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
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
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