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Variant emission: no duplicate copies from an output with a bound and a shared slot - #114
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…th a bound and a shared slot enumerated the bound slot, then overwrote it: 2,905 duplicate reaction nodes in deltasignal's canonical build) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…too (week review: the docstring said once each) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Found by the deltasignal week review (2026-10-15), verified by two independent skeptics.
In
_choices,free_outputsdropped an output only when ALL its slots were bound. An output complex with one slot bound to an input slot and one slot shared with the inputs stayed free, soreaction_choicesenumerated the bound slot and the binding loop then overwrote it: |members| identical choices per real copy, each minted as its own reaction node.20261012-1401_01206ca: 2,905 of ~57,000 reaction nodes are exact duplicates, across 36 pathways (e.g. RAF R-HSA-5674373: 12 copies, 6 distinct). Under the solver's OR-mean, a duplicated reaction counts 2–6x in its output's mean; 4 reactions were pushed pastLNG_MAX_VARIANTSand pooled only because of duplicates.test_output_with_a_bound_and_a_shared_slot_gives_no_duplicate_copies(fails on the old code).tests/test_network_invariants.py::...Class_I_MHC...fails on main as well (it reads existing output files: ratio 54.4 vs 50); unrelated.A deltasignal catalog rebuild and re-measurement follow before this is relied on.
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