Unable to save SpatialData object to zarr
Open
Nobody has claimed this yet.
needs: triage
priority: medium
- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
Hello,
Saving a spatialdata object to zarr file throws error.
Reproducible example with blobs() dataset:
from spatialdata.datasets import blobs
sdata_github = blobs()
sdata_github.write(path_zarr+"github_report_bug.zarr",overwrite=True)
Bug description:
It throws the error:
RuntimeError: `anndata.settings.allow_write_nullable_strings` is False, because writing of `pd.arrays.{StringArray,ArrowStringArray}` is new and not supported in anndata < 0.11, still use by many people. Opt-in to writing these arrays by toggling the setting to True.
Error raised while writing key '_index' of <class 'zarr.core.group.Group'> to /tables/table/obs
Session Info:
spatialdata_io version: 0.7.0
scanpy version: 1.11.2
pandas version: 3.0.2
numpy version: 2.3.5
anndata version: 0.12.16
spatialdata version: 0.7.3
spatialdata_plot version: 0.3.4
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
Run the reported blobs() example with the listed package versions and confirm the failure in the write(path_zarr+"github_report_bug.zarr", overwrite=True) path. Trace the write operation to the point where the error is raised for the _index key under /tables/table/obs. Done means the reproducible SpatialData object saves to zarr without this error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 62/100