Issue with sig.read_annotconfig in cell_type
- Dominant language
- Python
- Stars
- 50
- Forks
- 17
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 3
Description
Hi all, I've encounterd an issue with the **workbooks/celltype_annotation_besca.ipynb** notebook. Running the `sigconfig, levsk = bc.tl.sig.read_annotconfig(configfile)` chunk returns an empty `levsk` object.
```
-----
anndata 0.10.7
besca 2.5.3
matplotlib 3.7.1
numpy 1.26.4
pandas 2.2.2
scanpy 1.10.1
scipy 1.13.0
seaborn 0.13.2
sinfo 0.3.4
-----
IPython 8.18.1
jupyter_client 8.6.1
jupyter_core 5.7.2
jupyterlab 4.1.6
notebook 7.1.2
-----
Python 3.9.19
```
Many thanks!
Contributor guide
No contributing guide indexed for this repository
Research direction
Start with workbooks/celltype_annotation_besca.ipynb and run the sig.read_annotconfig(configfile) chunk using the reported environment. Trace why the returned levsk object is empty, then verify that the notebook produces the expected non-empty result.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100