CLI Reference

All commands use the autob executable.

`autob init`

Create or update ~/.autob/config.json.

Prompts for provider, API key, base URL when needed, model, timeout, and optional connectivity check.

Exit code: 0 on success; non-zero for invalid input, file write errors, or unexpected runtime errors.

`autob config show`

Show merged global/project configuration with source annotations and redacted API key.

Use this command to verify whether LLM inference can run. apiKey, baseUrl, and model must all be set after merging.

Exit code: 0 on success; non-zero for invalid JSON or validation errors.

`autob update [--check]`

Check for or install the latest published autobiology-cli package.

Options:

--check: check npm for a newer package and print the update notice without installing.

Without --check, the command runs npm install -g autobiology-cli@latest through npm without shell interpolation.

AutoBiology also checks for updates around normal CLI startup and caches the result for 24 hours in ~/.autob/update-check.json. Set AUTOB_DISABLE_UPDATE_CHECK=1 to skip automatic checks in CI or offline environments.

`autob run <sop-file> -o <output-dir>`

Run atomize, hypergraph, requirements, infer, and review in order.

Options:

-o, --output <dir>: required output directory.
--interactive: enable interactive candidate review in TTY sessions.

Exit code: 0 on success; non-zero for unreadable input, invalid JSON artifacts, output write errors, or unexpected runtime errors.

`autob atomize <sop-file> -o <output-dir>`

Parse SOP text into 01-ops.json.

`autob hypergraph <op-table> -o <output-dir>`

Convert 01-ops.json into 02-nodes.json and 03-hyperedges.json.

`autob requirements <nodes-file> <hyperedges-file> -o <output-dir>`

Generate deterministic requirements into 04-requirements.json.

`autob infer <requirements-file> -o <output-dir>`

Add LLM-assisted candidate requirements when JSON config is complete. Without LLM config, this command records a clarification and preserves existing requirements.

`autob review <requirements-file> -o <output-dir>`

Generate coverage artifacts, report, diagrams, and optional candidate review.

Options:

-o, --output <dir>: required output directory.
--interactive: prompt for candidate decisions in TTY sessions.

Help

autob --help
autob <command> --help