psyclaw 0.28.0 → 0.28.2

package/vendor/ars/pi/wrapper.js

@@ -100,6 +100,15 @@ export default function (pi) {
   });
 
   pi.on("input", (event) => {
+    // PsyClaw conversation mode: `ars: <task>` (entered via bare `ars` + Tab).
+    const modeMatch = event.text.match(/^ars:\s*([\s\S]*)$/i);
+    if (modeMatch) {
+      setArsActive(true);
+      const body = modeMatch[1].trim();
+      if (!body) return { action: "handled" };
+      return { action: "transform", text: body };
+    }
+
     const match = event.text.match(commandPattern);
     if (!match) {
       if (skillPattern.test(event.text)) setArsActive(true);

package/vendor/nature-skills/LICENSE

@@ -0,0 +1,201 @@
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package/vendor/nature-skills/NOTICE.md

@@ -0,0 +1,7 @@
+# Nature Skills (bundled subset)
+
+Source: https://github.com/Yuan1z0825/nature-skills  
+License: Apache-2.0 (see `LICENSE`)  
+Pinned commit: `28150f30f8b4017991fca8c7b2839f02c6586d2f`
+
+PsyClaw ships only the ARS gap-fill leaves (`nature-figure`, `nature-ref-verifier`, `nature-polishing`) plus the `nature-shared` support package they reference. Large example assets under `nature-figure/assets` are omitted from this bundle.

package/vendor/nature-skills/PSYCLAW_SOURCE.json

@@ -0,0 +1,19 @@
+{
+  "schemaVersion": "psyclaw/bundled-upstream/v1",
+  "name": "nature-skills",
+  "source": "https://github.com/Yuan1z0825/nature-skills",
+  "ref": "main",
+  "commit": "28150f30f8b4017991fca8c7b2839f02c6586d2f",
+  "contentSha256": "3dccb12c2dbfd430d2e133b434a9c8ef88ec9d0c31abded0776aba6e855f6509",
+  "license": "Apache-2.0",
+  "includes": [
+    "skills/nature-figure",
+    "skills/nature-ref-verifier",
+    "skills/nature-polishing",
+    "skills/nature-shared"
+  ],
+  "omissions": [
+    "skills/nature-figure/assets (chart-atlas / figures4papers / gallery examples omitted to keep the npm package small; runtime scripts and references remain)"
+  ],
+  "distribution": "Bundled in the PsyClaw npm package for offline ARS gap-fill; no runtime GitHub download is required."
+}

package/vendor/nature-skills/skills/nature-figure/README.md

@@ -0,0 +1,107 @@
+# `nature-figure` 技能
+
+[English](README_EN.md)
+
+`nature-figure` 用于设计、生成和审查投稿级科研图件，面向 Nature 系列、高影响力期刊、论文图版、机制示意图和 graphical abstract 草稿。
+
+## 适合用它做什么
+
+- 根据数据、图注或论文结论生成 Python / R 绘图脚本和可编辑图件。
+- 将已有图件重画为更清楚的多面板论文 figure。
+- 按“一张 Figure 回答一个 Results 级科学问题”的默认逻辑规划多面板证据链，让各 panel 分别承担主证据、control、正交验证、扰动、机制或边界等不同推理角色，而不是只把同一结果换指标重画。
+- 规划 Figure 1、机制图、workflow、graphical abstract 或补充图。
+- 检查面板标签、配色与视觉层级、逐面板误差线、最终 PDF 实际字号、统计标注、source data 和导出格式；多面板图在渲染时自动检查同行/同列轴框、宽高、panel 标签锚点和重复间距是否在 1.5 pt 容差内，每次生成或修改布局后再检测文字—文字、文字—线条/曲线、页面裁切及可疑色块/图片边缘重合。
+- 区分旗舰 `Nature` 初投稿、主图终稿和 Extended Data 的文件契约，并执行 `<250` 词图注上限。
+- 对 `Nature Machine Intelligence` 单独执行 6 个主 display、最多 10 个 Extended Data、初投稿/终稿边界、300 dpi/180 mm 和 source data 要求；当前官网未给独立图注数字，保留 2018 官方 `<300` 英文词为历史建议线，整张图注建议 150–250 词且不是每个 panel 分别计算。
+- 在用户明确要求时，通过 OpenRouter Images API 调用 `openai/gpt-image-2` 生成 AI 概念示意图草稿。
+- 对 AI 辅助 graphical abstract 先定义单一中心信息、图件类型、目标读者和证据边界，再比较构图与可访问配色；投稿前单独核验目标期刊最新 AI 政策、科学准确性、版权、披露和 provenance。`Nature Careers` 专栏仅作为实践建议，不等于投稿许可。
+
+## 工作方式
+
+绘图前先建立图件契约，而不是直接套模板：
+
+- 核心结论：这张图要证明什么。
+- 证据层级：哪些面板是主证据，哪些是补充解释。
+- 多面板架构：先写 figure-level claim，再决定每个 panel 的独特证据角色以及主图、另一张图或 Extended Data/SI 的去向。
+- 图件原型：散点、箱线、热图、机制图、流程图、多面板组合等。
+- 后端选择：Python 或 R；第一次选择后会作为默认偏好复用。
+- 数据完整性：默认保留全部观测和指定变量，任何排除都记录规则与前后计数。
+- 模板兼容性：先核对科学含义、数据结构和变换条件，再决定精确复用、结构适配或只继承样式。
+- 投稿约束：尺寸、字体、色彩、分辨率、矢量格式和 source-data 可追溯性。
+- 子图对齐门：由 Python axes 或 R patchwork/gtable 在最终尺寸下测量真实 panel 矩形；横排 3/4 张等跨度 panel 自动保证等宽，普通网格及“左二右一 / 左一右二”等跨行布局自动推断，可靠错位阻断导出，free-positioned hero panel、inset 和 colorbar 只能带理由豁免。
+- 渲染碰撞门：最终 PDF 每次重绘后都生成 collision JSON；可靠碰撞必须修复，可疑 overlay 必须逐项复核。
+
+## 典型请求
+
+- “把这组数据做成 Nature 风格多面板图，优先 Python。”
+- “参考 figures4papers 里 Nature Machine Intelligence 的布局，帮我补一个方法对比图。”
+- “重画这个机制示意图，导出 SVG/PDF，并给我 source data 表。”
+- “用 OpenRouter 生成 graphical abstract 草稿，但不要当作定量数据图。”
+
+## 示例预览
+
+| 方向 | 预览 | 可借鉴模式 |
+|------|------|------------|
+| 多面板论文图 | <a href="assets/gallery/fig1-material-mechanism-rich.png"><img src="assets/gallery/fig1-material-mechanism-rich.png" width="220" alt="Material design and physical validation"></a> | 机制示意、图像面板、定量结果和相关性放在同一证据链中 |
+| 图表类型 atlas | <a href="assets/chart-atlas/atlas-03-heatmaps.png"><img src="assets/chart-atlas/atlas-03-heatmaps.png" width="220" alt="Heatmap atlas"></a> | 热图、注释矩阵、聚类块和发散色标的组合模式 |
+| 第三方 figures4papers 参考 | <a href="assets/figures4papers/figure_VIGIL/figures/comparison_radar.png"><img src="assets/figures4papers/figure_VIGIL/figures/comparison_radar.png" width="220" alt="VIGIL comparison radar"></a> | 仅用于研究 layout、legend 和多指标比较语法；使用前阅读独立版权说明 |
+
+## 你需要提供
+
+- 原始数据、已有图、图注、论文 claim 或想表达的机制。
+- 目标期刊、单栏/双栏尺寸、输出格式和是否需要 source data。
+- Python / R 偏好；如果没有偏好，技能会先询问或沿用本机记录。
+
+## 产出
+
+- 可运行的 Python 或 R 绘图脚本。
+- SVG/PDF/TIFF/PNG 等图件文件，优先保留可编辑矢量版本。
+- 面板说明、source data 映射、排除计数、逐面板视觉审查表、alignment JSON/诊断 SVG、碰撞 JSON/诊断 PDF 和投稿前 QA 记录。
+- AI 示意图任务中，输出概念草稿和需要人工重画/核实的元素列表。
+
+## 内置参考
+
+- `references/api.md`：Python 配色、样式和绘图 helper 约定。
+- `references/asset-adaptation.md`：模板语义匹配、字段映射和数据完整性规则。
+- `references/multipanel-evidence-architecture.md`：从 Results 级问题到 panel 证据角色、图内闭环、跨 Figure claim escalation 和主图/Extended Data/SI 去向的规划与审计。
+- `references/template-catalog.md`：volcano、ROC、marker dot plot、marginal 和 paired 的已验证 Python CSV 模板。
+- `references/chart-types.md`：常见图型选择和视觉规则。
+- `references/demos.md`：第三方 `figures4papers` 示例索引、使用边界和原创适配模式。
+- `references/qa-contract.md`：导出前检查项、source-data 约束和静态预检入口。
+- `references/ai-graphical-abstract-workflow.md`：AI 图形摘要的信息简报、构图与配色、期刊政策门、人工科学核验、披露和 provenance 工作流。
+- `references/openrouter-image-generation.md`：OpenRouter / GPT Image 2 的 provider-specific 生成与 QA 路径。
+- `scripts/validate_figure.py`：Python/R 绘图源码的可复现静态 QA。
+- `scripts/audit_pdf_text.py`：扫描导出 PDF 的 `Tf` 操作符，发现 mathtext 上下标等低于 5 pt 的实际字形。
+- `scripts/audit_panel_alignment.py` 与 `scripts/panel_alignment.R`：在最终物理尺寸下测量 Matplotlib axes 或 R patchwork/gtable，对同行 3/4 panel 等宽、同行/同列边界、跨行面板共享外边界、panel 标签和重复间距执行阻断式自动审计。
+- `scripts/audit_figure_collisions.py`：对 Python/R 最终 PDF 执行自动几何碰撞审计，输出阻断性 FAIL、需复核 WARN、JSON 报告和可选带框诊断 PDF。
+- `scripts/figure_safety.py`：严格单调插值和基于数据/误差范围的标签高度 helper。
+- `assets/figures4papers/`：保留的第三方参考脚本与预览图；不自动适用本仓库 MIT License，使用前阅读 `THIRD_PARTY_NOTICES.md`。
+
+## 边界
+
+- 不会把 AI 生成图片当作真实实验结果或定量数据面板。
+- 不会把内部可用的 AI 草稿自动称为可投稿终稿；两者分别判定。
+- 不会凭空补统计检验、样本量、误差线含义或实验条件。
+- 不会为了渲染方便静默抽样、忽略变量或删除不完整观测。
+- 不会把自动校验通过当作视觉验收；对齐门只保证已声明的几何关系在容差内，最终交付仍需逐面板检查不确定性、标签碰撞、间距和显著性层级。
+- 私有模板可以在本机使用，但不应在面向用户输出中暴露私有路径、文件名或来源。
+- 第三方参考材料的版权和再使用条件以其来源及 `THIRD_PARTY_NOTICES.md` 为准；本仓库不额外授予这些文件的使用权。
+
+自动碰撞审计需要 PyMuPDF：
+
+```bash
+python -m pip install -r skills/nature-figure/requirements.txt
+```
+
+## 相关技能
+
+- `nature-statistics`：检查统计标注、n 定义和 p 值表述。
+- `nature-writing`：把图件结论放回手稿叙事。
+- `nature-paper2ppt`：把论文图件整理成汇报幻灯片。
+
+## 与其他技能的关系
+
+- 如果任务核心是统计解释、样本量定义或显著性表述，优先让 `nature-statistics` 先把文字审清，再回到 `nature-figure` 画图。
+- 如果图件已经定稿，但需要把结论组织成摘要、引言或结果段落，交给 `nature-writing` 继续承接。
+- 如果图件要直接转成组会材料或答辩汇报，再交给 `nature-paper2ppt` 组织成页面。
+- `nature-figure` 负责图件本身；它不替代统计审查，也不替代手稿叙事。

package/vendor/nature-skills/skills/nature-figure/README_EN.md

@@ -0,0 +1,107 @@
+# `nature-figure` Skill
+
+[中文说明](README.md)
+
+`nature-figure` designs, generates, and audits submission-grade scientific figures for Nature-series papers, high-impact journals, manuscript panels, mechanism schematics, and graphical-abstract drafts.
+
+## What To Use It For
+
+- Generate Python / R plotting scripts and editable figures from data, legends, or manuscript claims.
+- Redraw existing figures into clearer multi-panel manuscript figures.
+- Plan multi-panel evidence chains around the default that one figure answers one Results-level scientific question, with panels serving different inferential roles such as primary evidence, control, orthogonal validation, perturbation, mechanism, or boundary rather than merely redrawing the same result under new metrics.
+- Plan Figure 1, mechanism diagrams, workflows, graphical abstracts, or supplementary figures.
+- Check panel labels, color hierarchy, panel-by-panel uncertainty, actual PDF glyph sizes, statistical annotations, source data, and export formats; at render time, automatically enforce a 1.5 pt tolerance for comparable row/column axes rectangles, dimensions, panel-label anchors, and repeated gutters, then detect text-text, text-stroke/curve, page-clipping, and suspicious fill/image-edge overlaps after every generation or layout revision.
+- Separate flagship `Nature` initial, final main-figure, and Extended Data file contracts, including the under-250-word legend limit.
+- Apply `Nature Machine Intelligence` (NMI)'s separate six-main-display, up-to-ten Extended Data, initial/final, 300-dpi/180-mm, and source-data requirements; the current pages give no standalone legend number, so retain the official 2018 `<300`-English-word rule only as a historical advisory, count the whole legend rather than each panel, and aim for 150–250 words.
+- When explicitly requested, call `openai/gpt-image-2` through the OpenRouter Images API to draft AI concept schematics.
+- For AI-assisted graphical abstracts, define one central message, figure type, audience, and evidence boundary before comparing compositions and accessible palettes; then separately verify the target journal's current AI policy, scientific accuracy, copyright, disclosure, and provenance. Treat the *Nature Careers* column as practitioner advice, not submission permission.
+
+## Workflow
+
+Start with a figure contract rather than a template:
+
+- Core conclusion: what the figure must demonstrate.
+- Evidence hierarchy: which panels are primary evidence and which are explanatory.
+- Multi-panel architecture: write the figure-level claim first, then assign every panel a distinct evidence role and decide whether displaced material belongs in another figure or Extended Data/SI.
+- Figure prototype: scatter, box plot, heatmap, mechanism diagram, workflow, multi-panel composition, and so on.
+- Backend choice: Python or R; the first choice can be reused as the default preference.
+- Data integrity: preserve all observations and requested variables by default, and record every exclusion rule with before/after counts.
+- Template compatibility: compare scientific meaning, data shape, and transform constraints before exact reuse, structural adaptation, or style-only inheritance.
+- Submission constraints: size, typography, color, resolution, vector format, and source-data traceability.
+- Panel-alignment gate: Python axes or R patchwork/gtable measures real panel rectangles at final dimensions; horizontal rows of three or four equal-span panels must be equal width, regular grids and unequal-span `left two/right one` or mirrored layouts are inferred automatically, reliable misalignment blocks export, and free-positioned hero panels, insets, or colorbars require reasoned exemptions.
+- Rendered collision gate: regenerate a collision JSON after every final-PDF render; reliable collisions must be fixed and ambiguous overlays reviewed individually.
+
+## Typical Requests
+
+- "Make a Nature-style multi-panel figure from this dataset, preferably in Python."
+- "Use the figures4papers Nature Machine Intelligence layout as a reference and add a method-comparison figure."
+- "Redraw this mechanism schematic, export SVG/PDF, and give me the source-data table."
+- "Use OpenRouter to draft a graphical abstract, but do not treat it as a quantitative data figure."
+
+## Example Preview
+
+| Direction | Preview | Reusable Pattern |
+|-----------|---------|------------------|
+| Multi-panel manuscript figure | <a href="assets/gallery/fig1-material-mechanism-rich.png"><img src="assets/gallery/fig1-material-mechanism-rich.png" width="220" alt="Material design and physical validation"></a> | Mechanism schematic, image panels, quantitative results, and correlation in one evidence chain |
+| Chart-type atlas | <a href="assets/chart-atlas/atlas-03-heatmaps.png"><img src="assets/chart-atlas/atlas-03-heatmaps.png" width="220" alt="Heatmap atlas"></a> | Heatmaps, annotation matrices, cluster blocks, and diverging color scales |
+| Third-party figures4papers reference | <a href="assets/figures4papers/figure_VIGIL/figures/comparison_radar.png"><img src="assets/figures4papers/figure_VIGIL/figures/comparison_radar.png" width="220" alt="VIGIL comparison radar"></a> | Study layout, legend, and multi-metric comparison grammar only; read the separate copyright notice before use |
+
+## What You Need To Provide
+
+- Raw data, existing figure, legend, manuscript claim, or intended mechanism.
+- Target journal, single-column / double-column size, output format, and whether source data is required.
+- Python / R preference; if absent, the skill asks or reuses the local preference.
+
+## Outputs
+
+- Runnable Python or R plotting script.
+- SVG/PDF/TIFF/PNG figure files, with editable vector output preferred.
+- Panel notes, source-data mapping, exclusion counts, a panel-by-panel visual audit, alignment JSON/diagnostic SVG, collision JSON/diagnostic PDF, and a pre-submission QA record.
+- For AI-schematic tasks, a concept draft and a list of elements that need human redrawing or verification.
+
+## Built-In References
+
+- `references/api.md`: Python palette, style, and plotting-helper conventions.
+- `references/asset-adaptation.md`: semantic matching, field mapping, and data-integrity rules for templates.
+- `references/multipanel-evidence-architecture.md`: planning and audit from Results-level question to panel evidence roles, within-figure closure, cross-figure claim escalation, and main-figure/Extended-Data/SI placement.
+- `references/template-catalog.md`: validated Python CSV templates for volcano, ROC, marker dot plot, marginal, and paired figures.
+- `references/chart-types.md`: chart selection and visual rules.
+- `references/demos.md`: third-party `figures4papers` index, use boundaries, and original adaptation patterns.
+- `references/qa-contract.md`: export QA, source-data constraints, and static-preflight entry points.
+- `references/ai-graphical-abstract-workflow.md`: message brief, composition and color, journal-policy gate, human scientific verification, disclosure, and provenance for AI-assisted graphical abstracts.
+- `references/openrouter-image-generation.md`: provider-specific OpenRouter / GPT Image 2 generation and QA.
+- `scripts/validate_figure.py`: reproducible static QA for Python and R plotting source.
+- `scripts/audit_pdf_text.py`: scan exported PDF `Tf` operators for real glyph runs below the 5 pt floor, including reduced mathtext scripts.
+- `scripts/audit_panel_alignment.py` and `scripts/panel_alignment.R`: measure final-size Matplotlib axes or R patchwork/gtable geometry and block unequal widths in three/four-panel rows, row/column edges, shared outer edges of spanning panels, panel labels, or repeated-gutter misalignment.
+- `scripts/audit_figure_collisions.py`: automatic geometry audit for final Python/R PDFs, with blocking FAIL findings, review-required WARN findings, JSON output, and an optional marked diagnostic PDF.
+- `scripts/figure_safety.py`: strict monotone interpolation and data/uncertainty-driven label positioning helpers.
+- `assets/figures4papers/`: retained third-party scripts and previews; the repository MIT License does not automatically apply, so read `THIRD_PARTY_NOTICES.md` before use.
+
+## Boundaries
+
+- AI-generated images are not treated as real experimental results or quantitative data panels.
+- An internally useful AI draft is not automatically described as a submission-ready final asset; assess those two states separately.
+- The skill does not invent statistical tests, sample sizes, error-bar meanings, or experiment conditions.
+- The skill does not silently sample for rendering convenience, ignore requested variables, or remove incomplete observations.
+- Passing automated checks is not treated as visual acceptance; the alignment gate only proves declared geometric relationships are within tolerance, and uncertainty, label collisions, spacing, and salience still require panel-by-panel inspection.
+- Private templates can be used locally, but user-facing outputs should not expose private paths, filenames, or sources.
+- Third-party reference materials remain subject to their source terms and `THIRD_PARTY_NOTICES.md`; this repository grants no additional rights to those files.
+
+The automatic collision audit requires PyMuPDF:
+
+```bash
+python -m pip install -r skills/nature-figure/requirements.txt
+```
+
+## Related Skills
+
+- `nature-statistics`: check statistical annotations, n definitions, and p-value wording.
+- `nature-writing`: align figure conclusions with manuscript narrative.
+- `nature-paper2ppt`: turn manuscript figures into presentation slides.
+
+## Relationship With Other Skills
+
+- If the core task is statistical interpretation, sample-size definition, or significance wording, let `nature-statistics` audit the text before returning to `nature-figure`.
+- If the figure is finished but the user needs the claim written into an abstract, introduction, or results section, hand off to `nature-writing`.
+- If the figure should become a lab meeting deck or presentation slide, hand off to `nature-paper2ppt`.
+- `nature-figure` is responsible for the figure itself; it does not replace statistical review or manuscript narration.

package/vendor/nature-skills/skills/nature-figure/SKILL.md

@@ -0,0 +1,154 @@
+---
+name: nature-figure
+description: >-
+  Create, revise, audit, and export submission-grade scientific figures for Nature-family and other high-impact venues in Python (matplotlib/seaborn) or R (ggplot2/patchwork/ComplexHeatmap), including multi-panel plots, figures4papers-style work, and journal-ready SVG/PDF/TIFF outputs. Use for paper or scientific plots, manuscript data visualization, 论文配图、学术写作配图、科研绘图、科研作图、画图、作图、出图、论文图表、可视化. Define the conclusion, evidence logic, data integrity, template compatibility, export needs, and reviewer risks before plotting; honor or persist the Python/R backend choice. Also use the separate OpenRouter GPT Image 2 route for explicit AI-generated graphical abstracts, mechanism diagrams, concept schematics, 论文示意图、机制示意图、图形摘要; this route skips backend choice and treats outputs as drafts. Do not use for interactive dashboards, statistics-only analysis, data cleaning, literature review, code debugging, pure photo editing, or Illustrator/Figma-first infographics without manuscript-figure intent.
+---
+
+# Nature Figure Making — Router
+
+This skill is split into two layers:
+
+- A **static layer** under `static/` that holds versioned, reusable content fragments (the figure contract and default stance, plus a per-backend quick-start for Python and R).
+- A **dynamic layer** (this file plus `manifest.yaml`) that detects the plotting backend and loads only the fragment needed for the current job. The large design, API, pattern, and QA material lives in on-demand references.
+
+Do not try to apply the figure logic from memory or from this router. Always load fragments from disk as described below.
+
+## Routing protocol
+
+Follow these steps every time the skill is invoked.
+
+### 0. Check for graphical-abstract and AI-schematic routes
+
+For every graphical-abstract planning, generation, revision, or audit task that
+uses AI, read
+[references/ai-graphical-abstract-workflow.md](references/ai-graphical-abstract-workflow.md)
+first. It owns the message/audience brief, composition and palette workflow,
+policy gate, human scientific review, disclosure boundary, and provenance
+requirements. A Nature Careers article is practitioner advice, not submission
+clearance; verify the current official policy for the exact target journal.
+
+If the request is planning or auditing only, do not ask for Python or R unless
+the user also asks to render or revise a data-driven figure.
+
+If the user explicitly asks to generate a manuscript schematic, graphical abstract, mechanism diagram, concept illustration, or paper schematic with OpenRouter, GPT Image 2, an image-generation API, or similar wording, do **not** ask "Python or R?". This is a non-plotting AI-schematic route.
+
+For this route:
+
+1. Read [manifest.yaml](manifest.yaml) and the `always_load` files.
+2. Read [references/ai-graphical-abstract-workflow.md](references/ai-graphical-abstract-workflow.md).
+3. Read [references/openrouter-image-generation.md](references/openrouter-image-generation.md).
+4. Use [scripts/generate_openrouter_schematic.py](scripts/generate_openrouter_schematic.py) when the user wants a real API call or a reproducible payload.
+5. Treat output as a draft schematic / graphical abstract, not as a quantitative data panel. Do not invent experimental values, author logos, institutional marks, or unsupported mechanisms. Keep internal usefulness separate from submission eligibility.
+
+Only continue to the Python/R backend gate for plotting, charting, data visualization, or manuscript figure assembly tasks that are not explicit OpenRouter AI image-generation requests.
+
+### 1. Load the manifest and the core layer
+
+Read [manifest.yaml](manifest.yaml). It declares the `backend` axis, the allowed values, and the file paths each value maps to.
+
+Also read every file listed under `always_load` (`static/core/contract.md` and `static/core/stance.md`). These hold the figure contract, the backend gate, the missing-runtime rule, the privacy rule, and the default operating stance that apply to every figure job.
+
+### 2. Resolve the plotting backend
+
+Backend selection applies only to rendering or editing plotting code. Reuse a choice already established in the same task and its follow-ups; do not ask again merely because a new message omits the language. Read-only figure review and backend-independent data inspection may proceed without this choice. If the backend remains unresolved, retain the one-time Python/R question and pause only dependent plotting steps. Explicit approval requirements and backend exclusivity remain in force.
+
+Resolve the plotting backend from the current task before consulting the saved default. Decide the `backend` value in this order:
+
+1. If the current request explicitly chooses Python or R, use that backend and save it with `scripts/nature_figure_backend.py set python` or `scripts/nature_figure_backend.py set r`.
+2. If the request provides a clearly language-specific input file/workflow, use that backend and save it.
+3. Otherwise reuse a Python/R choice already established in this task. If none exists, run `scripts/nature_figure_backend.py get` and use a returned `python` or `r` preference.
+4. If neither a task choice nor a saved preference exists, ask exactly one concise question — **Python or R? I will remember this as your default.** — and pause only dependent plotting steps. After the user answers, save the answer before proceeding.
+
+- `python` — matplotlib / seaborn.
+- `r` — ggplot2 / patchwork / ComplexHeatmap.
+
+Do not guess or choose a backend by aesthetics alone. Only recommend a backend when the user explicitly asks you to choose; then use `references/backend-selection.md`, state the reason, save the selected backend, and proceed. Once selected, the backend is **exclusive** for all drawing, previewing, exporting, and visual QA (see `core/contract.md`). This gate does not apply to the explicit OpenRouter AI-schematic route above.
+
+### 3. Load the matching backend fragment
+
+After the backend is resolved, Read the mapped fragment (`static/fragments/backend/python.md` or `static/fragments/backend/r.md`). It carries the backend-only execution rule and the publication quick-start (rcParams/theme and export helper). Do **not** load the other backend's fragment.
+
+### 4. Build the figure using the loaded material
+
+Apply the loaded material in this order:
+
+1. Figure contract (`core/contract.md`) — write the core conclusion, map the evidence chain, classify the archetype, set the journal/export contract, before any code.
+2. Multi-panel evidence architecture — when planning, restructuring, or auditing a labelled multi-panel figure, load `references/multipanel-evidence-architecture.md`. Make the figure answer one Results-level scientific question; assign panels different inferential roles, not merely different metrics. When figure order must follow the manuscript argument, also load `../nature-shared/core/nature-results-discussion.md`.
+3. Default stance (`core/stance.md`) — archetype-first composition, hero panel, restrained palette, statistics/integrity as part of the figure.
+4. Backend fragment — the exclusive Python or R quick-start and execution rule.
+5. Template adaptation — when reusing built-in original examples, licensed external material, or user-provided plotting code, load `references/asset-adaptation.md` before mapping data or changing the script.
+6. Rendered QA and delivery preflight — load `references/qa-contract.md`, run the render-time panel-alignment gate for every multi-panel figure, `scripts/validate_figure.py` on the plotting source, `scripts/audit_pdf_text.py` on the exported PDF, and `scripts/audit_figure_collisions.py` on the same final PDF. Then inspect every panel and the complete figure at final physical size. Automated checks do not replace the panel-by-panel uncertainty, salience, spacing, and ambiguity audit.
+
+For every figure containing two or more comparable panels, measure the **final
+rendered plot-area rectangles** before export and preserve the alignment JSON.
+Python figures must call `require_matplotlib_panel_alignment()` from
+`scripts/audit_panel_alignment.py` after the final layout draw. R/patchwork
+figures must source `scripts/panel_alignment.R`, write the patchwork layout
+manifest at the final export dimensions, and run the same backend-neutral JSON
+auditor. Use a default physical tolerance of `1.5 pt` for shared edges, widths,
+heights, panel-label anchors and repeated gutters. `FIX BEFORE DELIVERY` or exit
+code `1` blocks export; `NOT AUDITABLE` or exit code `2` blocks any claim that
+alignment passed. A horizontal row of three or four equal-grid-span panels must
+have equal final plot-area widths as well as equal heights and gutters; an
+intentional unequal-width design requires a recorded `panel-width` exemption.
+Structured unequal-span grids—including two stacked panels
+beside one panel spanning both rows, in either column—must be inferred from
+shared grid start/stop boundaries and checked automatically. Nested grids,
+free-positioned hero panels, insets and colorbars may be excluded only through
+explicit comparable groups or a recorded exemption with a reason. Do not
+weaken the global tolerance to hide one intentional exception.
+
+After every generated or revised Python/R scientific figure, export the final
+PDF and run the collision audit again; this is mandatory after any change to
+data geometry, text, fonts, legends, annotations, axes, error bars, panel size
+or layout, not only at final submission. Use:
+
+```bash
+python skills/nature-figure/scripts/audit_figure_collisions.py figure.pdf \
+  --json-out figure.collision-audit.json \
+  --overlay-pdf figure.collision-audit.pdf
+```
+
+- `FIX BEFORE DELIVERY` or exit code `1`: repair the figure, re-export with the
+  selected plotting backend, and rerun all rendered QA.
+- `REVIEW REQUIRED`: inspect every WARN at final physical size; record why an
+  intentional overlay is acceptable. Use `--strict` when WARN must block.
+- `NOT AUDITABLE` or exit code `2`: report the dependency/PDF blocker and do not
+  claim collision validation. Install `requirements.txt` when PyMuPDF is absent.
+
+The collision audit reads PDF geometry for both Python and R output. It does not redraw
+the scientific figure or authorize cross-backend plotting. Its optional marked
+PDF is a QA-only diagnostic artifact and must never replace the selected
+backend's source or submission files.
+
+When the target is the flagship journal Nature, also load
+`references/nature-article-requirements.md`. It separates initial-review files
+from accepted-in-principle main and Extended Data production contracts and owns
+the flagship legend limit.
+
+When the target is Nature Machine Intelligence, instead load
+`../nature-shared/journal-formats/nature-machine-intelligence.md`. Apply its
+combined six-item main display budget, ten-item Extended Data maximum,
+initial-versus-production boundary, 300-dpi/180-mm production checks and source-
+data contract. NMI's current live pages do not assign a standalone per-legend
+number, but its official 2018 brief guide set a historical advisory ceiling of
+fewer than 300 English words per complete figure legend. Count the whole legend,
+not each panel; aim for 150–250 words and keep it below 300 unless the live
+submission system or editor gives a newer instruction. Do not import flagship
+Nature's limit.
+
+The chart serves the scientific logic; aesthetic polish is subordinate to making the core conclusion clear, defensible, and reviewable.
+
+### 5. Reach for references only when needed
+
+The files under `references/` are deep references, not defaults. Open them on demand per the `references.on_demand` table in the manifest — for example `references/figure-contract.md` to build the contract, `references/multipanel-evidence-architecture.md` to turn one Results-level question into complementary panel roles and a claim-escalating figure sequence, `references/asset-adaptation.md` to reuse a plotting template safely, `references/template-catalog.md` for validated Python CSV templates, `references/api.md` for the Python palette and numerical/layout safety helpers, `references/r-workflow.md` for R, `references/design-theory.md` for color/typography/export rationale, `references/common-patterns.md` and `references/chart-types.md` for layout/chart recipes, `references/nature-2026-observations.md` for real Nature page archetypes, `references/qa-contract.md` before final delivery, `references/nature-article-requirements.md` for exact flagship Nature stage and upload rules, `../nature-shared/journal-formats/nature-machine-intelligence.md` for exact NMI figure rules, `references/ai-graphical-abstract-workflow.md` for AI-assisted graphical-abstract planning, policy gating, human verification, and provenance, and `references/tutorials.md` / `references/demos.md` for worked examples.
+
+Do not infer flagship Nature or NMI requirements from a Nature Communications
+corpus or from the visual-style examples in this skill.
+
+## Why this split
+
+- The static layer is versioned and reviewable. The backend gate is now explicit in the manifest rather than buried in prose.
+- The dynamic layer keeps each invocation cheap: only the selected backend's quick-start enters context, and the 2,600+ lines of reference depth load only when a step needs them.
+- The router itself is short on purpose. Update fragments and references, not this file, when adding scope.
+- This structure mirrors `nature-writing`, `nature-polishing`, `nature-reader`, and `nature-paper2ppt`.

package/vendor/nature-skills/skills/nature-figure/agents/openai.yaml

@@ -0,0 +1,4 @@
+interface:
+  display_name: "Nature Figure"
+  short_description: "Create and audit submission-ready scientific figures"
+  default_prompt: "Use $nature-figure to create and audit a submission-ready scientific figure from these data."