pyproject.toml

[project]
name = "tiatoolbox"
version = "2.1.3"
description = "Computational pathology toolbox developed by TIA Centre."
readme = "README.md"
license = { text = "BSD-3-Clause" }
authors = [{ name = "TIA Centre", email = "TIA@warwick.ac.uk" }]
requires-python = ">=3.12, <3.15"
classifiers = [
  "Development Status :: 2 - Pre-Alpha",
  "Intended Audience :: Developers",
  "Natural Language :: English",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
]
dependencies = [
  "aiohttp>=3.8.1",
  "bokeh>=3.8.2",
  "click>=8.2.0",
  "dask>=2026.1.2",
  "defusedxml>=0.7.1",
  "filelock>=3.9.0",
  "flask>=2.2.2",
  "flask-cors>=4.0.0",
  "glymur>=0.12.7",
  "huggingface_hub>=0.33.3",
  "imagecodecs>=2022.9.26",
  "ipywidgets>=8.1.7",
  "joblib>=1.1.1",
  "jupyterlab>=3.5.2",
  "matplotlib>=3.10.0",
  "numba>=0.57.0",
  "numpy>=2.0.0",
  "opencv-python>=4.6.0",
  "openslide-bin>=4.0.0.2",
  "openslide-python>=1.4.0",
  "pandas>=2.0.0",
  "pillow>=9.3.0",
  "pydicom>=2.3.1",
  "pyyaml>=6.0",
  "requests>=2.28.1",
  "s3fs>=2024.12.0",
  "scikit-image>=0.26.0",
  "scikit-learn>=1.2.0",
  "scipy>=1.8",
  "shapely>=2.0.0",
  "simpleitk>=2.2.1",
  "sphinx>=9.0.0",
  "tifffile>=2026.6.1",
  "timm>=1.0.3",
  "torch>=2.5.0",
  "torchvision>=0.15.0",
  "tqdm>=4.64.1",
  "transformers>=5.15.0",
  "umap-learn>=0.5.3",
  "wsidicom>=0.18.0, <0.36.0",
  "zarr>=3.2.1",
]

[project.optional-dependencies]
deepspotm = ["deepspotm>=1.0.0"]
docs = [
  "furo>=2022.12.7",
  "myst-nb>=0.17.1",
  "myst-parser>=0.18.1",
  "sphinx-copybutton>=0.5.1",
  "sphinx-design>=0.3.0",
  "sphinx-toolbox>=3.2.0",
]
dev = [
  "tiatoolbox[docs]",
  "coverage>=7.0.0",
  "docutils>=0.18.1",
  "mypy>=2.3",
  "pip>=22.3",
  "poetry-bumpversion>=0.3.1",
  "pre-commit>=2.20.0",
  "pytest>=7.2.0",
  "pytest-cov>=4.0.0",
  "pytest-runner>=6.0",
  "pytest-xdist[psutil]",
  "ruff==0.16.10",
  "toml>=0.10.2",
  "twine>=4.0.1",
  "wheel>=0.37.1",
]

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

[project.urls]
Homepage = "https://github.com/TissueImageAnalytics/tiatoolbox"

[tool.uv]

[[tool.uv.index]]
name = "pytorch-cu126"
url = "https://download.pytorch.org/whl/cu126"
explicit = true

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

[tool.uv.sources]
# Linux/Windows get CUDA 12.6 wheels; macOS falls through to PyPI (MPS included)
torch = [
  { index = "pytorch-cu126", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
]
torchvision = [
  { index = "pytorch-cu126", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
]

[tool.pytest.ini_options]
  collect_ignore = ["setup.py", "benchmark/"]

[tool.coverage.run]
  branch = true
  source = ['tiatoolbox']
  omit = ['tests/*', 'tiatoolbox/__main__.py', '*/utils/env_detection.py', 'tiatoolbox/typing.py']

[tool.coverage.report]
  exclude_lines = [
    'if self.debug:',
    'pragma: no cover',
    'raise NotImplementedError',
    'if __name__ == .__main__.:',
  ]
  ignore_errors = true
  omit = ['tests/*', 'tiatoolbox/__main__.py', '*/utils/env_detection.py', 'tiatoolbox/typing.py']

[build-system]
  requires = ["setuptools"]
  build-backend = "setuptools.build_meta"

[tool.distutils.bdist_wheel]
  universal = true

[tool.poetry]
name = "TIA-Centre"  # uv does not accept space in name
version = "2.1.3"
description = "test"
authors = ["TIA Centre <TIA@warwick.ac.uk>"]

[tool.poetry_bumpversion.file."tiatoolbox/__init__.py"]
search = '__version__ = "{current_version}"'
replace = '__version__ = "{new_version}"'


[[tool.poetry_bumpversion.replacements]]
files = ["setup.py"]
search = 'version="{current_version}"'
replace = 'version="{new_version}"'

[[tool.poetry_bumpversion.replacements]]
files = ["CITATION.cff"]
search = 'version: {current_version}  # TIAToolbox version'
replace = 'version: {new_version}  # TIAToolbox version'

[[tool.poetry_bumpversion.replacements]]
files = [".github/workflows/docker-publish.yml"]
search = 'TOOLBOX_VER: {current_version}'
replace = 'TOOLBOX_VER: {new_version}'

[[tool.poetry_bumpversion.replacements]]
files = ["pyproject.toml"]
search = 'version = "{current_version}"'
replace = 'version = "{new_version}"'

[tool.ruff]
lint.select = [
  "A",     # flake8-builtins
  "B",     # flake8-bugbear
  "D",     # pydocstyle, need to enable for docstrings check.
  "E",     # pycodestyle - Error
  "F",     # pyflakes
  "G",     # flake8-logging-format
  "I",     # Isort
  "N",     # pep8-naming
  "S",     # flake8-bandit
  "W",     # pycodestyle - Warning
  "Q",     # flake8-quotes
  "C4",    # flake8-comprehensions
  "FA",    # flake8-future-annotations
  "EM",    # flake8-errmsg
  "PD",    # pandas-vet
  "PL",    # Pylint
  "PT",    # flake8-pytest-style
  "TD",    # flake8-todos
  "UP",    # pyupgrade
  "C90",   # mccabe
  "T10",   # flake8-debugger
  "T20",   # flake8-print
  "ANN",   # flake8-annotations
  "ARG",   # flake8-unused-arguments
  "BLE",   # flake8-blind-except
  "COM",   # flake8-commas
  "DTZ",   # flake8-datetimez
  "ERA",   # eradicate
  "FBT",   # flake8-boolean-trap
  "FIX",   # flake8-fixme
  "FLY",   # flynt
  "ICN",   # flake8-import-conventions
  "INP",   # flake8-no-pep420
  "INT",   # flake8-gettext
  "ISC",   # flake8-implicit-str-concat
  "NPY",   # NumPy-specific rules
  "PGH",   # pygrep-hooks
  "PIE",   # flake8-pie
  "PTH",   # flake8-use-pathlib
  "PYI",   # flake8-pyi
  "RET",   # flake8-return
  "RSE",   # flake8-raise
  "RUF",   # Ruff-specific rules
  "SLF",   # flake8-self
  "SIM",   # flake8-simplify
  "TID",   # flake8-tidy-imports
  "TCH",   # flake8-type-checking
  "TRY",   # tryceratops
  "YTT",   # flake8-2020
  "PERF",  # Perflint
  "SLOT",  # flake8-slots
  "ASYNC", # flake8-async
]
# Ignore rules which conflict with ruff formatter.
lint.ignore = ["COM812", "ISC001"]
# Allow Ruff to discover `*.ipynb` files.
include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]

# Allow autofix for all enabled rules (when `--fix`) is provided.
lint.fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
lint.unfixable = []

# Exclude a variety of commonly ignored directories.
exclude = [
    ".eggs",
    ".git",
    ".ruff_cache",
    ".svn",
    ".venv",
    "__pypackages__",
    "_build",
    "build",
    "dist",
    "venv",
]

# Ignore `F401` (import violations) in all `__init__.py` files.
lint.per-file-ignores = {"__init__.py" = ["F401"], "tests/*" = ["T201", "PGH001", "SLF001", "S101", "PLR2004"], "benchmarks/*" = ["T201", "INP001"], "pre-commit/*" = ["T201", "INP001"], "tiatoolbox/cli/*" = ["PLR0913"]}

# Same as Black.
line-length = 88

# Allow unused variables when underscore-prefixed.
lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

# Minimum Python version 3.12.
target-version = "py312"

[tool.ruff.lint.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 14

# need to enable for docstrings check.
[tool.ruff.lint.pydocstyle]
 # Use Google-style docstrings.
convention = "google"

[tool.ruff.lint.pylint]
max-args = 10

[tool.ruff.format]
exclude = [
    ".eggs",
    ".git",
    ".ruff_cache",
    ".svn",
    ".venv",
    "__pypackages__",
    "_build",
    "build",
    "dist",
    "venv",
    ".hg",
    ".mypy_cache",
    "buck-out",
    "docs",
    "data",
    "setup.py",
]
skip-magic-trailing-comma = false

[tool.mypy]
ignore_missing_imports = true
# Default local target: minimum supported Python (requires-python lower bound).
# CI overrides this per job with --python-version for 3.12-3.14.
python_version = "3.12"