Latest anndata version 0.12 introducing zarr3

With the latest anndata version 0.12 comes zarr3, a compression tool used to write the h5ad files. Until now zarr2 was used.

The problem is that our current cellxgene and cellxgeneVIP container running with cellxgene 1.1.1 do not support the latest anndata version/zarr3.

anndata 0.12 supports older h5ad files but anndata < 0.12 do not support newer h5ad files.

What can we do?

1. Update the cellxgene container to cellxgene 1.3.0
   • this seems to be working with older and newer h5ad files
2. Try updating the cellxgene vip continer to cellxgene 1.3.0 with anndata < 0.12 and see if it works or not
3. Updating the cellxgene container to cellxgene 1.3.0 with anndata >= 0.12 and see if VIP runs

Option 1 and 3 seem to be to most promising. If this does not work out we have to think about other options:

• We might have to somehow convert newer h5ad files to the older version e.g. export as mtx and tsv files and rebuild h5ad with older version.
• Adjust the container depending on the h5ad version
• Pin anndata <0.12