scverse / scverse/napari-spatialdata
Remove `_models.py`
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- Dominant language
- Python
- Stars
- 90
- Forks
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Description
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.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the legacy _models.py and the code paths that access layer metadata or call get_obs(), get_var(), and related methods. Trace annotation reads through layer.metadata['sdata'] and get_values(); the refactor is done when _models.py is no longer needed and the annotation-index mismatch described in issue #242 is addressed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100