docs: mark wave0.5 pending steps as historical

docs/ASSAY_PREREGISTRATION.md

@@ -28,7 +28,7 @@ non-reporting of negative results.
 | Selection algorithm | `pilot-panel` with similarity_threshold=0.75, max_per_seed=4 |
 | Selection date | [date of `make pilot` run] |
 | Selection locked at manifest | `outputs/phase3_manifest.json` |
-| Confident panel (post-external-predictor filter) | TBD after running CAMPR4 / AMPScanner / dbAMP |
+| Confident panel (post-external-predictor filter) | Historical placeholder; external predictor review later completed and summarized in `docs/METRICS_CURRENT.md` |
 
 ---
 

docs/PRE_WET_LAB_CHECKLIST.md

@@ -6,21 +6,19 @@
 > **Current status:** 53/100 breakthrough potential.
 > After completing this checklist: 55–65/100.
 >
-> **Estimated time:** 2–4 hours (all manual web submissions).
+> **Estimated time:** Historical estimate for the original manual-submission pass.
+> The external predictor portion has since been completed; remaining blockers are novelty/legal/expert review and wet-lab execution.
 
 ---
 
 ## Quick Start
 
 ```text
-1. Submit FASTA to 5 web tools           (~30 min)
-2. Record results in results CSV          (~10 min)
-3. Generate consensus report              (~1 min)
-4. APD3/DRAMP novelty BLAST               (~30 min)
-5. Invite expert reviewer                 (~1 week)
-6. Generate reviewer questionnaires       (~1 min)
-7. Lock pre-registration                  (~10 min)
-8. Order synthesis                        (vendor lead time)
+1. Review current external predictor evidence   (done historically; see current-state docs)
+2. Confirm full novelty / FTO posture           (~30-90 min depending on scope)
+3. Invite expert reviewer                       (~1 week)
+4. Lock pre-registration                        (~10 min)
+5. Order synthesis                              (vendor lead time)
 ```
 
 ---
@@ -371,8 +369,8 @@ make lint
 
 | Step | Score | Gate 6 | Gate 7 | Synthesis ready? |
 |------|:-----:|:------:|:------:|:----------------:|
-| Current | 53 | PENDING | PENDING | ❌ |
-| After Step 1 (predictors filled) | 56–58 | PASS/FAIL | PENDING | ❌ |
+| Historical baseline before external predictor completion | 53 | PENDING | PENDING | ❌ |
+| After external predictor completion | 56–58 | PASS/FAIL | PENDING | ❌ |
 | After Step 3 (expert review) | 60–65 | PASS/FAIL | PASS | ⚠️ conditional |
 | After Steps 4–6 (all gates pass) | 65–70 | PASS | PASS | ✅ |
 

docs/WAVE_0_5_BASELINE.md

@@ -5,7 +5,8 @@
 > Wet-lab validation by qualified collaborators is required before any biological claim.
 > Known/control candidates are not novelty claims.
 > High-risk candidates are labeled explicitly.
-> External predictor columns are PENDING — they require manual web-tool submission.
+> Historical note: this baseline freeze predates the completed Wave 0.5 external screen.
+> Current external-predictor status now lives in `docs/METRICS_CURRENT.md` and `docs/ROADMAP.md`.
 
 Generated: 2026-06-29
 
@@ -51,7 +52,7 @@ and classifies each candidate into a role that guides Wave 1 panel construction.
 |---|---|
 | LEAD | Novel scaffold with strong activity/safety balance. Priority for synthesis. |
 | HIGH_UPSIDE_RISKY | High predicted activity, but hemolysis or off-target risk flag present. |
-| PENDING | External predictor or safety data needed to finalize role. |
+| PENDING | Historical placeholder at the baseline-freeze date; superseded by later Wave 0.5 panel decisions. |
 | CONTROL | Known AMP (KWKLFKK/magainin class). Positive control for assay calibration. |
 | SAR_CONTROL | Known-variant (tachyplesin-like). SAR anchor, not a novelty lead. |
 | LOW_PRIORITY | Close relative to known AMPs. Useful but weak novelty position. |
@@ -66,16 +67,18 @@ and classifies each candidate into a role that guides Wave 1 panel construction.
 | SEED-003 | 2 | Tachyplesin-like — KNOWN_VARIANT | Retain as SAR_CONTROL |
 | SEED-005 | 1 | KWKLFKK-family close relative | CLOSE_RELATIVE, LOW_PRIORITY |
 | SEED-006 | 4 | Balanced novel helices — strongest current leads | Retain all 4 as LEAD |
-| SEED-007 | 4 | Temporin-G analogs — activity/safety mixed | PENDING: requires external predictor screen |
+| SEED-007 | 4 | Temporin-G analogs — activity/safety mixed | Historical baseline note; final Wave 1 disposition is recorded elsewhere |
 | SEED-008 | 4 | Trp-rich high-aromatic — high activity, HemoFinder risk | HIGH_UPSIDE_RISKY |
-| SEED-009 | 4 | Pro-rich intracellular-style — AntiCP off-target risk | PENDING: off-target concern |
+| SEED-009 | 4 | Pro-rich intracellular-style — AntiCP off-target risk | Historical baseline note; final Wave 1 disposition is recorded elsewhere |
 
 ---
 
 ## External Predictor Status
 
-All external predictor columns are currently PENDING.
-Manual web submission is required for:
+Historical baseline state only: at the time this file was frozen, external predictor fields had not yet been filled.
+That is no longer the current repo state. The completed Wave 0.5 external screen is summarized in `docs/METRICS_CURRENT.md`, `docs/ROADMAP.md`, and `docs/WAVE_0_5_EXTERNAL_PREDICTOR_SUMMARY.md`.
+
+The original manual-submission tool stack was:
 
 | Tool | URL | Notes |
 |---|---|---|

docs/WAVE_0_5_SCAFFOLD_DIVERSIFICATION_PLAN.md

@@ -29,7 +29,7 @@ correlated-failure risk. The goal is not more candidates — it is more independ
 | 2 — Scaffold Search | Defined 10 new independent families | (design parameters in `scripts/generate_wave0_5_candidates.py`) |
 | 3 — Candidate Generation | Generated 118 raw candidates | `outputs/wave0_5_raw_candidates.csv` |
 | 4 — Internal Filter | Shortlisted 60 at internal gates | `outputs/wave0_5_internal_shortlist.csv` |
-| 5 — External Predictors | Created PENDING submission templates | `outputs/wave0_5_external_predict_results.csv`, `docs/WAVE_0_5_EXTERNAL_PREDICTOR_SUMMARY.md` |
+| 5 — External Predictors | Planned manual submissions; later completed and summarized in current-state docs | `docs/WAVE_0_5_EXTERNAL_PREDICTOR_SUMMARY.md`, `docs/METRICS_CURRENT.md` |
 | 6 — Novelty Audit | Classified 60 shortlist vs 92 references | `outputs/wave0_5_novelty_audit.csv`, `docs/WAVE_0_5_NOVELTY_AUDIT.md` |
 | 7 — Panel Selection | Selected 24-candidate Wave 1 panel | `outputs/wave1_final_panel.csv`, `docs/WAVE_1_PANEL_RECOMMENDATION.md` |
 | 8 — Evidence Certificates | Generated machine-readable certs | `outputs/evidence_wave0_5/*.json` |
@@ -70,9 +70,9 @@ correlated-failure risk. The goal is not more candidates — it is more independ
 
 | Task | Status | Blocker |
 |---|---|---|
-| External predictor screen (all 60 shortlist) | PENDING | Manual web submissions to CAMPR4, AMPScanner, Macrel, AMPActiPred, HemoFinder, AntiCP |
-| Wave 0.5 Gate W0.5-3 (activity consensus) | PENDING | Requires external predictor results |
-| Wave 0.5 Gate W0.5-4 (safety annotation) | PENDING | Requires external predictor results |
+| External predictor screen (all 60 shortlist) | COMPLETE | Reflected in `docs/METRICS_CURRENT.md` and `docs/WAVE_0_5_EXTERNAL_PREDICTOR_SUMMARY.md` |
+| Wave 0.5 Gate W0.5-3 (activity consensus) | COMPLETE | Gate result recorded after external screen |
+| Wave 0.5 Gate W0.5-4 (safety annotation) | COMPLETE | Gate result recorded after external screen |
 | FTO (freedom-to-operate) for CLOSE_RELATIVE candidates | PENDING | Legal review |
 | Expert review of HIGH_UPSIDE_RISKY candidates | PENDING | Wet-lab collaborator |
 
@@ -107,9 +107,9 @@ activity_score >= 0.80 AND safety_score >= 0.65 → PASS_HIGH_UPSIDE
 | `outputs/wave0_5_raw_candidates.csv` | 118 raw generated candidates |
 | `outputs/wave0_5_internal_shortlist.csv` | 60 shortlisted candidates |
 | `outputs/wave0_5_internal_excluded.csv` | 58 excluded with reasons |
-| `outputs/wave0_5_external_predict_results.csv` | 60 rows, external columns PENDING |
-| `outputs/wave0_5_external_consensus.csv` | 60 rows, consensus columns PENDING |
-| `outputs/wave0_5_safety_consensus.csv` | 60 rows, safety columns PENDING |
+| `outputs/wave0_5_external_predict_results.csv` | Optional locally generated artifact from the completed external screen; not committed in every checkout |
+| `outputs/wave0_5_external_consensus.csv` | Optional locally generated artifact from the completed external screen; not committed in every checkout |
+| `outputs/wave0_5_safety_consensus.csv` | Optional locally generated artifact from the completed external screen; not committed in every checkout |
 | `outputs/wave0_5_novelty_audit.csv` | 60 rows with novelty classes |
 | `outputs/wave1_final_panel.csv` | 24 final panel candidates |
 | `outputs/wave1_reserve_panel.csv` | Reserve candidates |

docs/WAVE_1_PANEL_RECOMMENDATION.md

@@ -40,8 +40,8 @@ All candidates have:
 - Synthesis risk flags
 - Machine-readable evidence certificates (Phase 8)
 
-External predictor results (CAMPR4, AMPScanner, Macrel, AMPActiPred, HemoFinder, AntiCP) are
-PENDING and must be completed before wet-lab synthesis submission.
+External predictor review for Wave 0.5 was completed after this panel recommendation was first drafted.
+Treat this file as the panel-selection record; use `docs/METRICS_CURRENT.md` for the current external-consensus state.
 
 No antimicrobial activity is claimed until qualified wet-lab validation.
 

tests/test_docs_consistent.py

@@ -163,3 +163,21 @@ def test_doc_wave05_generated_outputs_claimed_only_if_present(self):
             assert "Machine-readable: `outputs/wave0_5_external_predict_results.csv`" not in metrics_text
             assert "PENDING (60 rows, all PENDING)" not in summary_text
             assert "Generated only after running `make wave0-5-fill-external`" in summary_text
+
+    def test_doc_wave05_historical_docs_do_not_pose_as_live_pending_state(self):
+        """Historical Wave 0.5 docs must label superseded pending steps as historical."""
+        baseline_text = (DOCS_DIR / "WAVE_0_5_BASELINE.md").read_text(encoding="utf-8")
+        scaffold_text = (DOCS_DIR / "WAVE_0_5_SCAFFOLD_DIVERSIFICATION_PLAN.md").read_text(
+            encoding="utf-8"
+        )
+        prereg_text = (DOCS_DIR / "ASSAY_PREREGISTRATION.md").read_text(encoding="utf-8")
+        checklist_text = (DOCS_DIR / "PRE_WET_LAB_CHECKLIST.md").read_text(encoding="utf-8")
+        wave1_text = (DOCS_DIR / "WAVE_1_PANEL_RECOMMENDATION.md").read_text(encoding="utf-8")
+
+        assert "Historical note: this baseline freeze predates the completed Wave 0.5 external screen." in baseline_text
+        assert "Historical baseline state only" in baseline_text
+        assert "External predictor screen (all 60 shortlist) | COMPLETE" in scaffold_text
+        assert "Wave 0.5 Gate W0.5-3 (activity consensus) | COMPLETE" in scaffold_text
+        assert "Historical placeholder; external predictor review later completed" in prereg_text
+        assert "The external predictor portion has since been completed" in checklist_text
+        assert "External predictor review for Wave 0.5 was completed after this panel recommendation was first drafted." in wave1_text