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Derived boundary edges go to boundary_edges.csv; add containment_structure.csv (deltasignal specs/044) - #104
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…cture.csv (deltasignal specs/044) logic_network.csv now holds only what curators curated. The edges the generator derives from complex/set structure at root inputs and terminal outputs (assembly, dissociation, composition) are tagged where they are emitted and written to boundary_edges.csv, same columns. Generation itself is unchanged: every export still sees the full network. containment_structure.csv is Reactome's structure one level at a time: parent, parent type, child, relation (component / member / candidate) and stoichiometry. containment.csv flattens to leaves and cannot tell a required subunit from one alternative of a set (code review F7). Verified: GPVI, NODAL and RAF regenerated from this branch; the union of the two files equals build 20260928-1110_06ccb63's logic_network.csv edge for edge by stable id; logic_network.csv has no assembly/dissociation edges. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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logic_network.csvnow holds only what curators curated. The edges the boundary pass derives from complex and set structure are tagged where they are emitted and written toboundary_edges.csv, with the same columns:assembly,dissociation, andcompositionwhen that switch is on. The edges are not recognised byedge_type, because specs/036's capped pools also useassembly. Generation itself is unchanged.containment_structure.csvis Reactome's structure one level at a time: parent, parent type, child, relation (component/member/candidate) and stoichiometry.containment.csvflattens to leaves, so it cannot tell a required subunit from one alternative of a set (code review F7).Merge after reactome/deltasignal
feat/044-boundary-edges, which teaches DeltaSignal to read the new file.Verified:
20260928-1110_06ccb63'slogic_network.csv, edge for edge by stable id.logic_network.csvhas no assembly or dissociation edges.Tests:
tests/test_boundary_edges_file.py(the tagging, the split, and a misaligned mask failing). 342 passed.Still in
logic_network.csv, though also inferred:depletionedges and set-pool nodes. Moving those is a separate decision.🤖 Generated with Claude Code