funtracks/pyproject.toml at f55268ccae1632a14e543cb74eb7bd2c05b4f263 · funkelab/funtracks · GitHub

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[build-system]
requires = ["setuptools>=70", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "funtracks"
dynamic = ["version"]
description = "Cell tracking data model"
readme = "README.md"
license = { text = "BSD 3-Clause License" }
requires-python = ">=3.10"
authors = [
    { name = "Caroline Malin-Mayor", email = "malinmayorc@janelia.hhmi.org" },
]
classifiers = [
    "Development Status :: 2 - Pre-Alpha",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Image Processing",
]

dependencies =[
    "numpy>=2,<3",
    "pydantic>=2,<3",
    "networkx>=3.4,<4",
    "psygnal>=0.14",
    "scikit-image>=0.25",
    "geff>=1.1.3,<2",
    "dask>=2025.5.0",
    "pandas>=2.3.3",
    "zarr>=2.18,<4",
    "numcodecs>=0.13,<0.16",
    "tracksdata[spatial]@git+https://github.com/royerlab/tracksdata@24d93ef8d3c4c44cedc346dc3229c98c1d3eaa5e",
]

[project.urls]
"Bug Tracker" = "https://github.com/funkelab/funtracks/issues"
"Documentation" = "https://funkelab.github.io/funtracks/"

[dependency-groups]
testing =[
    "pytest>=8,<9",
    "pytest-cov>=7,<8",
]
docs = [
    "mkdocs-material>=9,<10",
    "mike>=2,<3",
    "mkdocstrings[python]>=0.28.2",
    "mkdocs-api-autonav>=0.4.0"]
dev = [
    "ruff>=0.12",
    "pre-commit>=4,<5",
    "mypy>=1,<2",
    {include-group="testing"},
    {include-group = "docs"},
]

[tool.setuptools_scm]

[tool.ruff]
line-length = 90
target-version = "py310"
fix = true
src = ["src"]

[tool.ruff.lint]
select = [
    "E", "F", "W", #flake8
    "UP", # pyupgrade
    "I", # isort
    "BLE", # flake8-blind-exception
    "B", # flake8-bugbear
    "A", # flake8-builtins
    "C4", # flake8-comprehensions
    "ISC", # flake8-implicit-str-concat
    "G", # flake8-logging-format
    "PIE", # flake8-pie
    "SIM", # flake8-simplify
    "T20", # flake-print
    "D102", # undocumented public method
    "D103", # undocumented public function
    "D300", # enforces triple double quotes on docstrings
    "D414", # empty/missing docstring section
    "D417", # undocumented parameter
]

unfixable = [
  "B905", # currently adds strict=False to zips. Should add strict=True (manually)
]
[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D"]  # no docstrings in tests
"src/funtracks/data_model/tracks.py" = ["D"]  # Remove this when refactoring tracks
"src/funtracks/data_model/solution_tracks.py" = ["D"]  # Remove this when refactoring tracks
"__init__.py" = ["F401"]  # unused imports allowed in __init__.py

# https://docs.astral.sh/ruff/formatter/
[tool.ruff.format]

[tool.mypy]
ignore_missing_imports = true
python_version = "3.10"
explicit_package_bases = true

[tool.coverage.report]
exclude_also = [
    "if TYPE_CHECKING:",
]