Follow-up to the file-ordering fix. The from-scratch build writes each node's
community field straight from cluster()'s enumerate() after a STABLE size-sort,
so the hundreds of equal-sized small communities in a sparse graph were ordered
by the partitioner's (not seed-stable) enumeration order. Their integer IDs
permuted run-to-run, which reads as 77-88% "community churn" in a per-node cid
diff even though the actual grouping is reproducible.
Add a tuple(sorted(nodes)) tiebreak to make the sort a total order, so an
identical grouping always yields identical community IDs. Verified: with the
partition returned in shuffled order across 5 runs, the node->cid map is now
identical. (A separate ~0.06% community-count drift remains - likely
non-canonical edge weights upstream - tracked separately.)
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- hooks.py: drop --path-format=absolute (added git 2.31), validate no newlines in path, anchor relative paths on repo root (#907)
- detect.py: seed save_manifest from existing manifest before loop so incremental callers don't erase untouched file entries (#917)
- cluster.py: drop round(..., 2) from cohesion_score so split threshold 0.05 fires correctly; add resolution param to _partition and cluster; add exclude_hubs_percentile to cluster with majority-vote reattachment (#919)
- report.py: format cohesion with :.2f for display
- __main__.py: wire --resolution and --exclude-hubs into extract and cluster-only commands (#919)
- C++ inheritance already written to disk by analysis agent (#915)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Use safe JSON serialization fallbacks for deterministic sort keys in clustering and graph canonicalization, and skip invalid community IDs with a stderr warning instead of raising during update rebuilds.
Co-authored-by: Cursor <cursoragent@cursor.com>
Make `graphify update` idempotent by skipping output rewrites when graph/report content is unchanged, add `update --no-cluster`, and preserve community IDs across runs via overlap-based remapping with deterministic partition inputs.
Co-authored-by: Cursor <cursoragent@cursor.com>
* fix: suppress graspologic ANSI output that breaks PowerShell scrolling
graspologic's leiden() emits ANSI escape sequences (progress bars,
colored warnings) that corrupt PowerShell 5.1's scroll buffer on
Windows, disabling vertical scrolling. Redirect stdout/stderr to
StringIO during leiden() calls to prevent any escape codes from
reaching the terminal.
Add 2 tests verifying cluster() produces no stdout/stderr output.
Fixes#19
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* docs: add PowerShell troubleshooting section to Windows skill
Document the PowerShell 5.1 scrolling issue and provide 4
workarounds: upgrade graphify, use Windows Terminal, reset
terminal, or uninstall graspologic to use Louvain fallback.
Fixes#19
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
style: replace all em dashes with hyphens
fix: explain hidden .graphify/ folder in skill output and README
fix: rename .graphify/ to graphify-out/ so output is visible by default
Safi