LNG_BOUNDARY_HIERARCHY: hierarchical root-complex decomposition (off by default) - #97
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…el at a time -- join components the network already has, build missing nested complexes (deltasignal specs/030) Flat decomposition went straight to base leaves, so a species the pathway produces never reached the root complex that contains it (IFN alpha/beta: ISGF3 [cytosol] -> root ISGF3:KPNA1:KPNB1, no binding reaction in Reactome; 200 held-out cases severed). Off by default; downstream-reuse rule unchanged. Three tests. The one failing test (Class I MHC edges proportional) fails identically on main -- it checks stale generated output. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…228, 238/10, p=9e-58; +28 outside IFN alpha/beta; experimental +2) Flat-mode tests that stub every id as a Complex are pinned to LNG_BOUNDARY_HIERARCHY=0; the leaf-reuse tests run under the new default with a one-level component stub. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
adamjohnwright
marked this pull request as ready for review
September 26, 2026 13:06
…(two joins had welded a 162-node DSB loop); deterministic root order; nested complexes built per root; prefer a ROOT copy when joining (PDGFB: the pinned root copy never reached PDGF A/B heterodimer). All hierarchy-only; flat mode byte-identical. Three new tests, two mutation-checked. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… uuid string (a uuid4 is new every run, so the join landed on a different copy run to run); root-ness for the root-copy preference is the pathway's own non-depletion targets, not a live in-degree (which counted this function's joins, so choice followed stid sort order, and counted depletion). Three tests, all red on the previous commit. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Decompose a root complex one hasComponent level at a time: join components that already exist as nodes, build missing nested complexes, fall back to terminal leaves. Fixes the IFN alpha/beta severing (ISGF3 [cytosol] never reached root ISGF3:KPNA1:KPNB1). Off by default; A/B in deltasignal specs/030.
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