Docs: Small issues with examples / tutorials

Please provide the following

• Machine and OS: Ubuntu 22.04 VM
• binary_c: stable v2.2.3
• binary_c-python: v0.9.6

Discovered a few small issues on the docs website:

• API functionality tutorial: Last cell in docs shows a SystemError, even though it runs fine.
• Custom logging tutorial: Usage section seems to have itemize list, however, there's is probably an empty line missing since the listing is not displayed properly (right before cell [2]).
• Running populations with binary_c-python tutorial: Itemize issue again in section "Setting up the Population object".
• Extra features tutorial: TODOs are still present in here in: Example parse function and Dictionary modification sections