Issues

• Depletion edges are emitted before boundary expansion and suppress assembly for the complexes they target

  reactome/logic-network-generator#68 · Filter by author adamjohnwright opened on Sep 9, 2026

• Cache fingerprint: dead fast-path, fail-open reuse, adopted caches never re-validate, and PYTHONHASHSEED is recorded wrong

  reactome/logic-network-generator#63 · Filter by author adamjohnwright opened on Sep 9, 2026
  1

• Boundary assembly edges flatten a complex's internal EntitySet into co-required AND members

  reactome/logic-network-generator#60 · Filter by author adamjohnwright opened on Sep 9, 2026

• Curated input/output stoichiometry now emitted — needs regen + benchmark re-run

  reactome/logic-network-generator#48 · Filter by author adamjohnwright opened on Jul 20, 2026
  1

• Generator is non-deterministic (hash-seed-dependent); ~5.8% edges differ run-to-run

  reactome/logic-network-generator#42 · Filter by author adamjohnwright opened on Jul 14, 2026
  1

• [future] Cross-pathway connectivity via diagram Interaction links

  reactome/logic-network-generator#41 · Filter by author adamjohnwright opened on Jul 14, 2026

• Diagram-sourced reaction connectivity (A→product→B) to fill precedingEvent gaps

  reactome/logic-network-generator#39 · Filter by author adamjohnwright opened on Jul 14, 2026
  3