Unrecognized zarr version for example dataset in tutorial

[keviny2]

I get an error when I load the example .zarr as a SpatialData object in the tutorial. The link to the example dataset (https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zip) uses an unrecognized Version 0.6-dev. Here is the last part of the stack trace:

import matplotlib as mpl
import matplotlib.pyplot as plt
import spatialdata as sd
import spatialdata_plot

data_path = "mouse_liver.zarr"
sdata = sd.read_zarr(data_path)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
...
File ~/scratch/miniforge3/envs/spatialdata/lib/python3.10/site-packages/ome_zarr/format.py:21, in format_from_version(version)
     [19](~/scratch/miniforge3/envs/spatialdata/lib/python3.10/site-packages/ome_zarr/format.py:19)     if fmt.version == version:
     [20](~/scratch/miniforge3/envs/spatialdata/lib/python3.10/site-packages/ome_zarr/format.py:20)         return fmt
---> [21](~/scratch/miniforge3/envs/spatialdata/lib/python3.10/site-packages/ome_zarr/format.py:21) raise ValueError(f"Version {version} not recognized")

ValueError: Version 0.6-dev not recognized

[LucaMarconato]

Thanks @keviny2 for reporting. There was a misconfiguration in the pipeline that we use to generate and upload the datasets and a dev version of the package was used. I now re-run the job that is converting and uploading the datasets, so in 1-2 hours you should be able to download the correct datasets.

The format will be bumped at the next release of spatialdata, which will be able to read in the data.

CC @berombau

[keviny2]

Great. Thanks @LucaMarconato !

[stevenhuakui]

I got the same error for another two example datasets, Visium dataset, Xenium dataset, can you kindly regenerated them as well? @LucaMarconato , Many thanks!

BTW this package is fantastic! Thank you all for creating such an amazing tool!

[LucaMarconato]

@stevenhuakui thanks for the kind feedback, and for reporting. You are right, those two datasets are from a notebook that I didn't re-run. Now when the conversion job will conclude, all the datasets should be consistent.

[stevenhuakui]

Perfect! Thanks @LucaMarconato !

[zhangj1115]

i get the same error, when use the The link to the example dataset (https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zip)

[LucaMarconato]

@zhangj1115 thanks for reporting. The same problem reoccurred. It will be fixed in a few hours. I will make a release soon, which will address the issue at the root by providing a version of the library that is able to read the updated uploaded data.