Graphify-Labs/graphify · error · SystemExit

ERROR: refused to shrink graphify-out/graph.json (existing g

Error message

ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).

What it means

Deliberate shrink-guard (#479) in the graphify build export step. to_json(G, communities, 'graphify-out/graph.json') returns False without writing when the new graph has fewer nodes than the existing graph.json; the wrapper prints this ERROR, exits 1, and skips writing GRAPH_REPORT.md and .graphify_analysis.json so no artifact misdescribes the persisted graph (#1392).

Source

Thrown at tools/skillgen/expected/graphify__skill-droid.md:434

    raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
gods = god_nodes(G)
surprises = surprising_connections(G, communities)
labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)

# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
if not wrote:
    print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')
    print('If this shrink is intentional (you deleted files), re-run a full build with --force.')
    raise SystemExit(1)
report = generate(G, communities, cohesion, labels, gods, surprises, detection, tokens, 'INPUT_PATH', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
analysis = {
    'communities': {str(k): v for k, v in communities.items()},
    'cohesion': {str(k): v for k, v in cohesion.items()},
    'gods': gods,
    'surprises': surprises,
    'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```

If this step prints `ERROR: Graph is empty`, stop and tell the user what happened - do not proceed to labeling or visualization.

Replace INPUT_PATH with the actual path.

View on GitHub (pinned to 7fe58b0b0f)

Solutions

1. Intentional shrink: re-run a full build with --force to overwrite graph.json.
2. Verify INPUT_PATH matches the original build root.
3. Compare new vs existing node counts to find which files dropped out of extraction.
4. Remove graphify-out/ and rebuild from scratch if the state is stale.

Example fix

# before: shrink refused
wrote = to_json(G, communities, 'graphify-out/graph.json')
if not wrote:
    print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')
    raise SystemExit(1)

# after: intentional shrink -> full rebuild with --force

import json
from pathlib import Path

existing = Path('graphify-out/graph.json')
if existing.exists():
    old = len(json.loads(existing.read_text(encoding='utf-8')).get('nodes', []))
    if G.number_of_nodes() < old:
        raise SystemExit(f'shrink {old}->{G.number_of_nodes()} refused; use --force full rebuild if intentional')

When it happens

Trigger: Exporting a graph smaller than the on-disk graph.json: rebuild after source deletion, INPUT_PATH pointing at a smaller tree than the original build, or extraction dropping files.

Common situations: Post-prune rebuilds; building a subdirectory against a repo-root graph.json; partial re-extracts; stale larger graph.json from earlier work.

Related errors

• ERROR: refused to shrink graphify-out/graph.json (existing g
• ERROR: refused to shrink graphify-out/graph.json (existing g
• ERROR: refused to shrink graphify-out/graph.json (fewer node
• ERROR: refused to shrink graphify-out/graph.json (existing g
• ERROR: refused to shrink graphify-out/graph.json (existing g

AI-assisted analysis of Graphify-Labs/graphify@7fe58b0b0f (2026-08-14). Data as JSON: /api/errors/b42f1653e4259c90. Report an issue: GitHub.