panoptica/pyproject.toml at main · BrainLesion/panoptica · GitHub

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[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
build-backend = "poetry_dynamic_versioning.backend"

[tool.poetry-dynamic-versioning]
enable = true

[tool.poetry]
exclude = ["examples", "benchmark"]
version = "0.0.0"

[project]
name = "panoptica"
dynamic = ["version"]
description = "Panoptic Quality (PQ) computation for binary masks."
authors = [
    { name = "Hendrik Möller", email = "hendrik.moeller@tum.de" },
    { name = "Florian Kofler", email = "florian.kofler@tum.de" },
]
readme = "README.md"
requires-python = ">=3.10,<4.0"
license = { file = "LICENSE" }
keywords = ["panoptic", "quality", "segmentation", "medical imaging"]
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dependencies = [
    "numpy>=1.22,<2.3",
    "connected-components-3d>=3.12.3,<4.0.0",
    "scipy>=1.7.0,<2.0.0",
    "rich>=13.6.0,<14.0.0",
    "scikit-image>=0.22.0,<1.0.0",
    "ruamel.yaml>=0.18.6,<1.0.0",
    "plotly>=5.16.1,<6.0.0",
    "pandas>=2.1.0,<3.0.0",
    "typer>=0.15.0,<1.0.0",
    "tqdm>=4.62.3",
]

[project.urls]
repository = "https://github.com/BrainLesion/panoptica"
homepage = "https://github.com/BrainLesion/panoptica"
documentation = "https://panoptica.readthedocs.io/"

[dependency-groups]
nifti = [
    "nibabel>=5.1.0,<6.0.0",
    "pynrrd>=1.1.3,<2.0.0",
    "SimpleITK>=2.2.2,<3.0.0",
]
test = [
    { include-group = "nifti" },
    "pytest>=8.1.1",
    "joblib>=1.3.2,<2.0.0",
    "coverage>=7.0.1",
    "pytest-mock>=3.6.0,<4.0.0",
    "future>=0.18.3, <1.0.0",
]
lint = [
    "ruff>=0.11.0",
    "mypy>=1.10.0",
]
docs = [
    "Sphinx>=7.0.0",
    "sphinx-copybutton>=0.5.2,<1.0.0",
    "furo>=2024.8.6",
    "myst-parser>=2.0.0",
]
dev = [
    { include-group = "test" },
    { include-group = "docs" },
    { include-group = "lint" },
    "pre-commit>=2.20.0,<3.0.0",
    "torch>=2.1.0,<3.0.0",
]

[tool.poetry.group.nifti]
optional = true

[tool.poetry.group.test]
optional = true

[tool.poetry.group.docs]
optional = true

[tool.poetry.group.dev]
optional = true

[tool.poetry.group.lint]
optional = true


[project.optional-dependencies]
gpu = ["torch>=2.1.0,<3.0.0"]

[tool.poetry.scripts]
panopticacli = "panoptica.cli:app"


[tool.ruff]
line-length = 88
target-version = "py310"
extend-exclude = ["docs", "examples", "benchmark"]

[tool.ruff.lint]
# E/W: pycodestyle, F: pyflakes, UP: pyupgrade, B: bugbear.
# NOTE: import sorting (I) is intentionally NOT enabled. The package currently relies
# on a set of order-sensitive circular imports (_functionals <-> utils <->
# processing_pair <-> panoptica_result); reordering imports breaks `import panoptica`.
# Re-enable "I" once those cycles are decoupled.
select = ["E", "W", "F", "UP", "B"]
ignore = [
    "E501",  # line length is enforced by the formatter, not the linter
    "B905",  # zip(..., strict=) is 3.10+ only; not worth churning every call site
    "B008",  # calls in arg defaults are deliberate here (edge-case policy objects)
    "B024",  # _ProcessingPair is an intentional ABC without abstract methods
    "B028",  # explicit warnings.warn stacklevel is noise for this codebase
    "UP038", # Use X | Y instead of (X, Y) for isinstance
    "B017", # assert Exception in unittests...
]

[tool.ruff.lint.per-file-ignores]
# __init__.py re-exports are deliberate public API, not unused imports.
"__init__.py" = ["F401"]
# Tests favor readability over import hygiene (shared fixtures, re-imports).
"unit_tests/**" = ["F401", "F811", "E402", "F841"]

[tool.mypy]
python_version = "3.10"
# The package is clean under this configuration. It is pragmatic rather than strict:
# missing third-party stubs are ignored, and full annotation coverage is not enforced
# (tighten with e.g. disallow_untyped_defs incrementally). warn_unused_ignores is left
# off on purpose so optional deps (torch/nibabel/SimpleITK) not installed in a given
# environment don't turn their guarded `# type: ignore`s into spurious failures.
ignore_missing_imports = true
warn_redundant_casts = true
exclude = ["docs/", "examples/", "benchmark/", "unit_tests/"]