Dataset creation reproduction fails due to updated cell ontology

[gdewael]

Hi!

When running 01_download_data.ipynb, the notebook fails at the point where cell types are being filtered for being a subset of "native cell" (cell_types_to_remove = obs[~obs.cell_type.isin(find_child_nodes('native cell'))].cell_type.unique().tolist()).

I suspect this is due to the fact that the cell ontology has been updated since the writing of this notebook?
Can you specify which release version of the cell ontology has been used when creating the data (and update the link in the notebook accordingly)?

Gaetan

[felix0097]

Hi @gdewael,

sorry for the late reply! I've fixed the cell ontology version in the latest version of the notebook on the devel branch.
I checked it on my side, everything should run without errors again. Let me know if you have any further issues

Best,
Felix

[gdewael]

Thanks for the response!