upstream ci: Update Github actions

Github actions checkout v3.1.0 and setup-python v4.3.0 use deprecated
Node.js 16.

Bumping version to checkout v4.1.1 and setup-python v5.1.0 fixes the
workflows, as both use the recommended Node.js 20.

The checkout depth has been set to 1 (shallow copy) for all tasks that
do not require git history to be available.