bedapub / bedapub/besca

Issue with sig.read_annotconfig in cell_type

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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!

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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

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