Prepare existing formatting drift for read-only final validation #1682

The new read-only format-check in PR #1681 surfaces nine formatting differences already present on master 27d73ed. The old default tox silently formatted these files before testing. The single-suite policy deliberately requires formatting preparation and review before final validation.

Affected files:

• kg_microbe/transform_utils/madin_etal/madin_etal.py
• tests/test_bacdive_predicate_relations.py
• tests/test_foodon_native_categories.py
• tests/test_isolation_source_mapping_utils.py
• tests/test_kg_model_review_attribute_types.py
• tests/test_madin_pato_partition.py
• tests/test_merge_node_descriptions.py
• tests/test_ontology_category_authority.py
• tests/test_ontology_metadata_boundaries.py

Observed with Ruff 0.16.6 on the policy branch. Lock/config checks, lint, codespell and docstring coverage passed; format-check failed, so the new runner correctly did not start the full pytest stage. Resolve in a reviewed formatting preparation commit, preserving unrelated candidate work and scientific behavior. Do not bypass the check or silently combine formatting with an expensive test pass.