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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"
[project]
name = "wsinfer"
description = "Run patch-based classification on pathology whole slide images."
readme = "README.md"
requires-python = ">= 3.8"
license = { text = "Apache License, Version 2.0" }
authors = [
{ name = "Jakub Kaczmarzyk", email = "[email protected]" },
]
maintainers = [
{ name = "Jakub Kaczmarzyk", email = "[email protected]" },
]
classifiers = [
"Development Status :: 4 - Beta",
"Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Healthcare Industry",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Topic :: Scientific/Engineering :: Image Recognition",
"Topic :: Scientific/Engineering :: Medical Science Apps.",
]
dependencies = [
"click>=8.0,<9,!=8.1.4,!=8.1.5",
"h5py",
# This is when numpy.typing.NDArray was introduced.
"numpy>=1.21.0",
"opencv-python-headless>=4.0.0",
"pandas",
"pillow",
"scikit-image>=0.20.0",
"shapely",
# https://github.com/Bayer-Group/tiffslide/issues/72#issuecomment-1631015274
"tifffile>=2023.1.23",
"tiffslide>=2.2.0",
# https://github.com/Bayer-Group/tiffslide/issues/72#issuecomment-1630091390
"imagecodecs >= 2022.7.27 ; python_version<'3.9'",
# https://github.com/Bayer-Group/tiffslide/issues/72#issuecomment-1630091390
"imagecodecs >= 2023.7.10 ; python_version>='3.9'",
# The installation of torch and torchvision can differ by hardware. Users are
# advised to install torch and torchvision for their given hardware and then install
# wsinfer. See https://pytorch.org/get-started/locally/.
"torch>=1.7",
"torchvision",
"tqdm",
"wsinfer-zoo>=0.6.2",
]
dynamic = ["version"]
[project.optional-dependencies]
dev = [
"black",
"geojson",
"mypy",
"pandas-stubs",
"pre-commit",
"pytest",
"ruff",
"tiffslide",
"types-jsonschema",
"types-Pillow",
"types-tqdm",
]
docs = [
"pydata-sphinx-theme",
"sphinx",
"sphinx-autoapi",
"sphinx-click",
"sphinx-copybutton",
]
openslide = ["openslide-python"]
qupath = ["paquo"]
all = ["wsinfer[dev,docs,openslide,qupath]"]
[project.urls]
Homepage = "https://wsinfer.readthedocs.io"
Documentation = "https://wsinfer.readthedocs.io"
Repository = "https://github.com/SBU-BMI/wsinfer"
"Bug Tracker" = "https://github.com/SBU-BMI/wsinfer/issues"
[project.scripts]
wsinfer = "wsinfer.cli.cli:cli"
[tool.setuptools.package-data]
wsinfer = ["py.typed", "schemas/*.json"]
[tool.setuptools.packages.find]
include = ["wsinfer*"]
[tool.setuptools_scm]
write_to = "wsinfer/_version.py"
[tool.mypy]
disallow_untyped_defs = true
disallow_any_unimported = false
no_implicit_optional = true
check_untyped_defs = true
warn_return_any = true
warn_unused_ignores = true
show_error_codes = true
[[tool.mypy.overrides]]
module = [
"h5py",
"geojson",
"torchvision.*",
"openslide",
"shapely.*",
"zarr.storage",
]
ignore_missing_imports = true
[tool.ruff]
extend-exclude = ["_version.py", "scripts/"]
[tool.ruff.lint]
select = ["E4", "E7", "E9", "F", "B", "I"]
unfixable = ["B"]
[tool.ruff.lint.isort]
force-single-line = true