review-zoom-v7-fanin-render

Metadata

Status	done
Assigned	`agent-1141`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-07T19:43:27.928188576+00:00
Started	2026-05-07T20:09:08.495807991+00:00
Completed	2026-05-07T20:23:12.832924467+00:00
Tags	`review-zoom`, `review-zoom-v7`, `synthesis`, `render`, `eval-scheduled`
Eval score	0.94
└ blocking impact	0.93
└ completeness	0.95
└ coordination overhead	0.95
└ correctness	0.96
└ downstream usability	0.92
└ efficiency	0.90
└ intent fidelity	0.92
└ style adherence	0.94

Description

Fan in the v7 slide-feedback tasks and render the next review zoom deck.\n\nIntegrate these user-requested changes:\n- Slide 06a: replace the disliked violin/grouped view with clearer histogram-style PHR length distribution and visible 500 kb analysis-window ceiling.\n- Slide 08b: replace current bad view with original-style superpopulation-labeled MDS plus nearest same-superpopulation MDS-neighbor distance distribution.\n- Slide 09: use the same layout style as slide 08a, but MDS labels and colors by community, all communities labeled, 1:1 aspect.\n- Hi-C/3D: add or replace one confusing 3D validation slide using the best available 3D Hi-C/Dip-C/single-cell asset.\n- Gene enrichment: add/report-backed slide material so the deck references the strong methods/results reports and cleanly explains enriched/candidate gene-family/GO biology without overstating BH-significance.\n\nImplementation guidance:\n- Read every v7 fanout SLIDE_PATCH.md and use their generated assets.\n- Start from current v6 source/PDF and preserve successful v6 improvements unless directly superseded.\n- Keep one-figure-per-slide review-zoom style where possible.\n- Update REVISION_NOTES_V7.md with a concise changelog and key caveats.\n- Render PDF to slides/v2-review-zoom/BoG_2026_review_zoom_v7.pdf and export proof PNGs if the existing workflow does that.\n\nValidation:\n- PDF renders successfully.\n- Changed slides are nonblank and readable at slide scale.\n- Slide 08b metric is nearest same-superpopulation neighbor, not centroid/all-pairwise.\n- Slide 09 is MDS, not PCA.\n- Gene-enrichment claims are traceable to report/files and caveated correctly.\n- git diff --check passes.

Fan in the v7 slide-feedback tasks and render the next review zoom deck.\n\nIntegrate these user-requested changes:\n- Slide 06a: replace the disliked violin/grouped view with clearer histogram-style PHR length distribution and visible 500 kb analysis-window ceiling.\n- Slide 08b: replace current bad view with original-style superpopulation-labeled MDS plus nearest same-superpopulation MDS-neighbor distance distribution.\n- Slide 09: use the same layout style as slide 08a, but MDS labels and colors by community, all communities labeled, 1:1 aspect.\n- Hi-C/3D: add or replace one confusing 3D validation slide using the best available 3D Hi-C/Dip-C/single-cell asset.\n- Gene enrichment: add/report-backed slide material so the deck references the strong methods/results reports and cleanly explains enriched/candidate gene-family/GO biology without overstating BH-significance.\n\nImplementation guidance:\n- Read every v7 fanout SLIDE_PATCH.md and use their generated assets.\n- Start from current v6 source/PDF and preserve successful v6 improvements unless directly superseded.\n- Keep one-figure-per-slide review-zoom style where possible.\n- Update REVISION_NOTES_V7.md with a concise changelog and key caveats.\n- Render PDF to slides/v2-review-zoom/BoG_2026_review_zoom_v7.pdf and export proof PNGs if the existing workflow does that.\n\nValidation:\n- PDF renders successfully.\n- Changed slides are nonblank and readable at slide scale.\n- Slide 08b metric is nearest same-superpopulation neighbor, not centroid/all-pairwise.\n- Slide 09 is MDS, not PCA.\n- Gene-enrichment claims are traceable to report/files and caveated correctly.\n- git diff --check passes.

Depends on

Required by

Log

2026-05-07T19:43:27.900727406+00:00 Task paused
2026-05-07T19:43:48.924943395+00:00 Task published
2026-05-07T19:46:17.942602475+00:00 Added blocking dependency review-zoom-v7-hic-mapq0-method-slide for Erik's requested explanation of MAPQ0/multimapper Hi-C reanalysis before v7 fan-in render.
2026-05-07T20:09:08.495812550+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-07T20:09:28.046065052+00:00 Starting fan-in render: checking worktree state and v7 patch assets before editing the deck.
2026-05-07T20:11:29.307478823+00:00 FANOUT_DECISION: stay inline — upstream slide-specific tasks already produced assets; this task is the sequential deck integration and render.
2026-05-07T20:12:29.719287305+00:00 Integrated v7 source changes in Typst: 06a histogram, split 08b MDS/nearest-neighbor metric, slide 09 MDS community layout, MAPQ0 and Hi-C 3D slides, and report-backed gene-enrichment wording.
2026-05-07T20:19:11.808077431+00:00 Validated: Typst rendered v7 PDF and 46 proof PNGs; visual inspection and pixel scans passed for slides 06a, 08b, 08b.1, 09, 10m.1, 10m.2, 14m, 14a, 14b, and 14c.
2026-05-07T20:19:11.928924713+00:00 Validated: slide 08b.1 uses nearest same-superpopulation MDS neighbor distance with no self-neighbor rows; slide 09 validation_summary.tsv records classical MDS, coord_fixed_ratio=1, all C1-C15 labels, and pca_used=no.
2026-05-07T20:19:12.051849450+00:00 Validated: git diff --check passes.
2026-05-07T20:19:12.177430625+00:00 Validated: gene-enrichment section cites report-backed HPRCv2 gene-family support and caveats the canonical Fisher screen as 116 rows, 0 BH-significant rows; GO/ORA is framed as context/method contrast.
2026-05-07T20:22:12.811457787+00:00 Validated: no Cargo.toml found at repo depth 3; cargo build/test are not applicable for this deck/documentation render task.
2026-05-07T20:22:47.550200523+00:00 Committed: 63c8618 — pushed to remote branch wg/agent-1141/review-zoom-v7-fanin-render.
2026-05-07T20:23:12.832932262+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-07T20:25:20.885914942+00:00 PendingEval → Done (evaluator passed; downstream unblocks)