Add stages and split ruff hooks

Introduce default_stages and explicitly assign stages to hooks, marking safe checks as pre-commit/manual and file-modifying hooks as pre-commit-only. Add check-merge-conflict, set name-tests-test args, and ensure end-of-file-fixer/trailing-whitespace run only in pre-commit. Bump pyproject-fmt to v2.21.1 and update ruff pre-commit to v0.15.12, replacing the previous ruff entries with a clear split: local autofix/format hooks (pre-commit) and CI check-only variants (manual) with appropriate args. Remove the napari-plugin-checks entry and reorganize hooks for clearer local vs CI behavior.

Author: C-Achard

.pre-commit-config.yaml

@@ -1,36 +1,64 @@
+default_stages: [pre-commit]
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
+      # These are safe to run in both local & CI (they don't require "fix vs check" split)
       - id: check-added-large-files
+        stages: [pre-commit, manual]
       - id: check-yaml
+        stages: [pre-commit, manual]
       - id: check-toml
-      - id: end-of-file-fixer
+        stages: [pre-commit, manual]
+      - id: check-merge-conflict
+        stages: [pre-commit, manual]
       - id: name-tests-test
+        stages: [pre-commit, manual]
+        args: ["--pytest-test-first"]
+
+      # These modify files. Run locally only (pre-commit stage).
+      - id: end-of-file-fixer
+        stages: [pre-commit]
       - id: trailing-whitespace
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
-    hooks:
-      # Run the formatter.
-      - id: ruff-format
-      # Run the linter.
-      - id: ruff-check
-        args: [--fix,--unsafe-fixes]
+        stages: [pre-commit]
+
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.16.2
+    rev: v2.21.1
     hooks:
       - id: pyproject-fmt
+        stages: [pre-commit]    # modifies -> local only
+
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: v0.25
     hooks:
       - id: validate-pyproject
-  - repo: https://github.com/tlambert03/napari-plugin-checks
-    rev: v0.3.0
+        stages: [pre-commit, manual]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.12
     hooks:
-      - id: napari-plugin-checks
-  # https://mypy.readthedocs.io/en/stable/introduction.html
-  # you may wish to add this as well!
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v0.910-1
-  #   hooks:
-  #     - id: mypy
+      # --------------------------
+      # LOCAL AUTOFIX (developers)
+      # --------------------------
+      - id: ruff-check
+        name: ruff-check (fix)
+        args: [--fix, --unsafe-fixes]
+        stages: [pre-commit]
+
+      - id: ruff-format
+        name: ruff-format (write)
+        stages: [pre-commit]
+
+      # --------------------------
+      # CI CHECK-ONLY (no writes)
+      # --------------------------
+      - id: ruff-check
+        name: ruff-check (ci)
+        args: [--output-format=github]
+        stages: [manual]
+
+      - id: ruff-format
+        name: ruff-format (ci)
+        args: [--check, --diff]
+        stages: [manual]