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CLI Reference

ScholarAIO is designed to work best through an AI coding agent, but the CLI remains useful for scripting, inspection, and quick queries.

The authoritative source is always:

scholaraio --help
scholaraio <command> --help

The command groups below are aligned with the current codebase.

Core Commands

scholaraio index
scholaraio search
scholaraio search-author
scholaraio show
scholaraio embed
scholaraio vsearch
scholaraio usearch
scholaraio fsearch
scholaraio top-cited
  • search performs keyword search.
  • vsearch performs semantic vector search.
  • usearch performs fused keyword + semantic retrieval.
  • fsearch searches across the main library, proceedings, explore databases, and arXiv.
  • show supports layered reading from metadata to full text.

Ingest And Enrich

scholaraio pipeline [preset]
scholaraio enrich-toc
scholaraio enrich-l3
scholaraio backfill-abstract
scholaraio refetch
scholaraio translate
scholaraio attach-pdf
  • pipeline is the main composable ingest entrypoint.
  • Current preset values are full, ingest, enrich, and reindex.
  • Run scholaraio pipeline --help for pipeline options such as --steps, --dry-run, --no-api, and --rebuild.

Graph, Topics, And Explore

scholaraio refs
scholaraio citing
scholaraio shared-refs
scholaraio topics
scholaraio explore
  • Use refs, citing, and shared-refs for citation-graph analysis.
  • Use topics for BERTopic-based topic modeling and exploration.
  • Use explore for OpenAlex-backed literature exploration outside the main library.

Import, Export, And Workspaces

scholaraio import-endnote
scholaraio import-zotero
scholaraio export
scholaraio ws
  • import-endnote and import-zotero bring existing libraries into ScholarAIO.
  • export handles BibTeX, RIS, Markdown, and DOCX export.
  • ws manages paper subsets for focused projects and writing workflows.

Scientific Runtime And Documents

scholaraio toolref
scholaraio arxiv
scholaraio document
scholaraio style
  • toolref provides versioned scientific tool documentation lookup.
  • Current toolref subcommands are fetch, show, search, list, and use.
  • arxiv supports arXiv search and PDF fetch.
  • document provides Office-document utilities such as inspection.
  • style manages citation styles.

Audit, Setup, And Runtime Inspection

scholaraio audit
scholaraio repair
scholaraio rename
scholaraio setup
scholaraio insights
scholaraio metrics
scholaraio proceedings
scholaraio citation-check
  • setup is the environment check and setup wizard entrypoint.
  • insights analyzes research behavior such as hot keywords and reading trends.
  • metrics shows LLM token and runtime usage.
  • proceedings provides dedicated proceedings helpers.
  • citation-check verifies whether citations in text are backed by the local library.

Use the agent for the full workflow, and fall back to CLI commands when you want:

  • fast scripted access
  • a precise diagnostic check
  • direct inspection of intermediate results
  • reproducible command-line automation