Remove use of Python 3.9, include 3.13 in testing

[lrandersson]

Description

This PR bumps the Python dependencies used in the testing suite.

• Remove Python 3.9
• Include Python 3.9
• Removed a .txt file that was written for macOS but not used, and the test test_example_from_explicit seems to be Linux only.

Checklist - did you ...

• Add a file to the news directory (using the template) for the next release's release notes?
• Add / update necessary tests?
• Add / update outdated documentation?

[marcoesters]

I think we can use the opportunity here to update the minimum Python everywhere (pyproject.toml, meta.yaml).

[lrandersson]

I think we can use the opportunity here to update the minimum Python everywhere (pyproject.toml, meta.yaml).

Can we also remove scripts\run_examples.py? It looks very old and unused, it also references a few examples that I dont see referenced anywhere else.

[marcoesters]

I think we can use the opportunity here to update the minimum Python everywhere (pyproject.toml, meta.yaml).

Can we also remove scripts\run_examples.py? It looks very old and unused, it also references a few examples that I dont see referenced anywhere else.

I'm all for getting rid of things that are not used.