cluster-only ignores --no-viz flag and GRAPHIFY_VIZ_NODE_LIMIT env var on graphs ≥ 5000 nodes (v0.7.7)

[lijingwu2026]

Summary

graphify cluster-only always invokes to_html() regardless of --no-viz flag or GRAPHIFY_VIZ_NODE_LIMIT=0 env var. On graphs with ≥ 5000 nodes this raises ValueError and aborts the run after the new clusters are written to graph.json but before .graphify_labels.json is saved, leaving the graph in an inconsistent state.

Reproduce

Tested on graphifyy 0.7.7 (Python 3.13.12, macOS).

# graph.json with 7060 nodes, 22213 edges
graphify cluster-only . --no-viz                    # crashes
GRAPHIFY_VIZ_NODE_LIMIT=0 graphify cluster-only .   # crashes

Expected

Either flag/env should bypass to_html() entirely. Per v0.6.6 release notes:

--no-viz flag now works in cluster-only path — removes stale graph.html when passed (#565)
GRAPHIFY_VIZ_NODE_LIMIT env var — override the 5000-node HTML threshold (set to 0 to disable viz entirely, useful for CI) (#565)

Actual

Loading existing graph...
Graph: 7060 nodes, 22213 edges
Re-clustering...
Traceback (most recent call last):
  File "/opt/homebrew/bin/graphify", line 6, in <module>
    sys.exit(main())
  File ".../graphify/__main__.py", line 1415, in main
    to_html(G, communities, str(out / "graph.html"), community_labels=labels or None)
  File ".../graphify/export.py", line 395, in to_html
    raise ValueError(...)
ValueError: Graph has 7060 nodes - too large for HTML viz. Use --no-viz or reduce input size.

Likely cause

__main__.py:1415 calls to_html(...) unconditionally on the cluster-only branch — looks like the flag/env guards present elsewhere are missing on this code path (regression vs v0.6.6, or the v0.6.6 fix never reached cluster-only).

Side effect

graph.json is saved with the new cluster IDs (good), but .graphify_labels.json is not written (bad — community label persistence relies on it, per v0.6.6 fix #558). Subsequent --update runs lose human-readable labels.

Environment

• graphifyy 0.7.7 (pipx install)
• Python 3.13.12
• macOS Darwin 25.4.0
• Graph: 7060 nodes / 22213 edges / 314 communities

Workaround

None — graphs ≥ 5000 nodes cannot run cluster-only at all on v0.7.7.

[safishamsi]

Fixed in v0.7.8: cluster-only now loads existing .graphify_labels.json before clustering and writes it back after — human-readable labels survive re-clustering instead of resetting to 'Community N'.