manuscript-as-code

manuscript-as-code is a skill for Claude Code from foryourhealth111-pixel/Vibe-Skills. It costs 43 tokens per session (527 once invoked), scanned A, original, Apache-2.0.

A set of practices for managing a research paper like a software project, with organized files, version control, repeatable builds, and tracked sources for figures and results. It keeps the manuscript, generated files, and submission materials separate.

In plain words
What is it for?
Use it to structure a paper repository, rebuild PDF or HTML outputs, record figure inputs and parameters, and track submission and revision artifacts. Version control records changes so collaborators can review or restore earlier work.
Why use it?
It prevents confusing piles of renamed drafts and makes it clear which source files produced each figure or result. This is useful when several people collaborate or a paper goes through repeated revisions.

Skill for Claude Code

Written for Claude Code: allowed-tools in frontmatter.

Good fit Use it to structure a paper repository, rebuild PDF or HTML outputs, record figure inputs and parameters, and track submission and revision artifacts. Version control records changes so collaborators can review or restore earlier work.

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Install with agentmods
npx agentmods add skills/foryourhealth111-pixel/vibe-skills/manuscript-as-code
About the project

Vibe-Skills is a collection and routing system that helps AI agents discover, select, and coordinate specialized skills for completing tasks. It is intended for agents that need to organize workflows across many installed capabilities. The catalogue entries are skills and an agent belonging to this system.

foryourhealth111-pixel/Vibe-Skills · 3,235 stars · on GitHub

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add foryourhealth111-pixel/Vibe-Skills --skill manuscript-as-code
Clone the repo
git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for manuscript-as-code

README.md
[![agentmods](https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/manuscript-as-code/github.svg)](https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/manuscript-as-code)
Your own site
<a href="https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/manuscript-as-code"><img src="https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/manuscript-as-code/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for manuscript-as-code

Your own site · 80×15
<a href="https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/manuscript-as-code"><img src="https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/manuscript-as-code.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 43 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 527 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00043 $0.00527
Opus 5 $0.00022 $0.00264
Sonnet 5 $0.00009 $0.00105
Haiku 4.5 $0.00004 $0.00053

Measured 8d ago against content hash 81de88373ee7, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

manuscript-as-code scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

bundled/skills/manuscript-as-code/SKILL.md · 59 lines

What it actually says

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)

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/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)
Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 8d ago First seen · 59 lines · 43 tokens per session scan A 81de88373ee7

Subscribe to this mod's changes

manuscript-as-code is a skill published in the GitHub repository foryourhealth111-pixel/Vibe-Skills (3,235 stars, last pushed 11d ago), licensed Apache-2.0. It adds 43 tokens to every session and 527 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.