← graph

build-bog-v2-2

Build BoG v2 deck PDF via typst (polylux/touying)

Metadata

Statusdone
Assignedagent-813
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-05-06T01:20:17.064912618+00:00
Started2026-05-06T01:20:55.849021857+00:00
Completed2026-05-06T01:41:30.141164703+00:00
Tagsbog-this-week, bog-deck, render, eval-scheduled
Eval score0.92
└ blocking impact0.95
└ completeness0.95
└ constraint fidelity0.55
└ coordination overhead0.85
└ correctness0.95
└ downstream usability0.90
└ efficiency0.85
└ intent fidelity0.70
└ style adherence0.90

Description

GOAL: Render slides/v2/slide_NN_*.md (15 slides) into a single PDF deck via typst. Lead author Erik Garrison gives this talk at Biology of Genomes THIS WEEK; he wants a viewable PDF.

INPUTS:

  • slides/v2/slide_01_title.md … slide_15_concerted_evolution_thesis.md (15 markdown briefs with bullets / figure / speaker notes)
  • slides/v2/SLIDES_v2_PLAN.md (consolidated plan including time budget + narrative arc)
  • slides/v2/figure_manifest.md (every figure path + status; READY-TO-RENDER R scripts called out)
  • slides/v2/coherence_check.md (cross-slide flags)
  • slides/20260204_Subtelomics_overview_EG.pdf (now-tracked v1 deck — slides 02/03/09 may pull pages from this for diagrams)
  • paper_prep/figures/ (existing manuscript figures used by slides 04/07/10/11/12)
  • paper_prep/figures/nj_tree_arms/nj_tree_annotated.{pdf,png} (slide 07 NJ tree from upstream task)
  • /moosefs/guarracino/HPRCv2/PHR_III/similarity/ (off-tree alternates listed in figure_manifest)

PIPELINE — strict order:

  1. Render any READY-TO-RENDER figures called out in figure_manifest.md whose source R script is embedded in the slide markdown:

    • slide 03 ER-callout (n=18,827, p* ≈ 5.21e-4, 230× threshold) → slides/v2/slide_03_er_callout.{pdf,png}
    • slide 06 clade callouts → slides/v2/slide_06_clade_callouts.{pdf,png}
    • slide 09 clade legend → slides/v2/slide_09_clade_legend.{pdf,png}
    • slide 12 stage trajectory inset (lepto/zygo/pachy/diplo Mantel ρ) → slides/v2/slide_12_stage_trajectory.{pdf,png}
    • Optional composites (slide 07/08/10/11) — render only if straightforward. For each script: extract from the slide MD, execute with R, save outputs in slides/v2/. Log any failures with wg log and continue (use the upstream panel as fallback).

  2. Use typst (already at ~/.local/bin/typst v0.13.1 from render-manuscript-draft-4). Use polylux (https://polylux.dev/) — battle-tested presentation framework. Working dir: slides/v2/_typst/. Pick a clean professional theme suitable for a major scientific conference (Biology of Genomes, Cold Spring Harbor); polylux 'simple' or similar — no need for flashy styling.

  3. Generate slides/v2/_typst/deck.typ by integrating the 15 slide MDs. Mapping: each slide MD's '## Title' → polylux slide title; '## Bullets' → bullet list; '## Primary figure' → figure include (use the figure path from the slide MD or figure_manifest.md); '## Speaker notes' → polylux speaker-notes block (these don't appear in the rendered PDF but are preserved in the .typ source for Erik); '## Time budget' → as a comment at the top of the slide block.

  4. Compile: 'typst compile slides/v2/_typst/deck.typ slides/v2/BoG_2026.pdf' — log to slides/v2/_typst/render.log.

  5. MANDATORY VERIFICATION (lessons from render-manuscript-draft-4 figureless-PDF disaster): a. 'file slides/v2/BoG_2026.pdf' must report 'PDF document' b. 'pdfinfo slides/v2/BoG_2026.pdf' must show 15 pages c. 'pdfimages -list slides/v2/BoG_2026.pdf | wc -l' must show at least 12 image XObjects (slides 4,5,6,7,8,9,10,11,12,13,14 — 11 figure-bearing slides; allow some overcount). If <12, fail with the actual count and which slide is missing its figure. d. Run 'pdftoppm -r 100 slides/v2/BoG_2026.pdf slides/v2/_typst/page' to dump per-page screenshots; commit those alongside.

  6. Record slides/v2/BoG_2026.pdf as a wg artifact. Single commit message: 'feat: BoG v2 deck PDF via typst polylux'.

ACCEPTANCE:

  • slides/v2/BoG_2026.pdf exists; file reports PDF; 15 pages; ≥12 embedded images; per-page screenshots present in slides/v2/_typst/; wg artifact recorded.
  • If anything breaks irrecoverably (typst compile error, missing critical figure, etc.) — wg fail with the SPECIFIC error from the failing pipeline step. Do NOT silently produce a figureless PDF.

DO NOT:

  • Modify any slide_NN_*.md file (read-only inputs)
  • Modify any figure under paper_prep/figures/ (read-only)
  • Touch any file outside slides/v2/
  • Run heavy compute (no SBATCH; everything here is light R/ggplot2 + typst compile)
  • Build anything other than the deck (no .pptx, no beamer, no .key)

Depends on

Required by

Log