Update ruff to 0.6.1

[nsoranzo]

Since 0.6.0, ruff checks also Jupyter notebook files by default:

https://astral.sh/blog/ruff-v0.6.0

Fix test failures in #18578 .

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[nsoranzo]

Test failures unrelated.