pidgeon/pyproject.toml at main · cellgeni/pidgeon · GitHub

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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "pidgeon"
version = "0.1.0"
description = "image alignment with automatic match assessment and adaptive thumbnail estimation"
readme = "README.md"
requires-python = ">=3.12"
license = { text = "MIT" }
authors = [
    { name = "Martin Prete", email = "martin.prete@sanger.ac.uk" }
]

# Core deps are permissively licensed and torch-free.
dependencies = [
    "numpy>=2.1",
    "scipy>=1.13",
    "scikit-image>=0.24",
    "tifffile>=2024.8.30",
    "imagecodecs>=2024.9.22",
    "zarr>=3",
    "pyyaml>=6.0",
    "tqdm>=4.66",
]

[project.optional-dependencies]
# Learned matchers. NOTE: the standard SuperPoint+LightGlue/SuperGlue *weights*
# are released for non-commercial research use only. DISK / ALIKED / SIFT
# weights for LightGlue are more permissive. Pick deliberately.
glue = ["torch>=2.4", "lightglue @ git+https://github.com/cvg/LightGlue"]
# Detector-free dense matcher fallback. RoMa is MIT-licensed, but downloads
# model weights on first use; install deliberately in environments that allow it.
dense = ["torch>=2.4", "romatch[fused-local-corr]>=0.1.1"]
# License-safe classical fallback matcher (SIFT patent has expired).
sift = ["opencv-contrib-python>=4.10"]
plot = ["matplotlib>=3.8"]
spatialdata = ["spatialdata"]
# All optional runtime features. Keep dev tooling separate.
all = ["pidgeon[glue,dense,sift,plot,spatialdata]"]
dev = ["ruff>=0.6", "mypy>=1.11", "pytest>=8.3"]

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

[tool.hatch.build]
exclude = [
    "**/__pycache__",
    "**/*.pyc",
    "__MACOSX",
    "**/._*",
    "**/.DS_Store",
    "**/*.ipynb",
]

[tool.hatch.build.targets.wheel]
packages = ["src/pidgeon"]

[tool.hatch.metadata]
allow-direct-references = true

[tool.ruff]
target-version = "py312"
line-length = 100
src = ["src", "tests"]

[tool.ruff.lint]
select = ["E4", "E7", "E9", "F", "I"]

[tool.ruff.lint.isort]
known-first-party = ["pidgeon"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
line-ending = "auto"

[tool.mypy]
python_version = "3.12"
files = ["src/pidgeon"]
check_untyped_defs = true
no_implicit_optional = true
pretty = true
show_error_codes = true
warn_unused_configs = true

[[tool.mypy.overrides]]
module = [
    "cv2",
    "lightglue",
    "lightglue.*",
    "scipy.*",
    "skimage.*",
    "torch",
    "tqdm.auto",
]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = [
    "pidgeon.reader",
    "pidgeon.tiled",
]
# tifffile, zarr, and NumPy scalar stubs are stricter than these dynamic I/O
# adapter paths. Keep these modules in the mypy run while allowing the stub
# edge cases to be covered by focused runtime tests.
disable_error_code = [
    "arg-type",
    "assignment",
    "call-overload",
    "index",
    "operator",
    "return-value",
    "type-var",
]

[[tool.mypy.overrides]]
module = "pidgeon.plot"
# Plot helpers accept matplotlib objects and typed **kwargs that do not map
# cleanly onto matplotlib's broad runtime API.
disable_error_code = [
    "arg-type",
    "assignment",
    "attr-defined",
    "call-overload",
]

[dependency-groups]
dev = [
    "myst-nb>=1.4.0",
    "pydata-sphinx-theme>=0.19.0",
    "sphinx>=9.1.0",
    "sphinx-autodoc-typehints>=3.12.1",
    "sphinx-copybutton>=0.5.2",
]