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/manuscript-as-code

Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout. Helps teams avoid 'final_v7' chaos and ensures submission-ready artifacts.

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vibe-skills
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Install
$ npx -y skills add foryourhealth111-pixel/Vibe-Skills --skill manuscript-as-code --agent claude-code

How it fires

How this skill gets triggered: by you, by Claude, or both.

  • Fires itselfAuto-invocation. Claude auto-loads it when your prompt matches the work.Auto-invocation is when the right skill fires by itself at the right moment, driven by a FLOW.md router and a hook, instead of you invoking it by name. It is the difference between a skill being installed and a skill actually getting used.Read the full definition →
  • You can call itInvoke it directly when you want it.
  • Slash command/manuscript-as-code

Context preview

The summary Claude sees to decide when to auto-load this skill.

Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout. Helps teams avoid 'final_v7' chaos and ensures submission-ready artifacts.

SKILL.md

manuscript-as-code.SKILL.md
name: manuscript-as-code
description: "Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout. Helps teams avoid 'final_v7' chaos and ensures submission-ready artifacts."
allowed-tools: [Read, Write, Edit, Bash, Grep, Glob]

Manuscript as Code（论文工程化）

目标

把“写论文”升级成“交付可复现的出版工程”：

  • 结构清晰：任何人进仓库都知道哪里改正文、哪里改图、哪里改引用
  • 可复现：一条命令能构建 PDF/HTML；CI 自动验证
  • 可审计：每张图/每个结果都有来源（代码/数据/参数）

适用：

  • 多人协作写作（导师/合作者/跨机构）
  • 反复投稿/返修（需要明确改动轨迹）
  • 图表多、实验多、容易“找不到版本”的项目

---

推荐仓库结构（最小可行）

见 `templates/repo-structure.md`。核心思想：

  • `manuscript/`：只放正文与引用（source-of-truth）
  • `figures/`：每张图一个目录（source + out）
  • `build/`：所有生成物（可删除，可再生）
  • `submission/` 与 `revision/`：投稿与返修阶段产物

---

元规则（工程化的关键）

1) 生成物与源文件分离

  • 源：`figures/fig-02/src/plot.py`
  • 产物：`figures/fig-02/out/fig-02.pdf`
  • 禁止把产物当源文件编辑（比如在 PDF 上涂改）

2) 每张图都要能“重生成”

最少要求：

  • 一条命令 + 固定参数能导出最终图（PDF/TIFF）
  • 记录依赖版本与随机种子（如果有）

3) 把“投稿约束”写成配置

推荐维护：

  • `submission/submission-manifest.yml`（统一记录规格与完成度）

---

案例（推荐学习）

  • Manubot：`manubot/rootstock`（论文的 CI/协作写作范式）
  • Deep review：`greenelab/deep-review`（评审/返修视角）
Read it on GitHub ↗
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Repo: foryourhealth111-pixel/Vibe-Skills

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