aga_compare_paths: KeyError: 'aga_groups' and KeyError: 'aga_groups_order_original'
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
Hi,
I am following the example robustness.ipynb and I get the errors
KeyError: 'aga_groups' and KeyError: 'aga_groups_order_original'
when using the function aga_compare_paths in scanpy 0.4.4.
I read that aga_groups disappeared in version 0.3, but looks like aga_compare_paths is still using it?
Many thanks,
Maria
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with robustness.ipynb and the aga_compare_paths function in the scanpy 0.4.4 code. Trace where aga_groups and aga_groups_order_original are read, then reproduce the example to confirm the failure. Done means the example runs without either KeyError and the comparison produces its expected result.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100