RuntimeError in rule patchify_cellpose: add_image(), add_labels(), add_points() and add_shapes()

[suhridbuddha]

I am getting in this error at patchify stage:

RuntimeError: The functions add_image(), add_labels(), add_points() and
add_shapes() have been removed in favor of dict-like access to the elements.
Please use the following syntax to add an element:

    sdata.images["image_name"] = image
    sdata.labels["labels_name"] = labels
    ...

The new syntax does not automatically updates the disk storage, so you need to
call sdata.write() when the in-memory object is ready to be saved.
To save only a new specific element to an existing Zarr storage please use the
functions write_image(), write_labels(), write_points(), write_shapes() and
write_table(). We are going to make these calls more ergonomic in a follow up
PR.

any idea?

i am using snakemake-lsf profile (default setup) and xenium ome.tif

[quentinblampey]

Hello,

Yes, this is an issue related to the new version of Sopa (it solved a bug, but also created another one...).
Sorry for this second issue, I'll fix this on Wednesday!

[suhridbuddha]

Hello @quentinblampey thank you. the sopa i have now is Version: 1.0.6. Do you think downgrade may help?

Update: Another project of ours with the same xenium data and same sopa version is working fine on the same server. Do you think there are some lib dependencies as well?

[suhridbuddha]

even with the tuto.zarr i am getting the same error now.

[quentinblampey]

Hello @suhridbuddha, the newest releases of spatialdata and spatialdata-io introduced some breaking changes, so I need to update Sopa (I know that everything is broken right now, sorry for that). This will be done tonight or tomorrow morning.

These changes came with the publication of SpatialData, but now there shouldn't have breaking changes anymore! Wait for the next Sopa release and it should be all fixed 😊

[quentinblampey]

Hello @suhridbuddha, I released sopa==1.0.9, can you try?
It should now work, even though I still need to check some new functionalities from spatialdata, and perform additional checks.

NB: spatialdata is now using multiple tables, but the old sdata.table syntax is still supported

[suhridbuddha]

Thank you @quentinblampey. The new sopa has resolved the problem