Remove `region` from `adata.uns['spatialdata_attrs']`
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- Dominant language
- Python
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Description
As discussed here https://github.com/scverse/spatialdata/pull/410#discussion_r1430298422 and here https://github.com/scverse/spatialdata/pull/410#discussion_r1441517847, we are considering removing the region metadata.
We will still write it to disk to be used for cloud applications, but for in-memory uses we can have a method that is reading the levels of the column table.obs[REGION_KEY], which we will encourage (via warnings) or force to be a categorical.
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 reading the two discussions on pull request 410 and tracing uses of adata.uns['spatialdata_attrs'], table.obs[REGION_KEY], and the disk-writing path. Done means in-memory metadata no longer depends on region, while the disk representation remains available and the documented warning or categorical handling is covered.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100