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v0.5.51 — Virtual Assay Scope Document + Doc Drift Fix (Loop 30) - #145
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Phase 3 begins with a scope document defining what the virtual assay layer is and is not, with explicit uncertainty policy, ablation requirements, and integration modes. Accumulated doc drift fixed alongside. Changes: - docs/VIRTUAL_ASSAY_SCOPE.md — Phase 3 scope: 4 planned modules, 12 not-modeled effects, uncertainty gate (uncertainty>0.5 blocks selection), ablation requirement versus cheap baselines, 3 integration modes (off/info/weighted), calibration gate for weighted mode, 5 exit criteria. - docs/BENCHMARKING.md — Complete rewrite: all 19 benchmarks in 6 categories (core, honesty, selectivity, ablation, regression, deferred). Each has make target, purpose, target metric, verification command. - docs/METRICS_CURRENT.md — Test count corrected 1832+ → 1843. - docs/NOVELTY_AUDIT_GUIDE.md — Stale script reference fixed: download_uniprot_amps.py → download_novelty_dbs.py --uniprot. - docs/50_LOOP_PLAN.md — Loop 30 marked complete, Phase 3 now 'In progress', next is Loop 31 (membrane proxy). - docs/ROADMAP.md — v0.5.51 entry with all change details. - scripts/__init__.py — Populated with module docstring. 1843 tests passing. No pipeline code changes.
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Phase 3 begins with a scope document defining what the virtual assay layer is and is not.
Primary:
docs/VIRTUAL_ASSAY_SCOPE.md— Phase 3 scope: 4 planned modules, 12 not-modeled effects, uncertainty gate (uncertainty>0.5 blocks selection), ablation requirement vs cheap baselines, 3 integration modes (off/info/weighted), calibration gate for weighted mode, 5 exit criteria.Doc fixes:
docs/BENCHMARKING.md— Complete rewrite: all 19 benchmarks in 6 categoriesdocs/METRICS_CURRENT.md— Test count corrected 1832+ → 1843docs/NOVELTY_AUDIT_GUIDE.md— Broken script ref: download_uniprot_amps.py → download_novelty_dbs.pydocs/50_LOOP_PLAN.md— Loop 30 ✅, Phase 3 now 'In progress', next Loop 31docs/ROADMAP.md— v0.5.51 entryscripts/__init__.py— Populated with module docstring1843 tests passing. No pipeline code changes.