CLI Reference¶

All commands follow the pattern python -m cli <subcommand> [options].

Core Research¶

Command	Description
`research`	Automatically search arXiv, download PDFs, extract text, and generate AI summaries
`import`	Import papers by arXiv ID, DOI, or paper UID. Supports batch import from file
`ingest`	Full import pipeline: fetch metadata, run deep analysis, generate embeddings, and sync the knowledge graph
`search`	Search papers by query, year, source, tag, or parse status
`list`	List papers with filtering, sorting, and multiple output formats
`status`	Show database and queue status

Knowledge Graph¶

Command	Description
`kg`	Query, visualize, and manage the research knowledge graph
`cite-graph`	Build and visualize citation relationships
`citation-chain`	Build and visualize citation relationships
`citations`	Display papers cited by or citing a given paper
`cite-backfill`	Find papers without citation records and fetch forward citations from OpenAlex
`cite-import`	Import citations from file
`cite-fetch`	Fetch citation data for papers
`cite-stats`	Show citation statistics

Analysis¶

Command	Description
`gap`	Analyze papers to identify research gaps and suggest questions
`hypothesize`	Generate research hypotheses with experiment designs and risk assessments
`trend`	Analyze paper distribution, keyword trends, and citation velocity
`benchmark`	Detect and compare benchmark results across papers
`compare`	Compare multiple papers side-by-side
`analyze`	Orchestrate gap→trend→story→hypothesis analysis
`insight`	Extract and manage key insights from papers
`review`	Generate structured literature review for a research topic
`litreview`	Generate and maintain living literature reviews from subscription papers
`route`	Classify a research query and execute routed commands using LLM or embedding similarity

Chat & Interaction¶

Command	Description
`chat`	Ask questions about papers in your library with source citations
`chat-tui`	Launch a full-screen terminal chat interface for RAG-powered Q&A
`session`	Start, list, and manage research sessions for context-aware conversations
`ask`	Ask research questions with context awareness
`repl`	Interactive REPL for chained KG/paper exploration

Research Workflow¶

Command	Description
`roadmap`	Generate structured research roadmaps from questions and hypotheses
`story`	Generate narrative understanding from research papers
`pipeline`	Run gap analysis, generate hypotheses, and optionally create experiment records
`question`	Track and manage research questions from gap detection and manual entry
`journal`	Track research activities and thoughts
`narrative`	Aggregate all research state into narrative threads with phase tracking
`subscribe`	Subscribe to research topics and get AI-scored paper recommendations

Evolution & Gene Pool¶

Command	Description
`evoskill`	EvoSkill benchmark-driven skill discovery
`paper2code`	Generate code from paper
`rag`	RAG pipeline: paper → code → tests → benchmark
`lean`	Translate research hypotheses into Lean 4 code and verify them
`replicate`	Track paper replication attempts and results
`experiment`	Run and track experiments

Agents & Autonomy¶

Command	Description
`agent`	Run autonomous deep research agent with gap detection and session persistence
`daemon`	Start/stop autonomous research daemon that watches arXiv, runs gap detection, and evolves Gene Pool
`scout`	Search ArXiv for recent papers, score against Gene Pool capsules, recommend relevant ones
`signal`	Match live event keyword against historical capsules, cross-reference market data
`discover`	Cross-reference Gene Pool capsules, market data, and events to find correlations

Data Management¶

Command	Description
`queue`	Show and manage pending papers
`cache`	Manage paper metadata cache
`dedup`	Deduplicate papers by exact match
`dedup-semantic`	Deduplicate papers by semantic similarity
`merge`	Merge duplicate papers
`export`	Export papers in BibTeX or JSON format
`path`	Plan research reading order based on citation graph and relevance
`read-queue`	Manage paper reading queue

Financial & News¶

Command	Description
`jin10`	Real-time financial data via Jin10 MCP service
`intel`	Aggregate Jin10 news, market quotes, Gene Pool state, and academic papers
`digest`	Generate weekly research summary
`report`	Generate fresh report with latest Gene Pool data
`watch`	Watch papers.json and auto-rebuild KG on changes

Utilities¶

Command	Description
`stats`	Show database statistics
`validate`	Analyze research question novelty and feasibility
`influence`	Compute citation velocity = forward_citations / age_years
`slides`	Generate presentation slides from papers
`postprocess`	Run 6-stage research deep dive pipeline on a paper
`visual`	Visualize papers and knowledge graphs
`demo`	Load sample papers and Gene Pool capsules to explore Rairos
`friction`	Detect research friction points — failed commands, abandoned workflows
`argue`	Build structured arguments from evidence

Web & Dashboard¶

Command	Description
`dashboard`	Launch FastAPI web interface and open browser
`web`	Alias for dashboard

Quick Reference¶

# Install
pip install -e ".[all]"
rairos --help                    # Show all commands

# Paper operations
python -m cli import 2601.00155
python -m cli search "attention"
python -m cli list --status done

# Research
python -m cli research "RLHF alignment" --limit 5
python -m cli gap --papers "2601.00155"
python -m cli chat-tui

# Knowledge graph
python -m cli kg --query "transformer"
python -m cli cite-graph 2601.00155

# Gene Pool
python -m cli scout --topic "mixture of experts"
python -m cli daemon start