Publication-grade structural figure — KRAS Switch I/II with 3-layer QA

PASS · rubric SATISFIED1064sprompt: enartifact: en

Prompt (verbatim)

Using the input data in {DATA_DIR}, first use bioresearcher-python-setup-uv to install the scientific visualization dependencies (pymol-open-source, matplotlib, pymupdf, numpy, pillow, biopython). Then use bioresearcher-plot-making to create a publication-grade composite figure in figures/kras_inhibitors/ following the structural-biology_binder-visualization specification. Generate fig1_kras_landscape (.pdf, .svg, .png), run the bundled QA gates (audit_panel_alignment.py, audit_figure_collisions.py, and audit_pdf_text.py), and provide LEGENDS.md. Ensure all QA gates pass.

What happened

Chained bioresearcher-python-setup-uv (pymol-open-source, matplotlib, pymupdf, numpy, pillow, biopython) then bioresearcher-plot-making.
The TRUE session iterated through two collision-audit FAIL rounds (text overlaps) before finishing all-green — the QA gates bit.
Rubric flag verify-structural-figure-publication-quality adjudicated SATISFIED: pdf/svg/png + LEGENDS.md + audit JSON committed.

Evidence

Vector PDF collision audit	0 fail, 0 warn — PASS
Glyph size floor (>= 5.0 pt)	minimum found 5.2 pt — PASS
Panel alignment (<= 1.5 pt)	fail 0, warn 0, 4 comparisons — PASS

PDF · SVG · LEGENDS.md · alignment.json

Objective checks

checks passed: 5/5 · one rubric flag adjudicated SATISFIED post-run (recorded in result.json)

Fan-out mode	Sequential procedural chain: uv env bootstrap → plot-making render → QA gates
Provenance	`3380cc6` · opencode 1.18.29

Replay

node demos/run-demo.mjs --only agent-plot-making-en --publish

Manual-run only — this replay spends LLM tokens (real opencode CLI + network).

In the repository: README · transcript · result.json · artifact directory (permalink)