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render-bog-annotated

Render BoG annotated review deck — 16:9 wide, figure left, explanation right

Metadata

Statusdone
Assignedagent-941
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Modelclaude:sonnet
Created2026-05-06T14:53:18.620276017+00:00
Started2026-05-06T14:53:48.667076828+00:00
Completed2026-05-06T15:11:00.565596984+00:00
Tagsbog-this-week, bog-deck, render, review-mode, eval-scheduled
Eval score0.76
└ blocking impact0.80
└ completeness0.92
└ constraint fidelity0.85
└ coordination overhead0.70
└ correctness0.88
└ downstream usability0.75
└ efficiency0.80
└ intent fidelity0.76
└ style adherence0.92

Description

GOAL: Render an annotated review deck — slides/v2-review/BoG_2026_review.pdf — for the lead author to read end-to-end and fully understand what each slide presents. NOT a presentation deck. NOT a "figures full-bleed" zoom deck (that was build-bog-v2-3, which Erik says is too zoom-intense and wrong aspect). This is a reference document for review.

DESIGN — strict spec:

  • Page size: 16:9 WIDESCREEN. Suggested: 13.33in × 7.5in (or 1920×1080 ratio at any consistent inches; typst #set page(width: 13.33in, height: 7.5in)). NOT A4. NOT letter-landscape. EXPLICITLY 16:9.
  • Per-page LAYOUT: figure on the LEFT half, explanation on the RIGHT half. Two columns, side by side.
    • Left column (~50-55% of page width): the figure, sized to fit cleanly inside its column (use typst #image with fit:contain so it's never distorted, max-height = page minus margins, max-width = column width minus padding). Caption / source path in small grey type below the figure.
    • Right column (~45-50% of page width): a large slide TITLE at top (~24-28pt), then the SPEAKER NOTES prose from the slide MD (~150 words per slide, formatted as readable body text 11-12pt), then a small "## Why this slide matters" call-out (1-2 sentences extracted from the slide's "## Bullets" or "Notes for synthesizer" section).
  • One LOGICAL slide per page. Composite slides (07: heatmap+NJ, 08: PCA chrom+superpop, 10: Hi-C bulk+Mantel) get split into two pages each (07a left=heatmap right=explanation, 07b left=NJ tree right=explanation, etc.) — same as build-bog-v2-3 did.
  • Text-only slides (01 title, 15 thesis closer): full-page typeset of the title + speaker notes, no figure column.

INPUTS:

  • slides/v2/slide_01_title.md … slide_15_concerted_evolution_thesis.md (15 markdown briefs — each has ## Title, ## Bullets, ## Primary figure, ## Speaker notes, ## Time budget, ## Notes for synthesizer)
  • slides/v2/figure_manifest.md (figure paths + ready-to-render R scripts)
  • slides/v2/SLIDES_v2_PLAN.md (consolidated plan)
  • slides/20260204_Subtelomics_overview_EG.pdf (v1 deck — slides 02/03 may pull pages from this)
  • paper_prep/figures/ (existing figure assets)
  • paper_prep/figures/nj_tree_arms/nj_tree_annotated.{pdf,png} (slide 07 NJ)
  • slides/v2-zoom/_typst/ (build-bog-v2-3 may have rendered the missing R-script figures; reuse if present rather than re-rendering)

PIPELINE:

  1. Render any READY-TO-RENDER figures still missing per figure_manifest.md (slide 03 ER-callout, slide 06 clade callouts, slide 09 clade legend, slide 12 stage trajectory). Reuse from slides/v2-zoom/_typst/ or slides/v2/_typst/ if those tasks already produced them.
  2. typst is at ~/.local/bin/typst v0.13.1. Working dir: slides/v2-review/_typst/. Build slides/v2-review/_typst/review_deck.typ: #set page(width: 13.33in, height: 7.5in, margin: 0.5in) Custom layout function that takes (figure_path, title, speaker_notes, why_matters) and renders a two-column grid: figure on left, prose on right. For composite slides, emit two pages. For text-only slides, full-page typesetting.
  3. Compile: typst compile slides/v2-review/_typst/review_deck.typ slides/v2-review/BoG_2026_review.pdf 2>&1 | tee slides/v2-review/_typst/render.log
  4. MANDATORY VERIFICATION (lessons from render-manuscript-draft-2/4 and v2-3): a. file slides/v2-review/BoG_2026_review.pdf -> 'PDF document' b. pdfinfo shows page count between 15 and 25 (15 slides, some split for composites; ~18-20 expected). Page dimensions in pdfinfo MUST be 16:9 ratio (13.33×7.5 or whatever you used). If aspect ratio is wrong (e.g., A4 portrait, letter, square), FAIL the task — that's the bug Erik called out on v2-3. c. pdfimages -list shows >= 12 image XObjects (one figure per non-text-only slide). d. Per-page PNG screenshots: pdftoppm -r 100 BoG_2026_review.pdf slides/v2-review/_typst/page — commit alongside. e. ALSO check: each page's image is sized to roughly half the page width (rough check: image width ~= page width / 2 +/- 20%). If figures are still full-bleed (occupying >75% of page width), the layout is wrong and Erik will reject again.
  5. wg artifact records BoG_2026_review.pdf. Commit: 'feat: BoG annotated review deck — 16:9 wide, figure-left, explanation-right'.

ACCEPTANCE:

  • slides/v2-review/BoG_2026_review.pdf exists; page dimensions are 16:9; 15-25 pages; figures embedded and visible at ~half page width with explanation prose on the right; per-page screenshots present in slides/v2-review/_typst/; wg artifact recorded.
  • If the layout fails (figures wrong size, aspect ratio wrong, prose missing) — wg fail with the specific issue.

DO NOT:

  • Build a full-bleed figure deck (that's v2-3 — Erik already said that's wrong).
  • Use A4 portrait, letter portrait, or square pages — must be 16:9 widescreen.
  • Use top/bottom layout (figure top, prose below) — Erik specifically said NO. LEFT/RIGHT only. 16:9 means horizontally wide.
  • Modify slide_NN_*.md files or any figure under paper_prep/figures/ (read-only).
  • Touch files outside slides/v2-review/.
  • Use SBATCH (light: typst compile + light figure rendering).

Depends on

Required by

Log