[cchlanger]

Summary

Brings gertils in line with the other repositories behind looptrace, as #52 describes. gertils already formats with ruff format, lints with ruff check and type-checks with pyright, in the pre-commit hooks and in CI, and installs neither black, isort, pylint nor mypy. What remained were the versions and the line length, in the first two commits. The third removes # noqa comments that the reformatting showed to be fragile:

Commit	Change
ca179bb	Pins ruff 0.7.4 and pyright 1.1.411, the versions that looptrace and spotfishing pin. gertils locked ruff 0.3.7 and pyright 1.1.414. gerlichlab/looptrace#557 is where the shared versions are chosen.
2125286	Removes line-length = 100, so that ruff formats at its default of 88, and reformats the code: 8 of 15 files, 114 lines added and 42 removed.
f040948	Tells ruff that numpydoc_decorator's @doc gives functions their docstrings, with pydocstyle's ignore-decorators setting, so that the six # noqa: D103 comments on decorated functions go. When the formatter split a signature, it moved one of them off the line where ruff reports the rule. Classes keep their # noqa: D101, as the setting applies only to functions.

Nothing changes for users of gertils, so this needs no release: besides the layout, the code changes only in its # noqa comments.

Testing

• With ruff 0.7.4 and pyright 1.1.411, all checks pass before the reformatting, without changes to the code, and pyright --verifytypes gertils still finds 100% of the public API typed.
• After each commit, all pre-commit hooks and the 122 tests pass.
• With ignore-decorators, ruff still reports a public function that has neither a docstring nor @doc.
• 61 lines are still longer than 88 characters: strings, comments and docstrings, which ruff doesn't wrap. As before, the configuration doesn't check line length (E501).

Merging

Please don't squash: main can be fast-forwarded to the branch, which keeps the three commits as they are.

Closes #52

[Copilot]

🟢 Approval recommended

The tooling updates are consistent, formatting preserves behavior, and no blocking issues were identified.

No open issues 🎉

What changed in this PR

Aligns gertils with the shared formatting and type-checking standards in #52, without changing runtime behavior.

Changes:

• Pins Ruff 0.7.4 and Pyright 1.1.411.
• Adopts Ruff’s default 88-character formatting.
• Replaces function-level docstring suppressions with decorator-aware configuration.

File	Description
typings/​zarr/​__init__.pyi	Reformats a stub signature.
tests/​test_pixel_value_statistics.py	Reformats statistics tests.
tests/​test_pathtools.py	Reformats path tests.
tests/​test_get_fov_sort_key.py	Reformats imports and tests.
pyproject.toml	Pins tools and updates Ruff settings.
poetry.lock	Locks the selected tool versions.
gertils/​zarr_tools.py	Reformats code and removes a docstring suppression.
gertils/​types.py	Reformats exception construction.
gertils/​pixel_value_statistics.py	Reformats code and removes docstring suppressions.
gertils/​pathtools.py	Reformats code and removes docstring suppressions.

_{Review effort: Balanced}