scverse / scverse/spatialdata

Unrecognized zarr version for example dataset in tutorial

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Description

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

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the example notebook linked in the tutorial and reproduce the failure using the mouse_liver.zip dataset and sd.read_zarr. Check where the dataset's Version 0.6-dev is introduced and determine what update is needed so the tutorial loads the example successfully; verify by rerunning the notebook.

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Assessment

Tech stack
python
Domain
documentation
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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