pyproject.toml

[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 = "jakub.kaczmarzyk@stonybrookmedicine.edu" },
]
maintainers = [
    { name = "Jakub Kaczmarzyk", email = "jakub.kaczmarzyk@stonybrookmedicine.edu" },
]
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",
    "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",
    "flake8",
    "geojson",
    "isort",
    "mypy",
    "pytest",
    "tiffslide",
    "types-Pillow",
    "types-tqdm",
    "Flake8-pyproject",
]
docs = [
    "pydata-sphinx-theme",
    "sphinx<6.0.0",
    "sphinx-autoapi",
    "sphinx-click",
    "sphinx-copybutton",
]
openslide = ["openslide-python"]

[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", "patchlib/presets/*.csv", "schemas/*.json"]

[tool.setuptools.packages.find]
include = ["wsinfer*"]

# Flake8-pyproject (https://pypi.org/project/Flake8-pyproject/)
[tool.flake8]
max-line-length = 88
extend-ignore = ['E203']
exclude = "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",
    "cv2",
    "geojson",
    "torchvision.*",
    "openslide",
    "pandas",
    "safetensors.*",
    "scipy.stats",
    "shapely.*",
    "skimage.morphology",
    "tifffile",
    "zarr.storage",
]
ignore_missing_imports = "True"

[tool.setuptools_scm]
write_to = "wsinfer/_version.py"

[tool.isort]
profile = "black"
force_single_line = "True"