytorch.org/whl/cu128"
explicit = true

[tool.uv.sources]
torch = [
    { index = "pytorch-cu128", marker = "sys_platform == 'linux'" },
]
torchvision = [
    { index = "pytorch-cu128", marker = "sys_platform == 'linux'" },
]

[tool.uv.extra-build-dependencies]
flash-attn = ["setuptools", "wheel", "packaging", "ninja", "torch"]

[[tool.uv.dependency-metadata]]
name = "flash-attn"
version = "2.7.4"
requires-dist = ["torch", "einops"]


[tool.taskipy.tasks]
cli = "python -m wsi_toolbox.cli"
app = "streamlit run wsi_toolbox/app/main.py --server.address 0.0.0.0 --server.port ${PORT:-8501}"
watcher = "python -m wsi_toolbox.watcher"
clean = "rm -rf build/ dist/ *.egg-info/ __pycache__/ && find . -name '*.pyc' -delete && find . -name '__pycache__' -delete"
build = "python -m build"
check = "python -m twine check dist/*"
lint = "ruff check . --extend-ignore F401"
lint-strict = "ruff check ."
fix = "ruff check --fix . && ruff format ."

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.sdist]
exclude = [
    ",/",
    "data/",
    "out/",
    "weights/",
    "*.h5",
    "*.ndpi",
    "*.svs",
    "*.tiff",
]

[tool.hatch.build.targets.wheel]
packages = ["wsi_toolbox"]

[dependency-groups]
dev = [
    "fastapi>=0.115.0",
    "ipython>=9.1.0",
    "jupyterlab>=4.1.6",
    "ruff>=0.8.0",
    "taskipy>=1.14.1",
    "uvicorn>=0.32.0",
]
build = [
    "build>=1.0.0",
    "twine>=5.0.0",
]

# Slide-level encoding (CLI only) - uv-only feature, not uploaded to PyPI
# $ uv sync --group gigapath
gigapath = [
    "gigapath @ git+https://github.com/prov-gigapath/prov-gigapath.git@5d77be0",
    "flash-attn>=2.7.4",
    "einops>=0.8.1",
    "fairscale>=0.4.13",
]

[tool.ruff]
# Exclude common directories
exclude = [
    ".git",
    ".venv",
    "__pycache__",
    "build",
    "dist",
    "*.egg-info",
]

# Same as Black.
line-length = 120

[tool.ruff.lint]
# Enable specific rule categories
select = [
    "F",        # Pyflakes (unused imports, undefined names, etc.)
    "I",        # isort (import sorting)
    "E402",     # Module level import not at top of file
    "PLC0415",  # Import outside toplevel (import in function)
]

# Ignore specific rules
ignore = []

[tool.ruff.lint.per-file-ignores]
# Optional/heavy imports that need lazy loading
"wsi_toolbox/app/main.py" = ["E402", "PLC0415"]  # Streamlit app with special import patterns
"wsi_toolbox/utils/progress.py" = ["PLC0415"]  # Optional dependency (streamlit) lazy loading
"wsi_toolbox/commands/umap_embedding.py" = ["PLC0415"]  # Heavy import (umap) lazy loading

[tool.ruff.lint.isort]
known-first-party = ["wsi_toolbox"]