uvx paper-pilot

pip install paper-pilot

graph LR
    A[Prompt] --> B[Search 6 databases]
    B --> C[Resolve OA PDFs]
    C --> D[Download & read]
    D --> E[Extract evidence]
    E --> F[Render figures]
    F --> G[Markdown report]
    G --> H[Zotero sync]

Research retrieval-augmented generation, deep-read the top papers, and compare the methods.

{
  "mcpServers": {
    "paper-pilot": {
      "command": "uv",
      "args": ["--directory", "/path/to/paper-pilot", "run", "paper-pilot"],
      "env": {
        "OPENALEX_EMAIL": "you@example.com",
        "UNPAYWALL_EMAIL": "you@example.com",
        "ZOTERO_LOCAL": "true",
        "SCIHUB_ENABLED": "false"
      }
    }
  }
}

claude mcp add --scope user paper-pilot -- uv --directory /path/to/paper-pilot run paper-pilot

[mcp_servers.paper_pilot]
command = "uv"
args = ["--directory", "/path/to/paper-pilot", "run", "paper-pilot"]

[mcp_servers.paper_pilot.env]
OPENALEX_EMAIL = "you@example.com"
ZOTERO_LOCAL = "true"

paper-pilot --transport streamable-http --host 127.0.0.1 --port 8000

SCIHUB_ENABLED=true

OPENALEX_EMAIL=you@example.com        # Required for polite API access
UNPAYWALL_EMAIL=you@example.com       # Required for OA resolution
SEMANTIC_SCHOLAR_API_KEY=             # Optional, higher rate limits

# Local Zotero
ZOTERO_LOCAL=true
ZOTERO_LIBRARY_TYPE=user

# Web Zotero API (alternative)
ZOTERO_LIBRARY_ID=
ZOTERO_API_KEY=

# Sci-Hub (disabled by default)
SCIHUB_ENABLED=false

# Storage
PAPER_PILOT_DATA_DIR=./data

# Institutional networks
HTTP_PROXY=
HTTPS_PROXY=
SSL_CERT_FILE=

src/paper_pilot/
  server.py              MCP tools and pipeline orchestration
  config.py              Environment and settings
  services/
    academic.py          Multi-source scholarly search
    open_access.py       OA resolution and PDF downloads
    scihub.py            Sci-Hub paper resolution (opt-in)
    deep_read.py         Full-text extraction and page rendering
    zotero.py            Local and web Zotero integration
    reporting.py         Markdown report generation
    libgen.py            Supplementary LibGen support