Lukas Heumos

### Report ``` ps_space = ps.compute( pert_embeddings, target_col="perturbations", # more parameters ) ps.label_transfer( psadata_classifier, column="gene_programme", target_val="Unknown", ) ``` maybe `target_col?` instead of `column`? ### Version information _No response_

### Description of feature Implement a new more modular and well tested version of DIALOGUE - [ ] Sketch user facing and internal API design and discuss it with Lukas...

### Report Raised by @emdann in https://github.com/scverse/pertpy/pull/682#issuecomment-2569982972 The model doesn't complain if you try to specify a complex interaction contrast on a model that wasn't fit with the interaction in...

I had disabled the ehrapy cellrank CI job for a while as it was broken and I wanted to wait for a proper release and not with development versions. Today,...

Deprecate save parameter of plots

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- [X] Closes #1508 - [X] Tests included - Deprecates the `save` parameter of plotting functions - Suggests to use `sc.pl.plot(show=False).figure.savefig()` instead - Uses a Futurewarning instead of a Deprecationwarning...

Python 3.13 support

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**Is your feature request related to a problem? Please describe.** I would like to kindly request Python 3.13. support. It's been out for a while and is supported by all...

new module: demuxem

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### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...

new module: seurat/htodemux

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### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...

Add plots for ehrdata

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### Description of feature - [ ] Check whether our existing plots that we got from scanpy even make sense for 3D EHRData - [ ] Vibe code a few...

### Description of feature @eroell recent transition results in tons of test warnings. We should update our tests and get rid of the warnings.