Graph node still exists when deleting multiple files

[lau1944]

I am refactoring the current codebase, with a lot of deletion of the files, and i use graphify update . command to update the graph. But taking a look on the result, some nodes are deleted but it still exists on the graph.

What is the best practice in case of the file deletion, do I need to delete the /graphify-out and rebuild it again?

[safishamsi]

Good question — and I dug into this on current v8 (0.9.13) but couldn't reproduce genuine stale nodes. Here's what I found and the best practice.

graphify update . does handle deletions — you do not need to delete graphify-out/ and rebuild. I verified three scenarios, all correct:

• Delete several files at once → their nodes are all evicted.
• Delete a file whose classes/functions are still imported by a surviving file → the deleted file's nodes are still evicted.
• Delete a base class's file while a surviving subclass still inherits from it → the base's real node (and its methods) are evicted.

The one case where a node looks like it 'survives': if a surviving file still references a symbol from the deleted file (e.g. class Sub(Base) after you delete base.py), you'll see a Base node remain — but check its source_file: it'll be empty (""), not base.py. That's a fresh unresolved-reference stub standing in for the now-external Base your code still names — the original base.py-sourced node was removed. It's expected (your code does still reference Base); once you delete the reference too, it goes away.

If you're seeing a genuinely stale node — one whose source_file still points at a file you deleted — that's a real bug and I'd like to fix it. Could you share:

1. your graphify version (graphify --version),
2. whether you ran plain graphify update . or the git-hook path, and
3. one stale node's source_file value from graph.json after the update?

Leaving this open pending that. If it's the sourceless-stub case above, it's working as intended.