Daily diary: 2026-07-21

A whole-day entry with four hands on the wheel. @jwildfire published Diary #7 in the morning, closing a loose end that had carried since the 17th. A midday design pass turned the FDA Standard Safety Tables & Figures Integrated Guide into a full static-displays strategy — an 82-display inventory, an 8-chart-engine reduction, and a drafted design PR for requirement #9. Then the evening session ran two siblings in parallel: an Opus agent took the gsm.safety v1.0.0 RC from two red checks and 7-of-9 renderer coverage to fully green with complete parity — uncovering and fixing an upstream ECG data corruption on the way — while a Fable agent shipped a portfolio executive overview, modernized roadmap.html, and took live direction that set the stage model for the run to R/Pharma: Stage 2 closes when safety.viz is fully shipped; Stage 3 is the autonomy experiments.

📊 Session report: the in-session record for 07-21 could not be frozen next-day (oa#32 — --report lacks a --date flag); the 2026-07-22 report covers the closeout.

Work completed

Blog Diary #7 published (morning, @jwildfire). R/Pharma Diary #7 — Papers → Prompts → Prototypes went live: blog PR #9 merged at 09:15 with follow-up PR #10 (reviewed content + keynote card) right behind it. The three-sibling release-train story is now public (hub #22).

FDA ST&F static-display strategy (midday design pass). The strategy report is live on the hub with a machine-readable inventory of all 60 tables and 22 figures from the Integrated Guide v2.0: the figures reduce to 8 reusable chart engines; pharmaverse cardinal covers only 26/60 tables and 4/22 figures; 15 figures have no static-R implementation anywhere — and 12 of those 15 already have a shipped safety.viz interactive twin, which is the proposed Phase 1. Architecture recommendation: shared R derivation layer + thin renderers, mirroring gsm.kri. The pass also drafted hub PR #42 — the requirements/design/9_design.html doc for hub #9 — now waiting on review and the D1–D4 decisions (package placement, shared-layer depth, scope, output formats). Process note: this pass ran outside the session heartbeat, so the wrapup delta — not the scratchpad — accounted for it; named gap, no transcript mining needed.

gsm.safety v1.0.0 RC hardened to the merge gate (👯🤖 gs39-rc-cleanup, Opus 4.8). PR #39 is now fully green (13 checks) and parks as a draft at @jwildfire's merge+tag gate:

• CI: the workflow-template drift was real — R-CMD-check 0.4.1→0.4.2 and workflow-template-check 0.4.1→0.5.0 synced byte-exact from gsm.utils@actions-v1; the ubuntu oldrel R 4.3.3 failure was a transient pak download flake, proven by re-running the identical commit to a pass. No package code was at fault.
• Renderer parity 7/9 → 9/9: safety.viz v1.4.0 ships nine renderers but gsm.safety bound seven. Widget_AeExplorer (gs#41) and Widget_QtExplorer (gs#42) landed with full R/JS/schema/workflow/example/pkgdown/test lanes, a new ExampleData("adeg") ECG dataset, and a re-vendored adae carrying the 37 AE-free placeholder rows the ae-explorer denominator contract requires. A guard test now fails loudly if a future bundle bump adds a renderer without a binding. Tests 230 → 324; devtools::check() 0E/0W.
• Site: all 9 pkgdown example pages rendered and browser-verified (live widgets, no console errors); the RC evidence bundle refreshed on the hub (ac6bf97); a real screenshot thumbnail gallery landed on the pkgdown home (ca4ba52), superseding the stale codex PR #29 — @jwildfire marked it superseded on the thread. Two papercuts fixed en route (missing pkgdown URL in DESCRIPTION; a docs/ ignore leak that pushed 88 MB into R CMD check).

Late addendum: after its close-out the sibling kept rolling on @jwildfire's direction — the hub evidence bundle got a further late-night refresh (ba395da) covering the thumbnail gallery and the first pass of the corrected ECG data.

ECG data corruption found and fixed (same sibling, at @jwildfire's live direction). Reviewing the QT example page surfaced QTcF/QTcB values inflated ~80 ms: pharmaverseadam's rederived QTc params were computed from a corrupt RR column (implying HR 113.6 bpm against a recorded median of 72). Filed as sv#79 and fixed in sv PR #80: QTc now derives from the sane RRR param (median QTcF 561→468 ms), the ECG logic moved to a tested demo-data-lib.mjs with the corrupt values as the negative case, and assertRrSane() fails the build if RR ever contradicts HR again. No library code touched — a clean v1.4.1 patch. @jwildfire's call: ship the fix and document the residual limitation (the pilot cohort's measured QT median of 444 ms still crosses ICH E14 categories; no correction formula fixes source data, and provenance beats synthesis).

Portfolio executive overview + the stage model (👯🤖 roadmap-exec-overview, Fable 5). The executive overview is live: accomplishments, status, short/medium-term proposals, and seven roadmap gaps (G1–G7 — recommended, not executed). roadmap.html's generator went to 1.8.0: the Tasks column now reads the GitHub sub-issues rollup, plus an Updated column, still-open flags, and attention-first ordering. Live direction from @jwildfire then set the frame for everything ahead — Stage 2 = safety.viz fully shipped (gs v1.0 merge+tag, closeouts, the QTc fix, Diary #8); Stage 3 = autonomy experiments (--auto on /session-init, a /goal command; Goal 1 = keep adding charts, Goal 2 = the user-facing safetyGraphics-replacement app, with open.gismo on the same arc); Phase 4 = September talk prep. Decision records posted on #10, #18, and #34; memories updated the same hour.

PRs / issues touched

• Merged (@jwildfire, morning): blog PR #9 + PR #10 — Diary #7 live.
• Opened: gs#41, gs#42 (both on PR #39's Closes line), sv#79, sv PR #80, hub PR #42 (design doc for #9).
• Advanced: gs PR #39 (red CI → fully green; 7/9 → 9/9 renderers; evidence refreshed), hub #28 → Review (moved at this wrapup), gs#28 (gallery shipped in the RC; findings comment posted), gs PR #29 (marked superseded by @jwildfire).
• Reports: FDA ST&F strategy, executive overview, refreshed RC1 evidence.

Blockers / risks

• sv PR #80 is merge-blocked — the auto-mode permission classifier denies gh pr merge, so the gate-approved v1.4.1 train (merge → dev→main promotion → tag) is parked, and the adeg re-vendor + final gs PR #39 data refresh queue behind it. Resolved the next morning: the merge-permission scaffold shipped and v1.4.1 released through the new lane — see the 2026-07-22 entry.
• QT demo realism is bounded by its source — even corrected, the pilot cohort's measured QT crosses ICH E14 categories; documented as a known limitation rather than synthesized away.
• Hub #41 is board-Released but still open — the one-click close is @jwildfire's.
• Board closeout lag — #2/#3/#21/#30 open-but-Released; the exec overview's G1–G7 fixes await @jwildfire's read.

Next session: loose ends

1. Keynote-plan report on the hub (hub #10) — the stage model is decided; write it down as the plan of record.
2. Autonomy design — --auto /session-init + /goal for hub #18's Design section.
3. open.gismo plan rewrite, app-first (hub #34) — Stage-3 Goal 2 framing, then the Phase 1–4 requirements.
4. Stage-2 close checklist: gs PR #39 merge+tag (hub #28); sv #80 → v1.4.1 → adeg re-vendor → final #39 refresh; hub PR #42 review + D1–D4 on #9; Diary #8 (hub #22); closeouts (#41 and the board-lag set).
5. Queued (carried): board hygiene G1/G5; nep #35 pre-flight → ⚡️ Phase-1 build; safety.viz-release skill draft.

🙋 ToDo (@jwildfire)

• gs PR #39 merge + tag v1.0.0 — fully green, 9/9 renderers, evidence current.
• sv PR #80 — merge + cut v1.4.1 done 07-22 AM: merged and released as v1.4.1 through the new merge lane.
• Hub PR #42 — review the #9 design doc; decide D1–D4.
• Hub #41 one-click close; gs PR #29 close closed 07-22 AM as superseded.
• Admin carried: obotclaw installs (open.gismo + jwildfire.github.io); Gilead PR #151; hub #3 §7; LinkedIn; deletions approval.

This diary entry was drafted by Claude Code using Fable 5 during a live working session and reviewed by @jwildfire.