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LNG_DIAGRAM_SUBPATHWAYS: read sub-pathway diagrams for drawn hand-offs (default off) - #119
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…wn hand-offs (default off, deltasignal specs/070) A covering diagram draws a sub-pathway that has its own diagram as one box, so the shared-glyph hand-offs inside it were never read. deltasignal specs/070 counts 450 such curator-drawn hand-offs missing from the canonical catalog (PTEN released by R-HSA-6807126 feeding R-HSA-6807106, drawn on PTEN Regulation's diagram, is a dead-end copy). Pairs are still restricted to the pathway's own reactions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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diagram_shared_product_pairsread only the covering diagram, where a sub-pathway with its own diagram is a box, so hand-offs drawn on that diagram were never joined (450 of 459 missing shared-glyph hand-offs, deltasignal specs/070).Under
LNG_DIAGRAM_SUBPATHWAYS=1it also reads each sub-pathway's own diagram, still restricted to the pathway's own reactions. Default off: armdsubfailed its gate (curator held-out −171, experimental −19), because the joined loops are recycling loops the solver cannot yet handle. Kept as the faithful variant for the solver work that follows. Two tests added; the one failing test (test_main_edges_proportional_to_best_matches[...983169]) also fails on main.🤖 Generated with Claude Code