improved ILP problems + LLM-generated predicates

[sfluegel05]

This PR includes some minor fixes/improvements of the learning pipeline as well as

• LLM-generated predicates. You can ask an LLM to define new predicates for specific ChEBI classes (and provide the Python program for it) The predicate_set option llm_generated_fgs adds those predicates to the learning process
• update to popper version 5. This means you will need Python version >=3.14