scverse/napari-spatialdata

Remove `_models.py`

LucaMarconato opened this issue · 4 comments

LucaMarconato commented

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: #242.

melonora commented

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.

LucaMarconato commented

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.

This is resolved now, correct? @melonora

giovp commented

I think @melonora did some magic and indeed it automagically disappeared. But I am not sure this was pushed/merged.

melonora commented

Jup during the ghent hackathon

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