chore: extend pre-commit hooks and enable its updates via dependabot

.github/dependabot.yml

@@ -1,44 +1,39 @@
 # Run dependencies versions update
 version: 2
 
-updates:
-  - package-ecosystem: "uv"
-    directories:
-      - "/"
-      - "/examples/*/"
+# Multi-ecosystem group: all version updates land in a single combined PR.
+# Security updates are alert-driven and unaffected by this grouping; the uv
+# `security-updates` group below keeps them batched in their own PR.
+multi-ecosystem-groups:
+  all:
     schedule:
       interval: "weekly"
       day: "monday"
     commit-message:
       prefix: "chore(deps)"
+
+updates:
+  - package-ecosystem: "uv"
+    directories:
+      - "/"
+      - "/examples/*/"
+    patterns:
+      - "*"
+    multi-ecosystem-group: "all"
     groups:
       security-updates:
         applies-to: security-updates
         patterns:
           - "*"
-      test-dependencies:
-        applies-to: version-updates
-        patterns:
-          - "pytest*"
-      doc-dependencies:
-        applies-to: version-updates
-        patterns:
-          - "properdocs*"
-          - "mike*"
-      dev-dependencies:
-        applies-to: version-updates
-        patterns:
-          - "*"
 
   - package-ecosystem: "github-actions"
-    directory: "/.github/workflows"
-    schedule:
-      interval: "weekly"
-      day: "monday"
-    commit-message:
-      prefix: "chore(deps)"
-    groups:
-      github-actions-dependencies:
-        applies-to: version-updates
-        patterns:
-          - "*"
+    directory: "/"
+    patterns:
+      - "*"
+    multi-ecosystem-group: "all"
+
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    patterns:
+      - "*"
+    multi-ecosystem-group: "all"

.pre-commit-config.yaml

@@ -30,20 +30,29 @@ repos:
         types_or: [ python, pyi ]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
-      - id: check-docstring-first
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
       - id: check-executables-have-shebangs
+      - id: check-illegal-windows-names
       - id: check-json
       - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-vcs-permalinks
       - id: detect-private-key
       - id: check-shebang-scripts-are-executable
       - id: check-toml
       - id: check-yaml
       - id: debug-statements
+      - id: destroyed-symlinks
       - id: end-of-file-fixer
         types: [python]
       - id: fix-byte-order-marker
+      - id: name-tests-test
+        args: [--pytest-test-first]
+        exclude: '^tests/(toy_backends\.py|toy_models/|utilities/)'
       - id: no-commit-to-branch
       - id: requirements-txt-fixer
       - id: trailing-whitespace
@@ -52,17 +61,12 @@ repos:
         args: [--fix=lf]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.33.0
+    rev: 0.39.0
     hooks:
     - id: check-dependabot
     - id: check-github-workflows
 
-  # - repo: https://github.com/thlorenz/doctoc
-  #   rev: v2.2.0
-  #   hooks:
-  #     - id: doctoc
-  #       args: [ --github, --update-only ]
-
+  # Strip output from Jupyter and IPython notebooks
   - repo: https://github.com/kynan/nbstripout
     rev: 0.9.1
     hooks: