/paper-assembly

name: paper-assembly
description: 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.
argument-hint: [paper-directory]

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

1. Scan the paper directory for existing artifacts 2. Identify which phases are complete vs pending 3. 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: 1. Save output artifacts to the paper directory 2. Propagate results to downstream phases 3. 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

1. Merge all sections into main.tex 2. Verify all \includegraphics files exist 3. Verify all \cite keys exist in .bib 4. Compile to PDF 5. 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](../paper-compilation/), [self-review](../self-review/)
• See also: [research-planning](../research-planning/)