Update and run all pre commit hooks#121
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Remove legacy packaging and test config files (setup.cfg, requirements.txt, .isort.cfg, napari_cellseg3d/_tests/pytest.ini, and its conftest). Migrate and update metadata in pyproject.toml: bump supported Python classifiers to 3.10–3.12, add napari manifest entry-point, include napari.yaml in package data, simplify dynamic fields, adjust optional dependencies (add PyQt6, pyside6, move pydensecrf2 to crf extra) and streamline dev dependencies (remove black/isort as direct dev deps). Update tooling rules (ruff token change) and remove redundant tool configs. Update tox.ini to target py310/311/312 across linux/windows/macos, expose platform mappings for GH Actions, and switch to using extras for test/crf/pyqt6 while keeping usedevelop and running pytest as the test command.
Skip a test that causes GitHub Actions to freeze by importing pytest and marking it skipped (needs to be fixed or removed). In worker_inference, replace np.reshape(...) with the ndarray.reshape(...) call and remove an obsolete commented reshape for clarity. In dev_scripts/correct_labels, initialize a napari.Viewer and add the image via viewer.add_image instead of calling napari.view_image(), ensuring the image layer is properly created.
Bump and extend pre-commit configuration and migrate pyproject to a PEP 621 style layout. .pre-commit-config.yaml: update pre-commit-hooks rev, replace/update ruff hook to astral-sh/ruff-pre-commit with auto-fix and unsafe-fixes, add ruff-format, mdformat (with mdformat-myst), pyproject-fmt and validate-pyproject hooks; keep napari-plugin-checks. pyproject.toml: add [build-system], normalize project metadata (name, license, requires-python, classifiers), move authors to [[project.authors]], declare dynamic version, reorganize and deduplicate dependencies and optional-dependencies, add project.urls and napari entry-point, add [tool.setuptools] packaging settings, move and refine ruff configuration under [tool.ruff.lint], and add [tool.pyproject-fmt] settings. Overall this modernizes packaging and enables enhanced linting/formatting via pre-commit hooks.
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