Graphify-Labs/graphify · error · ValueError

graph.json contains 0 nodes

Error message

graph.json contains 0 nodes

What it means

Graph-existence preflight in the /graphify path command of the aider fragment (tools/skillgen/fragments/core/aider.md:1062). Shortest-path queries load graphify-out/graph.json via networkx json_graph; the guard raises SystemExit(1) up front if that file is missing, instead of letting the loader throw a confusing FileNotFoundError.

Source

Thrown at graphify/callflow_html.py:1659

    if not paths["graph"].exists():
        raise FileNotFoundError(
            f"graphify output not found: {paths['graph']}. "
            "Run graphify first or pass --graph /path/to/graph.json."
        )

    # Load data
    nodes, edges, hyperedges, meta = load_graph(paths["graph"])
    labels = load_labels(paths["labels"])
    lang = detect_lang(args.lang, nodes, labels)
    if paths["sections"]:
        sections = load_sections(paths["sections"])
    else:
        sections = derive_sections_from_communities(nodes, labels, lang, args.max_sections)
    sections = normalize_sections(sections, lang)
    report_text = load_report(paths["report"])

    if not nodes:
        raise ValueError("graph.json contains 0 nodes")
    if len(sections) <= 1:
        raise ValueError("no sections defined")

    if verbose and len(nodes) >= 5000:
        print("WARNING: Large graph -- Mermaid rendering may be slow. Consider --max-sections 5.", file=sys.stderr)

    node_ids = {node.get("id") for node in nodes}
    missing_endpoint_edges = [edge for edge in edges if edge.get("source") not in node_ids or edge.get("target") not in node_ids]
    if verbose and missing_endpoint_edges:
        print(f"WARNING: {len(missing_endpoint_edges)} edges reference nodes not present in graph.json.", file=sys.stderr)

    meta["project_name"] = infer_project_name(str(paths["graph"]), meta)
    meta["node_count"] = len(nodes)
    meta["edge_count"] = len(edges)
    meta["hyperedge_count"] = len(hyperedges)

    if args.output:
        output_path = Path(args.output).expanduser()

View on GitHub (pinned to 7fe58b0b0f)

Solutions

1. Build the graph first with /graphify <path>, then re-run the path query.
2. cd to the directory that contains graphify-out/ (the preflight and loader both use relative paths).
3. If the build previously failed, resolve that failure (extraction/shrink) before querying.
4. Rebuild the graph if it was cleaned: /graphify <path>.

Example fix

# before
/graphify path auth session
# ERROR: No graph found ...

# after
/graphify .
/graphify path auth session

from pathlib import Path

if not Path('graphify-out/graph.json').is_file():
    raise SystemExit('build the graph first: /graphify <path>')
print('ok - safe to run shortest-path traversal')

When it happens

Trigger: Invoking /graphify path <conceptA> <conceptB> when graphify-out/graph.json does not exist in the current working directory — graph never built, built under a different root, or deleted.

Common situations: Querying before any build; wrong cwd (relative path miss); graphify-out removed by git clean/CI; earlier build exited at the empty-graph or shrink guard so graph.json was never written.

Related errors

• graphify output not found: {paths['graph']}. Run graphify fi
• no sections defined
• deduplicate_entities: nodes span multiple repos {sorted(repo
• file_hash requires a file, got: {p}
• graph.json {p} is {size} bytes, exceeds {_MERGE_MAX_BYTES}-b

AI-assisted analysis of Graphify-Labs/graphify@7fe58b0b0f (2026-08-14). Data as JSON: /api/errors/8d2eff75f3f81363. Report an issue: GitHub.