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Agent skill

Manuscript As Code

by foryourhealth111-pixel in foryourhealth111-pixel/Vibe-Skills

Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout.

Apache-2.0Auto-check: notesDevelopment

Install Manuscript As Code

skills CLI
$ npx skills add foryourhealth111-pixel/Vibe-Skills --skill manuscript-as-code -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install foryourhealth111-pixel/Vibe-Skills manuscript-as-code --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/bundled/skills/manuscript-as-code .claude/skills/manuscript-as-code && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
manuscript-as-code
GitHub stars
3.6k
Token cost
~281 tokens
SKILL.md length
47 words
Files
2
Skills in repo
81
Repo updated
First seen
Licence
Apache-2.0

At a glance

Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout.

  • Works in 3 steps: 生成物与源文件分离 → 每张图都要能“重生成” → 把“投稿约束”写成配置
  • Tasks that involve Git workflow
  • SKILL.md covers 目标, 推荐仓库结构（最小可行）, 元规则（工程化的关键） and 案例（推荐学习）
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Manuscript As Code is an agent skill from foryourhealth111-pixel/Vibe-Skills. Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout. Helps teams avoid 'finalv7' chaos and ensures submission-ready artifacts.

Its SKILL.md is about 280 tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files (for example `templates/repo-structure.md`).

It sits in Development, covering Git workflow. The repository describes itself as: Intelligent Skill routing and workflow orchestration for AI agents — +21.12 pp reward, −29.6% tokens on SkillsBench with DeepSeekV4Flash-VE. The licence is Apache-2.0.

When your agent uses it

  • Tasks that involve Git workflow

Example prompts

  • “finalv7”
  • “/manuscript-as-code”

Requirements

  • Pre-approved tools (allowed-tools): Read, Write, Edit, Bash, Grep, Glob

Workflow steps

3 steps, taken from the step headings in SKILL.md.

  1. 生成物与源文件分离
  2. 每张图都要能“重生成”
  3. 把“投稿约束”写成配置

What it can do on your machine

Read from SKILL.md and the folder at commit ddcaa2a. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Read
    • Write
    • Edit
    • Bash
    • Grep
    • Glob

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Manuscript As Code loads about 281 tokens when it runs. Until then it costs about 53 tokens; SKILL.md has 47 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~53
When it runs · the whole SKILL.md, loaded when a task matches
~281

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
    allowed-tools: Read, Write, Edit, Bash, Grep, Glob

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from foryourhealth111-pixel/Vibe-Skills at commit ddcaa2a, republished under its Apache-2.0 licence (© foryourhealth111-pixel). 47 words, ~281 tokens.

Download SKILL.mdSave it as .claude/skills/manuscript-as-code/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.
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）

© foryourhealth111-pixel, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file in bundled/skills/manuscript-as-code of foryourhealth111-pixel/Vibe-Skills.

  • SKILL.md
  • templates/repo-structure.md

Open the folder on GitHubat commit ddcaa2a

Compare with similar skills

Manuscript As Code next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Manuscript As Code compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Manuscript As Code this skillforyourhealth111-pixel/Vibe-Skills3.6k—~281Automated safety check: NotesApache-2.0
Finishing a Development Branchobra/superpowers297k5 repos~1.9kAutomated safety check: PassMIT
Code Design Rationale Investigatorcursor/plugins10k9 repos~2.6kAutomated safety check: PassNone
Contributor-First PR MergeHKUDS/OpenHarness16k1 repos~847Automated safety check: PassMIT
Migrate Internal Package into GhostTryGhost/Ghost56k—~3.8kAutomated safety check: PassMIT
Create Pull Requestcline/cline70k1 repos~1.6kAutomated safety check: PassApache-2.0

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Categories

Questions about Manuscript As Code

What does Manuscript As Code do?

Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout. Manuscript As Code is an agent skill from foryourhealth111-pixel/Vibe-Skills. Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout.

When should I use Manuscript As Code?

Manuscript As Code fits situations like: tasks that involve Git workflow.

How do I install Manuscript As Code in Claude Code?

Run `npx skills add foryourhealth111-pixel/Vibe-Skills --skill manuscript-as-code -a claude-code`. Or copy the skill folder (bundled/skills/manuscript-as-code in foryourhealth111-pixel/Vibe-Skills) into .claude/skills/manuscript-as-code in your project. Claude Code loads it when a task matches its description.

How do I install Manuscript As Code in Codex?

Run `npx skills add foryourhealth111-pixel/Vibe-Skills --skill manuscript-as-code -a codex`. Or copy the skill folder (bundled/skills/manuscript-as-code in foryourhealth111-pixel/Vibe-Skills) into .agents/skills/manuscript-as-code in your project. Codex loads it when a task matches its description.

Can I use Manuscript As Code in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add foryourhealth111-pixel/Vibe-Skills --skill manuscript-as-code -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/manuscript-as-code, .gemini/skills/manuscript-as-code, .github/skills/manuscript-as-code and .opencode/skills/manuscript-as-code in your project.

What does Manuscript As Code need to run?

SKILL.md names no scripts, command-line tools or credentials: Manuscript As Code is instructions for the agent only. Its frontmatter pre-approves these tools: Read, Write, Edit, Bash, Grep, Glob.

Does Manuscript As Code access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Manuscript As Code safe to install?

Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Manuscript As Code use?

Manuscript As Code is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Manuscript As Code use?

About 281 tokens (SKILL.md is roughly 1.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Manuscript As Code?

Skills that share tags, products or a category with Manuscript As Code: Finishing a Development Branch (obra/superpowers, 297k stars), Code Design Rationale Investigator (cursor/plugins, 10k stars), Contributor-First PR Merge (HKUDS/OpenHarness, 16k stars) and Migrate Internal Package into Ghost (TryGhost/Ghost, 56k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Manuscript As Code?

foryourhealth111-pixel (a GitHub user) maintains it in foryourhealth111-pixel/Vibe-Skills, which has 3,612 GitHub stars. The repository holds 81 skills in this directory. The repository was last updated on August 31, 2026.

Source: foryourhealth111-pixel/Vibe-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.