proposal: use (dask/geo) DataFrames for shapes (and polygons?)
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- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
right now the Shapes model is an anndata. We are just saving the coordinates in adata.obsm["spatial"] and the metadata in uns. I feel this is overkill and we don't really have plans to extend this spec further (but we did discuss to potentially move it to geodataframe or as points -> dask dataframes). I'd suggest by release to convert Shapes to GeoDataFarme or DaskDataFrame
@scverse/spatialdata
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 reviewing the Shapes model and its current anndata representation, including coordinates in adata.obsm["spatial"] and metadata in uns. Compare the proposed GeoDataFrame and Dask DataFrame directions, including the possibility of representing shapes as points. Done means agreeing on and implementing a replacement representation for Shapes before the targeted release.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100