Honest Scholar

Research you can defend.

Honest Scholar helps you keep research honest — especially now that AI is in the loop. You (not the AI) make and sign off every material decision, and you must be able to explain and defend the work; the tool keeps the accounts, advises, and probes. It supports honest, disclosable AI-assisted research — it does not certify that any work is honest.

This package is the CLI / tooling behind the honest-scholar Claude Code plugin. The plugin (skills + methodology) stays pure-markdown; this package provides the honest-scholar command it calls — literature, dataset, defend, backlog, and doctor — installed isolated, so it never touches your project's ML environment.

Install

uv tool install honest-scholar     # recommended (isolated tool env)
# or: pipx install honest-scholar
# or: pip install honest-scholar

honest-scholar --version
honest-scholar doctor              # reports python / uv / rclone

Documentation: https://honest-scholar.science/

CLI

honest-scholar --version
honest-scholar doctor                                           # environment report
honest-scholar literature resolve|cites|refs|enrich|neighbors   # citation graph (OpenAlex + S2)
honest-scholar dataset    validate|ingest|emit                  # manifest + Croissant
honest-scholar dataset    fetch|verify|mirror|audit             # SHA-256 retrieval + rclone mirror
honest-scholar defend     record                                # understanding-status record
honest-scholar backlog    park|add|list|rank|promote|drop       # exploration backlog
honest-scholar keys       set|list|check|unset|path             # API-key & credential store

Every command is implemented and emits JSON (the skills parse it). Network- and rclone-backed commands degrade gracefully when a key or the binary is absent.

API keys & credentials

Some services throttle hard without a key. Providing one is optional (the tooling degrades gracefully) but lifts the ceiling:

Keys live in a CLI-managed JSON store at .honest-scholar/keys.json (gitignored, created 0600), read with os.environ > store > unset precedence, so an environment variable always wins. Manage it with keys:

honest-scholar keys set S2_API_KEY        # hidden prompt, or reads piped stdin
echo "$MY_KEY" | honest-scholar keys set S2_API_KEY
honest-scholar keys set < keys.json       # a JSON object sets many at once
honest-scholar keys list                  # presence + source (never the value)
honest-scholar keys check | unset | path

The value is read only from stdin or a hidden prompt — never argv — so it never hits your shell history or the process list, and list/check/doctor report presence only.

Plaintext at rest. The store is not encrypted; gitignore + 0600 limit exposure but are not a vault. OS-keychain backing is a planned follow-up (#49).

Learn more

• Documentation: https://honest-scholar.science/
• User guide: https://honest-scholar.science/get-started/user-guide
• Plugin, source & full design record: https://github.com/davorrunje/honest-scholar
• Disclose your AI use & cite Honest Scholar: https://github.com/davorrunje/honest-scholar/blob/main/DISCLOSURE.md

Changelog

https://github.com/davorrunje/honest-scholar/blob/main/CHANGELOG.md

License

Apache-2.0.