pyproject.toml

# https://peps.python.org/pep-0517/
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools>=70", "setuptools-scm>=8"]

# https://peps.python.org/pep-0621/
[project]
name = "cellpose-runner"
description = "Run CellPose with formalized configuration logging and visualization."
readme = "README.md"
requires-python = ">=3.12"
license = { text = "BSD 3-Clause License" }
authors = [
    { email = "malinmayorc@janelia.hhmi.org", name = "Caroline Malin-Mayor" },
]
keywords = []
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: BSD License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Typing :: Typed",
]
dynamic = ["version"]
dependencies = [
    "cellpose>=4.1,<5",
    "coolname>=2,<6",
    "janelia-pathlib",
    "numpy>=1.26,<3",
    "pydantic>=2.7,<3",
    "tifffile>=2024.1,<2027",
    "tomli-w>=1,<2",
    "zarr>=3,<4",
]

[tool.uv.sources]
janelia-pathlib = { git = "ssh://git@github.com/JaneliaSciComp/janelia-pathlib.git" }

[project.optional-dependencies]
report = ["pandas>=2,<3", "panel>=1.4,<2"]
view = ["neuroglancer>=2.39,<3"]

[project.urls]
homepage = "https://github.com/JaneliaSciComp/cellpose_runner"
repository = "https://github.com/JaneliaSciComp/cellpose_runner"
documentation = "https://JaneliaSciComp.github.io/cellpose_runner/"

# https://peps.python.org/pep-0735/
[dependency-groups]
test = ["pytest>=8.3,<10", "pytest-cov>=6,<8"]
docs = [
    "mkdocs-material>=9.6,<10",
    "mkdocstrings-python>=1.16,<3",
    "mkdocs-api-autonav>=0.3,<1",
    "mkdocs-include-markdown-plugin>=7.1,<8",
    "mkdocs-autorefs>=1.0,<2",
    "mike>=2.1,<3",
]
dev = [
    { include-group = "test" },
    { include-group = "docs" },
    "ipython>=8,<10",
    "mypy>=1.15,<3",
    "pre-commit>=4,<5",
    "ruff>=0.13,<1",
]

# enables dynamic versioning from git tags
[tool.setuptools_scm]

# https://docs.astral.sh/ruff/rules/
[tool.ruff]
line-length = 100
target-version = "py312"
fix = true
src = ["src"]

[tool.ruff.lint]
extend-select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "I",    # isort
    "UP",   # pyupgrade
    "C4",   # flake8-comprehensions
    "B",    # flake8-bugbear
    "A001", # flake8-builtins
    "RUF",  # ruff-specific rules
    "TID",  # tidy imports
    "TC",   # type checking
    "T201", # print statements
    "D102", # undocumented public method
    "D103", # undocumented public function
    "D300", # enforces triple double quotes on docstrings
    "D414", # empty/missing docstring section
    "D417", # undocumented parameter
]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D", "ANN"]
"scripts/*.py" = ["D"]
# these scripts report to stdout for CI to consume
".github/scripts/*.py" = ["D", "T201"]

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

# https://docs.pytest.org/en/stable/reference/customize.html
[tool.pytest.ini_options]
minversion = "7.0"
testpaths = ["tests"]
pythonpath = ["tests"]
addopts = "-m 'not slow'"
markers = [
    "slow: runs real cellpose end to end; excluded by default, run with `-m slow`",
]
filterwarnings = [
    "error",
    # if needed, add global ignores here, for example:
    # "ignore:Some message:SomeCategory",
]

# https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
files = "src/cellpose_runner"
strict = true
disallow_any_generics = false
disallow_subclassing_any = false
show_error_codes = true
pretty = true

# cellpose ships no type information, so calls into it are untyped.
[[tool.mypy.overrides]]
module = ["cellpose.*", "janelia_pathlib.*", "neuroglancer.*", "pandas.*", "panel.*"]
ignore_missing_imports = true

# https://coverage.readthedocs.io/en/latest/config.html
# These exclusions are limited to code that provably cannot run under the test
# suite. Deliberately *not* excluded: `except ImportError` (optional-dependency
# fallbacks are exactly the paths that break for users without the extra) and
# `pass` (which would also hide untested branches like `if edge_case: pass`).
[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",           # explicit opt-out
    "if TYPE_CHECKING:",          # never executes at runtime
    "@overload",                  # typing-only stub signatures
    "raise NotImplementedError()",# abstract methods; the bare form only
    '^\s*\.\.\.\s*$',             # lines with ONLY ellipses, any surrounding whitespace
]

[tool.coverage.run]
source = ["src/cellpose_runner"]