Lukas Heumos

For new term requests, please provide the following information: ## Preferred term label CosMx SMI ## Synonyms CosMx ## Textual definition CosMx SMI is a high-plex in situ analysis platform...

Hopefully fixes `uv`

### Report > ep.settings.set_figure_params(figsize=(4, 4), vector_friendly=True, dpi_save=300) doesn't seem to have the same effect as the scanpy version. Reported by @juzb ### Version information _No response_

> Further instructions on using this template can be found in the dev docsincluded in the project.

Python 3.12 support

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### Description of feature - [ ] Check whether tests and use-cases run with Python 3.12. It might be annoying to rerun all tutorials so let's primarily keep it to...

Feature pertpy use-cases in our tutorial

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### Description of feature We have such great use-cases that combine several of pertpy's modules, but they're hidden in our reproducibility repository. It'd be great if we could find a...

### Description of feature https://github.com/velten-group/crispat

AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'. Did you mean: 'get_data_files'?

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#### Problem description Trying to build my documentation with `uv` which also installs gensim as a transitive dependency. #### Steps/code/corpus to reproduce `uv pip install gensim` but it leads to...

Attempting to parse EFO 3.67.0 from http://www.ebi.ac.uk/efo/releases/v3.67.0/efo.owl using Pronto, which is the defacto standard in Python, results in an error. Note that all past versions including 3.66.0 still work. ```...

### Description of feature It's time. 3.13 is around the corner. Adapt CI then.