CI: Fix python version for pre-commit

[gmuloc]

Change Summary

• Fix python version for pre-commit to 3.9 as for the others rather than relying on ubuntu-latest default
• Bump checkout and python-version actions to latest
• Some yamllint fixes

Related Issue(s)

Fixes #653

Component(s) name

ci

Proposed changes

cf summary

How to test

Ci passes

Checklist

Repository Checklist

• [x] My code has been rebased from devel before I start
• [x] I have read the CONTRIBUTING document.
• [x] My change requires a change to the documentation and documentation have been updated accordingly. (check the box if not applicable)
• [x] I have updated molecule CI testing accordingly. (check the box if not applicable)