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theislab / cellrank_notebooks

Tutorials and examples for CellRank.
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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CytoTRACE tutorial outdated #43

Closed WeilerP closed 1 year ago

WeilerP commented 2 years ago

Description

If I am not mistaken, the API for the CytoTRACE kernel changed with theislab/cellrank#791. Previously, the all statistics were calculated when instantiating the kernel, i.e.,

ctk = CytoTRACEKernel(adata)

To achieve the same behaviour, the following code needs to be used

ctk = CytoTRACEKernel(adata).compute_cytotrace()

The tutorial has not yet been updated accordingly.

WeilerP commented 2 years ago

@michalk8, is there a similar change in other kernels?

michalk8 commented 2 years ago

@michalk8, is there a similar change in other kernels?

As far as I remember, no, only this has been split from the __init__.

Marius1311 commented 2 years ago

Thanks for spotting this @WeilerP! Would you mind updating the tutorial accordingly?

WeilerP commented 2 years ago

@michalk8, is this even possible? As far as I can tell, the notebooks at stable and latest are the same, right? So changing the notebook would change it for the stable docs as well even though there, the new API is not yet used. Or am I missing something?

michalk8 commented 2 years ago

@michalk8, is this even possible? As far as I can tell, the notebooks at stable and latest are the same, right? So changing the notebook would change it for the stable docs as well even though there, the new API is not yet used. Or am I missing something?

You're right, the notebooks aren't versioned into master/dev, so it's not possible. Think we should sooner or later make master the development branch again.

michalk8 commented 1 year ago

closed via #65