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CLI reference

The binary is sciogen. Typer handles routing; all output goes through a Rich console. Only indexing shows the banner + progress flow; query commands print their result table and nothing else.

Every command here can also be run as python -m sciogen <command> — useful when the sciogen binary is not on PATH (see the quickstart troubleshooting section for how to fix PATH permanently).

sciogen / sciogen index [path]

Build or incrementally update the knowledge graph. Bare sciogen (no subcommand) is shorthand for sciogen index ..

Flag Default Effect
path . Project directory to index
--rebuild off Discard the existing index and rebuild from scratch (use after a schema change or embedder switch)

Output ends with the completion summary a coding agent reads:

✓ Done! 1,204 nodes · 3,456 edges · indexed in 4.2s
  Ready. Your codebase is now queryable.

Files that fail to parse are skipped with a single ⚠ line and logged to SQLite; indexing continues.

sciogen search <query>

Semantic or hybrid search.

Flag Default Effect
--path, -p . Indexed project directory
--mode, -m semantic semantic or hybrid (graph-expanded)
--granularity, -g all file | class | function | chunk
--top, -k 10 Number of results

sciogen callers <symbol>

Who calls a symbol.

Flag Default Effect
--path, -p . Indexed project directory
--depth, -d 1 Hops up the call chain
--min-confidence, -c 0.0 Drop edges below this confidence

sciogen impact <symbol>

Full blast radius if a symbol changes: transitive callers plus direct subclasses, implementors, tests, and mutators. Same flags as callers, with --depth defaulting to 5.

sciogen deps <file>

Direct files, transitive files, and external modules a file imports.

sciogen symbol <name>

Typed node info for one symbol plus its immediate relations.

Flag Default Effect
--path, -p . Indexed project directory
--file, -f — Narrow to a specific defining file when the name is ambiguous

sciogen explore [path]

Generate the interactive graph GUI and open it in the browser. path may be a subdirectory of an indexed project to scope the view. Writes a self-contained HTML file under .sciogen/ and opens it — no server. See architecture.md.

sciogen mcp [path]

Run the MCP server over stdio for agent integration. See mcp.md.

Global

Flag Effect
--version Print version and exit
--help Command help (instant — no heavy imports)