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scverse / napari-spatialdata

Interactive visualization of spatial omics data
https://spatialdata.scverse.org/projects/napari/en/latest/
BSD 3-Clause "New" or "Revised" License
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Remove `_models.py` #248

Open LucaMarconato opened 3 weeks ago

LucaMarconato commented 3 weeks ago

As discussed during the VIB Ghent 2024 hackathon with @giovp and @melonora, removing the legacy _models.py from the codebase, and access the data directly form layer.metadata['sdata'] would improve the robustness of the code.

In particular we should rely on get_values() for fetching annotations instead of the currently used get_obs(), get_var() etc.

A positive implication of this refactoring is that the mismatch between the annotation indices shown by napari, and the indices used by SpatialData, would disappear, therefore fixing this bug: https://github.com/scverse/napari-spatialdata/issues/242.

melonora commented 3 weeks ago

get_values won't entirely work. It requires a refactor because currently if you pass on an element it is not allowed to be a table.