heliosdb-nano-code-graph

name	heliosdb-nano-code-graph
description	Index a repository's source code as an AST symbol graph in HeliosDB-Nano. Covers grammar registration (Rust / Python / TypeScript / Go / Markdown / SQL), full-project indexing (`code_index`), LSP-shaped queries (`lsp_definition`, `lsp_references`, `lsp_call_hierarchy`, `lsp_hover`), the git-hook helper (`heliosdb-nano code-graph hook`), and the `_hdb_code_symbols` / `_hdb_code_symbol_refs` tables. Use this when the user wants AI-grade "where is this defined / used / called" queries across a codebase, or wants to wire a code-graph into a Claude Code / MCP workflow.
allowed-tools	Bash(heliosdb-nano *), Bash(git *), Read

Code-Graph Indexing

When to use

• Build an index over a project's source so an AI agent can answer "definition", "references", "callers", "hover" with grounded results.
• Run an MCP server (heliosdb-nano-mcp) that exposes code-graph queries.
• Pair the index with embeddings (code-embed feature) for semantic + structural search.

Prerequisites

• Cargo feature: code-graph required.

  cargo install heliosdb-nano --features code-graph
  

• For embeddings: add --features code-embed.
• For MCP serving: add --features mcp-endpoint.

Verify:

heliosdb-nano code-graph --help \
  && echo "code-graph: ENABLED" \
  || echo "rebuild with --features code-graph"

Verbs

Verb	Surface	One-liner
git-hook ingest	CLI	git diff-tree --no-commit-id --name-only -r HEAD | heliosdb-nano code-graph hook --data-dir .helios-index/heliosdb-data --source-table src
register grammar (lib)	Rust	db.register_grammar("rust", tree_sitter_rust::language())?
list registered (lib)	Rust	db.registered_grammars()
project index (lib)	Rust	let stats = db.code_index()?;
LSP: definition	Rust	db.lsp_definition("rust", "src/foo.rs", line, col)?
LSP: references	Rust	db.lsp_references("rust", "src/foo.rs", line, col)?
LSP: call hierarchy	Rust	db.lsp_call_hierarchy(...)?
LSP: hover	Rust	db.lsp_hover(...)?
refresh content hash	Rust	db.code_graph_merkle_refresh()?
query symbol table	SQL	SELECT * FROM _hdb_code_symbols WHERE name = 'foo'
query refs	SQL	SELECT * FROM _hdb_code_symbol_refs WHERE from_symbol = 42

Recipes

Recipe 1: One-shot full-repo index (Rust embedded)

use heliosdb_nano::EmbeddedDatabase;

let db = EmbeddedDatabase::new("./.helios-index/heliosdb-data")?;

// Built-in grammar registration is automatic for the languages compiled
// in via the `code-graph` feature; you can also register custom grammars:
// db.register_grammar("kotlin", tree_sitter_kotlin::language())?;

// Tell the indexer where to find your sources (you maintain a `src` table):
db.execute("CREATE TABLE IF NOT EXISTS src (path TEXT PRIMARY KEY, body TEXT, lang TEXT)")?;
// (populate src however you want; for git-tracked repos see Recipe 3)

let stats = db.code_index()?;
println!("symbols: {}, refs: {}, files: {}/{} ({} unchanged, {} skipped)",
    stats.symbols_written, stats.refs_written,
    stats.files_parsed, stats.files_seen,
    stats.files_unchanged, stats.files_skipped);

Recipe 2: LSP-style queries

// "definition of the symbol at line 42, column 18 in src/foo.rs"
let defs = db.lsp_definition("rust", "src/foo.rs", 42, 18)?;
for d in defs {
    println!("{}:{}:{}", d.path, d.line, d.col);
}

// "every reference to that symbol"
let refs = db.lsp_references("rust", "src/foo.rs", 42, 18)?;

// "who calls fn `bar`"
let calls = db.lsp_call_hierarchy("rust", "src/foo.rs", 42, 18, /*incoming=*/true)?;

// "hover info" (signature, doc comment)
let hov = db.lsp_hover("rust", "src/foo.rs", 42, 18)?;

Recipe 3: Git hook — incremental on every commit

mkdir -p .helios-index
heliosdb-nano init .helios-index/heliosdb-data

# .git/hooks/post-commit (or pre-push)
#!/usr/bin/env bash
git diff-tree --no-commit-id --name-only -r HEAD \
  | heliosdb-nano code-graph hook \
      --data-dir .helios-index/heliosdb-data \
      --repo-root . \
      --source-table src
chmod +x .git/hooks/post-commit

Each commit prints CodeIndexStats { files_seen, files_parsed, files_unchanged, files_skipped, symbols_written, refs_written }.

Recipe 4: Force-reparse (rebuild from scratch)

# 1. drop the index data dir
rm -rf .helios-index/heliosdb-data
heliosdb-nano init .helios-index/heliosdb-data

# 2. feed every tracked file (not just diff-tree)
git ls-files \
  | heliosdb-nano code-graph hook \
      --data-dir .helios-index/heliosdb-data \
      --source-table src

Use this when adding a new grammar (existing files need re-parsing) or after upgrading Nano (schema bumps).

Recipe 5: Inspect via SQL

-- top-10 most-referenced symbols in the project
SELECT s.name, COUNT(r.id) AS refs
  FROM _hdb_code_symbols s
  JOIN _hdb_code_symbol_refs r ON r.to_symbol = s.id
 GROUP BY s.name
 ORDER BY refs DESC LIMIT 10;

-- find every symbol called `parse` in Rust
SELECT * FROM _hdb_code_symbols
 WHERE name = 'parse' AND lang = 'rust';

Recipe 6: Branch-scoped queries (FR-3 ON BRANCH '<n>')

LSP queries can be pinned to a branch — useful for asking "what does this look like on the feature-x branch":

let defs = db.lsp_definition_on_branch("rust", "src/foo.rs", 42, 18, "feature-x")?;

The branch guard restores the previous active branch on Drop, so any later queries continue against the original branch.

Pitfalls

• heliosdb-nano code-graph hook is opt-in — it's only present if the binary was built with --features code-graph. If users see "unknown subcommand", reinstall.
• Languages: Phase-1 ships Rust, Python, TypeScript, Go, Markdown, SQL. Adding a language requires registering its tree-sitter grammar via register_grammar.
• Large repos: first full index can take minutes. Subsequent commits are fast (Merkle-hashed file diffing skips unchanged files — files_unchanged in the stats).
• bulk_insert_tuples direct-write path: ingest writes via the in-process bulk path, not via INSERT … VALUES. Don't try to ingest from outside the same OS process while the indexer is running.
• FK in transaction (v3.21.x bug, fixed in v3.22.1): cascading deletes inside a transaction once raised phantom FK violations. Pin to >=3.22.1 for the per-file delete-stale path.
• Cross-process INSERT … ON CONFLICT (path) DO UPDATE is still racy. The hook subcommand and SDK both run in-process, so this only matters if you wrap your own multi-process ingester.

See also

• heliosdb-nano-graph-rag — wraps the symbol graph with seed/expand/rerank for RAG retrieval.
• heliosdb-nano-mcp — exposes code-graph results to AI agents via MCP tools.
• heliosdb-nano-vector — pair with embeddings for semantic similarity over symbols.
• docs/code_graph/{overview,pilot,troubleshooting}.md — design + troubleshooting docs.
• tests/code_graph_phase2.rs — acceptance fixtures (incremental, force-reparse, populated KB).