make sure metadata from formatting is saved to disk

[ckmah]

Metadata such as indexing columns generated as columns in spatialdata shapes are ignored when written to file using SpatialData.write() in version spatialdata==0.0.15. For now bento-tools will also reindex when loading data with bt.io.read_zarr().

Solution may be as simple as upgrading to spatialdata>=0.1.0.

[ckmah]

Looks like this is an open issue scverse/spatialdata#311 that still needs to be addressed scverse/spatialdata#293. Could also migrate all our annotations to Table elements and retrieve with get_values() instead but will be a significant refactor.

[LucaMarconato]

scverse/spatialdata#542 will solve the issue of columns lost when saving shapes.

[LucaMarconato]

The linked PR is now ready 😊

[ckmah]

closed by #149