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[Bug]: Python files can disappear from the graph when a class is used before it's defined

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@Mpasha17 is already working on this.

Since Oct 11, 2026.

  • #4343 by @Mpasha17 — open

Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
72/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Active
Tech stack
python
Domain
devtools

Research direction

Start by running graphify update . on the two-file reproduction in the issue and inspect graphify-out/graph.json to trace how the class reference before its definition affects file and class nodes. Find the Python parsing and graph construction entry points that handle those references; the issue does not name specific source files or tests. Done means widget.py remains in the graph, references resolve to its Widget class, and the missing call from Helper.make appears.

Written by the indexing model from the issue text.

Description

What's happening

In some Python projects, whole files go missing from the graph, and the classes inside them get tangled up. There's no error, so it's easy to miss.

I noticed it on rich: when I ran graphify update rich/rich, two of its main files, markdown.py and syntax.py, weren't in the graph at all.

When it happens:

  • the file itself disappears from the graph
  • the class with the same name as the file ends up "containing" itself and every other class in the file
  • other files that import it look like they import the class instead of the file
  • some calls made from inside that file are quietly left out

When it happens

All three of these at once:

  1. The file is directly in the folder you point graphify at, not in a subfolder
  2. It has a class with the same name as the file, like Widget in widget.py
  3. Something earlier in that file mentions the class before it's defined, like a type hint w: Widget

Naming a file after its main class is pretty common, like console.py with Console, so this shows up in real projects.

How to see it for yourself

Make a folder with these two files and run graphify update .:

widget.py

from __future__ import annotations

class Helper:
    def make(self, w: Widget) -> None:
        w.draw()

class Widget:
    def draw(self):
        return 1

app.py

from widget import Widget

def use(w: Widget):
    w.draw()

Then look at graphify-out/graph.json:

  • there's no widget.py node
  • Widget "contains" itself and Helper
  • app.py imports Widget the class instead of widget.py the file
  • the call from Helper.make to Widget.draw is missing, while the same call from app.py is there

What should happen

widget.py should be in the graph like any other file, and the Widget it mentions should just point to the class defined lower down in the same file.

How much it matters

I checked graphify's call links against Jedi on rich. On 0.9.85, with this fixed, graphify finds 54 more correct calls, going from 64.6% to 68.6%, with no wrong links added and none lost. Both missing files come back too.

Version: graphify 0.9.85 · macOS 26.4 · Python 3.14

Dominant language
Python
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Forks
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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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