update pre-commit

.pre-commit-config.yaml

@@ -1,17 +1,14 @@
 repos:
-
 # Empty notebookds
 - repo: local
   hooks:
-    - id: clear-notebooks-output
-      name: clear-notebooks-output
-      files: tools/.*\.ipynb$
-      stages: [commit]
-      language: python
-      entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
-      additional_dependencies: [jupyter]
-
-
+  - id: clear-notebooks-output
+    name: clear-notebooks-output
+    files: tools/.*\.ipynb$
+    stages: [commit]
+    language: python
+    entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+    additional_dependencies: [jupyter]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.6.0
   hooks:
@@ -23,13 +20,11 @@ repos:
   - id: no-commit-to-branch # Prevent committing to main / master
   - id: check-added-large-files # Check for large files added to git
   - id: check-merge-conflict # Check for files that contain merge conflict
-
 - repo: https://github.com/psf/black-pre-commit-mirror
   rev: 24.4.2
   hooks:
-    - id: black
-      args: [--line-length=120]
-
+  - id: black
+    args: [--line-length=120]
 - repo: https://github.com/pycqa/isort
   rev: 5.13.2
   hooks:
@@ -38,43 +33,37 @@ repos:
     - -l 120
     - --force-single-line-imports
     - --profile black
-
-
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.4.6
   hooks:
   - id: ruff
-    exclude: '(dev/.*|.*_)\.py$'
+    # Next line if for documenation cod snippets
+    exclude: '^(dev/.*|[A-Za-z].*_)\.py$'
     args:
     - --line-length=120
     - --fix
     - --exit-non-zero-on-fix
     - --preview
-
 - repo: https://github.com/sphinx-contrib/sphinx-lint
   rev: v0.9.1
   hooks:
-    - id: sphinx-lint
-
+  - id: sphinx-lint
 # For now, we use it. But it does not support a lot of sphinx features
 - repo: https://github.com/dzhu/rstfmt
   rev: v0.0.14
   hooks:
-    - id: rstfmt
-      exclude: 'cli/.*' # Because we use argparse
-
+  - id: rstfmt
+    exclude: 'cli/.*' # Because we use argparse
 - repo: https://github.com/b8raoult/pre-commit-docconvert
-  rev: "0.1.4"
+  rev: "0.1.5"
   hooks:
   - id: docconvert
     args: ["numpy"]
-
 - repo: https://github.com/b8raoult/optional-dependencies-all
   rev: "0.0.6"
   hooks:
   - id: optional-dependencies-all
-    args: ["--inplace", "--exclude-keys=dev,docs,tests", "--group=dev=docs,tests"]
-
+    args: ["--inplace", "--exclude-keys=dev,docs,tests", "--group=dev=all,docs,tests"]
 - repo: https://github.com/tox-dev/pyproject-fmt
   rev: "2.1.3"
   hooks: