Record #295 closure in HANDOFF.md - #314
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Phase 5 (#295) is closed as delivered-by-Phase-2: both its figures (shift_by_site_heatmap_zoom, validation_titer_fold_change) shipped in PR #309 and were verified constant-by-constant against its spec. Updates the two stale references that flagged #295 as awaiting a close/repurpose call. The second note is rewritten rather than dropped so the Figure 4 zoom regions and the Figure 5 x-axis warning stay discoverable, and records that the manuscript's ">1,000-fold" A419S claim refers to measured titers rather than the model's predicted enrichment ratio. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Docs-only sync following the close of Phase 5 (#295) as delivered-by-Phase-2.
HANDOFF.mdcarried two stale references flagging #295 as awaiting aclose/repurpose call. The DAG owner has now made that call — close it — so both
are updated:
⚠️ emptied by Phase 2 — needs an explicit close/repurpose call→✅ closed as delivered-by-Phase-2 (figures shipped in PR #309).warned that Phase 5 of EPIC #290: Shift-by-site heatmap and titer validation figures #295's body is the only record of the Figure 4 zoom regions and
the Figure 5 x-axis warning, so the note now points at the (closed) body and
its audit comment instead of dropping those facts. It also records that the
manuscript's ">1,000-fold" A419S claim refers to measured titers, not the
model's predicted enrichment ratio (predicted: Delta 0.854 / BA.1 0.132 /
BA.2 0.137) — a distinction that is easy to misread as a failed replication.
The log-x requirement for Figure 5 was explicitly dropped, not deferred; no
follow-up issue was filed. Over
xlim=[0.1, 1.3]— barely one decade — linear isthe better rendering.
No code, config, or pipeline files are touched, so nothing invalidates the fit
cache.
Deviations from spec
The spec (#295) called for building Figures 4 and 5. No figure work was
performed — an audit confirmed Phase 2 (PR #309) had already shipped both,
verified constant-by-constant, so the issue was closed as already-satisfied
rather than implemented. This PR carries only the resulting documentation sync.
Three spec items that Phase 2 resolved differently (the
predicted_func_scoreblocker routed around via
collection_muts.csv, the titer CSVs fetched at apinned commit rather than vendored, and the unnecessary
'142L' -> 'D142L'fixup) are recorded in the #295 audit comment and required no action here.
Yolo trail: work-issue stub gate STOPped to the user (scope call, not a workflow gate) — full log in _ignore/yolo/295.log