Agent skill

papi

CLI reference for paperpipe (papi). Use BEFORE MCP RAG tools. For listing, searching, showing, adding papers.

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Install this agent skill to your Project

npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/development/papi

SKILL.md

Paper Reference Assistant (CLI)

Entry point skill. Use papi CLI first; MCP RAG tools only when CLI is insufficient.

For specialized workflows, invoke dedicated skills:

  • /papi-ask — RAG queries requiring synthesis
  • /papi-verify — verify code against paper
  • /papi-compare — compare papers for decision
  • /papi-ground — ground responses with citations
  • /papi-curate — create project notes

Setup

bash
papi path   # DB location (default ~/.paperpipe/; override via PAPER_DB_PATH)
papi list   # available papers
papi list | grep -i "keyword"  # check if paper exists before searching

When NOT to Use MCP RAG

  • Paper name known → papi show <paper> -l summary
  • Exact term search → papi search --rg "term"
  • Checking equations → papi show <paper> -l eq
  • Only use RAG when above methods fail or semantic matching required

Decision Tree

Question Tool
"What does paper X say about Y?" papi show X -l summary, then papi search --rg "Y"
"Does my code match the paper?" /papi-verify skill
"Which paper mentions X?" papi search --rg "X" first, then leann_search() if no hits
"Compare approaches across papers" /papi-compare skill or papi ask
"Need citable quote with page number" retrieve_chunks() (PQA MCP)
"Cross-paper synthesis" papi ask "..."

Search Commands

bash
papi search --rg "query"              # exact text (fast, no LLM)
papi search --rg --regex "pattern"    # regex (OR, wildcards)
papi search "query"                   # ranked BM25
papi search --hybrid "query"          # ranked + exact boost
papi ask "question"                   # PaperQA2 RAG
papi ask "question" --backend leann   # LEANN RAG
papi notes {name}                     # open/print implementation notes

Search Escalation (cheapest first)

  1. papi search --rg "X" — exact text, fast, no LLM
  2. papi search "X" — ranked BM25 (requires papi index --backend search first)
  3. papi search --hybrid "X" — ranked + exact boost
  4. leann_search() — semantic search, returns file paths for follow-up
  5. retrieve_chunks() — formal citations (DOI, page numbers)
  6. papi ask "..." — full RAG synthesis

MCP Tool Selection (when papi CLI insufficient)

Tool Speed Output Best For
leann_search(index, query, top_k) Fast Snippets + file paths Exploration, finding which paper to dig into
retrieve_chunks(query, index, k) Slower Chunks + formal citations Verification, citing specific claims
papi ask "..." Slowest Synthesized answer Cross-paper questions, "what does literature say"
  • Check indexes: leann_list() or list_pqa_indexes()
  • Embedding priority: Voyage AI → Google/Gemini → OpenAI → Ollama

Adding Papers

bash
papi add 2303.13476                   # arXiv ID
papi add https://arxiv.org/abs/...    # URL
papi add --pdf /path/to.pdf           # local PDF
papi add --pdf "https://..."          # PDF from URL
papi add --from-file papers.bib       # bulk import

Per-Paper Files

Located at {db}/papers/{name}/:

File Best For
equations.md Code verification
summary.md Understanding approach
source.tex Exact definitions
notes.md Implementation gotchas
figures/ Architecture diagrams, plots

If agent can't read ~/.paperpipe/, export to repo: papi export <papers...> --level equations --to ./paper-context/ Use --figures to include extracted figures in export.

See commands.md for full reference.

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