foryourhealth111-pixel/manuscript-as-code
bundled/skills/manuscript-as-code/SKILL.md
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.
$ install --global
skillsauthnpx skillsauth add foryourhealth111-pixel/vco-skills-codex manuscript-as-codeInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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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）
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