add top class option for chebi graph, set molecular entity as default

[sfluegel05]

Currently, the ChEBI graph includes all classes in ChEBI, including roles, chemical entities (which include atoms, chemical substances, groups and molecular entities) and subatomic particles.

As discussed in the March 26 Strontex meeting, it does not make sense for our models to learn the classification of subatomic particles, atoms, chemical substances or groups. Roles are also a different classification task.

Therefore, I changed the default ChEBI graph to be the subgraph of molecular entity (excluding molecular entity itself). By setting the top class, one can get other graphs if needed.

[sfluegel05]

@copilot unittests are failing, fix

[Copilot]

@copilot unittests are failing, fix

Fixed in a464207. I investigated the CI failures, reproduced them locally, and updated build_chebi_graph to handle missing top_class in partial ontologies by returning the full graph instead of raising a NetworkX error. I also ran ruff format, ruff check, targeted tests, and the full test suite (65 passed).