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pyproject.toml
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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "wsidata"
description = "Data structures and I/O functions for whole-slide images (WSIs)."
readme = "README.md"
requires-python = ">=3.10"
license = "MIT"
authors = [
{name = "Yimin Zheng", email = "[email protected]"},
{name = "Ernesto Abila", email = "[email protected]"},
{name = "André F. Rendeiro", email = "[email protected]"},
]
keywords = ["histopathology", "whole slide image", "image analysis", "data structure"]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Topic :: File Formats",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
Documentation = "https://wsidata.readthedocs.io"
repository = "https://github.com/rendeirolab/wsidata"
dynamic = ["version"]
dependencies = [
"spatialdata>=0.3.0",
"opencv-python-headless",
"openslide-python",
"openslide-bin",
"tiffslide",
"rich",
"numba>=0.61.0",
"torch>=2.0.0",
]
[project.optional-dependencies]
stain = ["torchstain"]
bioformats = ["scyjava"]
cucim = ["cucim"]
plot = ["matplotlib", "legendkit"]
[tool.hatch.version]
path = "wsidata/__init__.py"
[tool.hatch.build.targets.sdist]
exclude = [
"docs",
"data",
"assets",
"tests",
"scripts",
".readthedocs.yaml",
".github",
".gitignore",
]
include = [
"README.md",
"LICENSE",
"pyproject.toml",
"wsidata",
]
[tool.hatch.build.targets.wheel]
packages = ["wsidata", "README.md", "LICENSE", "pyproject.toml"]
[tool.ruff]
lint.ignore = ["F401"]
line-length = 88
[tool.taskipy.tasks]
hello = "echo Hello, World!"
test = "pytest tests"
doc-build = "sphinx-build -b html docs/source docs/build"
doc-clean-build = "python docs/clean_up.py && sphinx-build -b html docs/source docs/build"
doc-serve = "python -m http.server -d docs/build"
fmt = "ruff format docs/source wsidata tests"
[tool.uv]
default-groups = ["dev", "docs"]
[dependency-groups]
dev = [
"jupyterlab>=4.3.5",
"pre-commit>=4.1.0",
"pytest>=8.3.4",
"ruff>=0.9.4",
"taskipy>=1.14.1",
"pytest-cov>=6.0.0",
"torchvision>=0.21.0",
"torchstain>=1.4.1",
"matplotlib>=3.10.0",
"legendkit>=0.3.4",
"pyright>=1.1.393",
]
docs = [
"sphinx>=8.1.3",
"sphinx-copybutton>=0.5.2",
"sphinx-design>=0.6.1",
"myst-nb>=1.1.2",
"numpydoc>=1.8.0",
"pydata-sphinx-theme>=0.16.1",
"sphinx>=8.1.3",
"sphinx-copybutton>=0.5.2",
"sphinx-design>=0.6.1",
]