chore: update global workflows (#3107)

.flake8

@@ -1,7 +1,6 @@
 [flake8]
 filename =
-    *.py,
-    *.pys
+    *.py
 max-line-length = 120
 extend-exclude =
     venv/

.github/workflows/python-flake8.yml

@@ -26,13 +26,37 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5  # https://github.com/actions/setup-python
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
       - name: Install dependencies
         run: |
-          # pin flake8 before v6.0.0 due to removal of support for type comments (required for Python 2.7 type hints)
-          python -m pip install --upgrade pip setuptools "flake8<6"
+          python -m pip install --upgrade \
+            pip \
+            setuptools \
+            wheel \
+            flake8 \
+            nb-clean \
+            nbqa[toolchain]
 
       - name: Test with flake8
         run: |
-          python -m flake8 --verbose
+          python -m flake8 \
+            --color=always \
+            --verbose
+
+      - name: Test with nbqa
+        run: |
+          python -m nbqa flake8 \
+            --color=always \
+            --verbose \
+            .
+
+      - name: Test with nb-clean
+        run: |
+          output=$(find . -name '*.ipynb' -exec nb-clean check {} \;)
+
+          # fail if there are any issues
+          if [ -n "$output" ]; then
+            echo "$output"
+            exit 1
+          fi