papi

Original：🇺🇸 English
Translated

This skill should be used when the user wants to interact with their paper database — listing papers, searching content, showing paper details, adding papers, or exporting context. Matches queries like "search papers for X", "add this arXiv paper", "show equations from paper Y", "what papers do I have". Prefer CLI over MCP RAG tools for direct lookups.

7installs
Sourcehummat/paperpipe
Added on

NPX Install

npx skill4agent add hummat/paperpipe papi

Tags

Translated version includes tags in frontmatter
paper-managementcli-toolrag-systemarxiv-integrationdocument-retrieval

SKILL.md Content

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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

QuestionTool
"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"              # literal text match (fast, no LLM) — NOT regex by default!
papi search --rg --regex "pattern"    # regex patterns (add --regex explicitly)
papi search "query"                   # ranked BM25
papi search --hybrid "query"          # ranked + exact boost
papi search "query" -p paper1,paper2  # limit search to specific papers
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)

ToolSpeedOutputBest For
leann_search(index_name, query, top_k)
FastSnippets + file pathsExploration, finding which paper to dig into
retrieve_chunks(query, index_name, k)
SlowerChunks + formal citationsVerification, citing specific claims
papi ask "..."
SlowestSynthesized answerCross-paper questions, "what does literature say"
  • Check available 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 2303.13476 1706.03762 "Attention Is All You Need"  # multiple at once (mixed sources OK)
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}/
: 
equations.md
, 
summary.md
, 
source.tex
, 
notes.md
, 
paper.pdf
, 
figures/
.
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 
references/commands.md
for full command reference and per-file details.