---

name: papi description: Help with paper references using paperpipe (papi). Use when user asks about papers, wants to verify code against a paper, needs paper context for implementation, or asks about equations/methods from literature. allowed-tools: Read, Bash, Glob, Grep

Paper Reference Assistant

Use this skill when the user:

• Asks "does this match the paper?" or similar verification questions
• Mentions a paper name, arXiv ID, or method from literature
• Wants to implement or verify an algorithm from a paper
• Asks about equations, formulas, or methods from scientific papers
• Needs paper context loaded into the conversation

Workflow

Decision Rules (Use the Cheapest Thing That Works)

1. Prefer papi show <paper> -l eq|tex|summary (prints to stdout); use direct files under {db}/papers/{name}/ if needed.
2. Prefer retrieval-only MCP chunks over full papi ask when you only need “top passages about X”.
3. Use papi ask only when explicitly requested to run a RAG backend (PaperQA2 via --backend pqa, or LEANN via --backend leann).

1. Find the paper database location

papi path

2. List available papers

papi list

Or search for specific topics:

papi search "surface reconstruction"

2b. Audit generated content (optional)

If summaries/equations/tags look suspicious, run an audit to flag obvious issues:

papi audit
papi audit --limit 10 --seed 0

2c. LLM configuration (optional)

export PAPERPIPE_LLM_MODEL="gemini/gemini-3-flash-preview"
export PAPERPIPE_LLM_TEMPERATURE=0.3

3. For code verification

1. Identify which paper(s) the code references (check comments, function names, README)
2. Run papi show {name} -l eq — compare symbol-by-symbol with implementation
3. If ambiguous, run papi show {name} -l tex for exact definitions
4. Check {db}/papers/{name}/notes.md for local implementation gotchas (or run papi notes {name})

4. For implementation guidance

1. Run papi show {name} -l summary for high-level approach
2. Run papi show {name} -l eq for formulas to implement
3. Cross-reference with papi show {name} -l tex if equation details are unclear

5. For cross-paper questions

papi search "query"      # fast text search
papi index               # build/update PaperQA2 index (backend: pqa)
papi ask "question"      # PaperQA2 RAG (backend: pqa, if installed)
papi index --backend leann
papi ask "question" --backend leann

Adding New Papers

papi add 2303.13476                           # name auto-generated
papi add https://arxiv.org/abs/2303.13476     # URLs work too
papi add 2303.13476 --name my-custom-name     # override auto-name
papi add 2303.13476 --update                  # refresh existing paper in-place
papi add 2303.13476 --duplicate               # add a second copy (-2/-3 suffix)
papi add --pdf /path/to/paper.pdf --title "Some Paper" --tags my-project  # local PDF ingest

See Also

Read commands.md in this skill directory for the full command reference.