Paper Pilot

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