Coordinate arrays of type object can not be written, read, and then written again with zarr<3
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needs mcve
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Description
What happened?
Coordinate arrays of type object can not be written, read, and then written again.
Minimal Complete Verifiable Example
import xarray as xr
import numpy as np
data = xr.DataArray(data=np.zeros((2, 2)),
dims=['x', 'y'],
coords=dict(
y=np.array(['a', 'b'],
dtype=object)))
data.to_zarr("test.zarr", mode="w")
data = xr.open_zarr("test.zarr")
data.to_zarr("test2.zarr", mode="w")
# File "numcodecs/vlen.pyx", line 104, in numcodecs.vlen.VLenUTF8.encode
# TypeError: expected unicode string, found 2
MVCE confirmation
- Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
- Complete example — the example is self-contained, including all data and the text of any traceback.
- Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
- New issue — a search of GitHub Issues suggests this is not a duplicate.
- Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Environment
xarray==2025.9.0
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 by running the minimal Python example using DataArray.to_zarr and xr.open_zarr, then inspect the object-coordinate serialization path indicated by the numcodecs.vlen.VLenUTF8 traceback. Done means an object-typed coordinate can be written to Zarr, reopened, and written to a second Zarr store without the TypeError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100