paper-assembly

Q: How do I install paper-assembly?

Run npx skills add https://github.com/lingzhi227/agent-research-skills --skill paper-assembly in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/paper-assembly/ (personal) or .claude/skills/paper-assembly/ (project).

by lingzhi227Education & Science

Orchestrate the full paper pipeline end-to-end. Manage state propagation between phases (literature → plan → code → experiments → figures → tables → writing → review), support checkpointing and resumption. Use for assembling a complete paper from components.

Installs: 1.6K
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Install

Works with every agent the skills CLI supports.

npx skills add https://github.com/lingzhi227/agent-research-skills --skill paper-assembly

01
Install
Run the command in your project. The CLI asks which agents to install for.
02
Describe the task
Ask your agent for something this skill covers. It loads paper-assembly automatically when relevant.
03
Review the result
The agent follows the SKILL.md steps, scripts and references bundled with the skill.

SKILL.md

The instructions your agent reads when the skill is triggered.

Paper Assembly

Orchestrate the entire paper pipeline end-to-end with state management and checkpointing.

Input

$0 — Paper project directory or paper plan

References

Orchestration patterns and state management: ~/.claude/skills/paper-assembly/references/orchestration-patterns.md

Scripts

Check pipeline completeness

python ~/.claude/skills/paper-assembly/scripts/assembly_checker.py --dir paper/ --output checkpoint.json
python ~/.claude/skills/paper-assembly/scripts/assembly_checker.py --dir paper/ --verbose

Scans paper directory, checks 9 pipeline phases, reports missing artifacts, suggests next steps.

Workflow

Step 1: Assess Current State

Scan the paper directory for existing artifacts
Identify which phases are complete vs pending
Build a dependency graph of remaining work

Step 2: Execute Pipeline Phases

Run phases in dependency order:

Phase	Skill	Input	Output
1. Literature	literature-search, literature-review	Topic	Knowledge base, BibTeX
2. Planning	research-planning	Knowledge base	Paper structure, task list
3. Code	experiment-code	Plan	Training/eval pipeline
4. Experiments	experiment-design	Code	Results JSON/CSV
5. Figures	figure-generation	Results	PNG figures
6. Tables	table-generation	Results	LaTeX tables
7. Writing	paper-writing-section	All above	main.tex sections
8. Citations	citation-management	Draft	references.bib
9. Formatting	latex-formatting	Draft	Formatted LaTeX
10. Compilation	paper-compilation	All	PDF
11. Review	self-review	PDF	Review scores

Step 3: State Propagation

After each phase completes:

Save output artifacts to the paper directory
Propagate results to downstream phases
Update the progress checkpoint file

Step 4: Quality Gates

Before proceeding to the next phase:

Verify all required outputs exist
Check for consistency (e.g., all cited keys in .bib)
Validate figures/tables match experimental results

Step 5: Final Assembly

Merge all sections into main.tex
Verify all \includegraphics files exist
Verify all \cite keys exist in .bib
Compile to PDF
Run self-review for quality check

Orchestration Patterns

Sequential Pipeline (AI-Scientist)

generate_ideas → experiments → writeup → review

Multi-Agent State Broadcasting (AgentLaboratory)

# Propagate results to all downstream agents
set_agent_attr("dataset_code", code)
set_agent_attr("results", results_json)

Copilot Mode (AgentLaboratory)

Human can intervene at any phase boundary for review/correction.

Checkpoint Format

{
  "project": "paper-name",
  "phases_completed": ["literature", "planning", "code"],
  "current_phase": "experiments",
  "artifacts": {
    "literature": "knowledge_base.json",
    "plan": "research_plan.json",
    "code": "experiments/",
    "results": null
  },
  "last_updated": "2024-01-15T10:30:00Z"
}

Rules

Never skip phases — each depends on previous outputs
Save checkpoints after every phase completion
Human review is recommended at phase boundaries
All numbers in the paper must trace to actual experiment logs
Re-run downstream phases if upstream changes

Related Skills

Upstream: all other skills (this is the orchestrator)
Downstream: paper-compilation, self-review
See also: research-planning

FAQ

What does the paper-assembly skill do?

How do I install paper-assembly?

Run npx skills add https://github.com/lingzhi227/agent-research-skills --skill paper-assembly in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/paper-assembly/ (personal) or .claude/skills/paper-assembly/ (project).

Which AI agents can use paper-assembly?

Any agent that supports the open Agent Skills format (a folder with a SKILL.md file), including Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Windsurf, Cline, OpenCode and more.

Is paper-assembly safe to install?

No partner security audit is available yet. Skills can run commands and scripts, so read the SKILL.md and any bundled files before installing.

Who maintains paper-assembly?

It is published by lingzhi227 in lingzhi227/agent-research-skills. It has 1,582 recorded installs.