The dependencies and dependents in the Insights -> Dependency graph of my repository do not match the expectations

[myhloli]

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Bug

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repository：https://github.com/opendatalab/MinerU
There is a pyproject.toml file in the root directory of my repository, and it complies with the PEP standards.
However, the Dependency Graph feature is completely malfunctioning. I cannot see the PyPI packages that my project depends on in the "dependencies" section, nor can I see other projects that depend on our project in the "dependents" section (the PyPI package name "mineru" is not available as an option in dependents).

[github-actions[bot]]

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[AniXDex]

Hi @myhloli

This is a known problem with GitHub's dependency detection system. Even with PEP 621 compliant pyproject.toml files, the dependency graph often fails to work properly.

Quick Fixes to Try:
Force Re-indexing

Make a small commit to your pyproject.toml (add a comment)

This sometimes triggers GitHub to re-scan dependencies

Add requirements.txt

Generate: pip freeze > requirements.txt

Commit this file - GitHub handles requirements.txt more reliably than pyproject.toml

Verify Format

Ensure dependencies are under [project] section with proper array format

Check file is in repository root (which yours is)

Root Cause
GitHub's PEP 621 support is still buggy despite being officially supported since 2023. The dependents detection is particularly unreliable for PyPI packages.

Best Solution
File a GitHub Support ticket mentioning:

Repository URL: https://github.com/opendatalab/MinerU

PyPI package "mineru" not showing in dependents

Dependencies not appearing despite valid pyproject.toml

This usually requires manual intervention from GitHub's team to fix the indexing.

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