pydata / pydata/xarray

Error converting zarr v3 to zarr v2: zarr 2 does not support "Serializer"

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bug topic-zarr
Dominant language
Python
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Description

What happened?

I'm trying to convert a Zarr dataset in the Zarr format/version 3 to 2. Xarray can successfully read zarr v2 or v3. I can make an xarray dataset in memory and write to disc in either zarr v2 or v3. I seem to find this problem only when reading an existing zarr v3 and and attempting to write to a zarr v2. However i can successfully convert the opposite direction by reading an existing zarr v2 and writing to zarr v3. Given that all the other read/write scenarios that i've tried work fine, i'm guessing there's some internal config set when reading a dataset from zarr v3 which maybe doesn't exist or has an incompatible default for in zarr v2.

What did you expect to happen?

I expected this to be possible

xr.open_zarr('v3path.zarr', zarr_format=3).to_zarr('v2path.zarr', zarr_format=2)
Minimal Complete Verifiable Example
import xarray as xr
import numpy as np

# generate a random array and write it to zarr v3
arr = np.random.rand(100, 100)
(
    xr
    .DataArray(arr, dims=['x', 'y'], name='data')
    .to_zarr(
        './test-v3.zarr',
        zarr_format=3
    )
)

# now try to convert it to a zarr 2
(
    xr
    .open_zarr('./test-v3.zarr')
    .to_zarr('test-v2.zarr', zarr_format=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.
Relevant log output
ValueError: Zarr format 2 arrays do not support `serializer`.
Anything else we need to know?

No response

Environment

This is on a google colab machine but i've also replicated this on so Mac and Windows installations

INSTALLED VERSIONS ------------------ commit: None python: 3.11.12 (main, Apr 9 2025, 08:55:54) [GCC 11.4.0] python-bits: 64 OS: Linux OS-release: 6.1.123+ machine: x86_64 processor: x86_64 byteorder: little LC_ALL: en_US.UTF-8 LANG: en_US.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.14.6 libnetcdf: None

xarray: 2025.3.1
pandas: 2.2.2
numpy: 2.0.2
scipy: 1.15.3
netCDF4: None
pydap: None
h5netcdf: 1.6.1
h5py: 3.13.0
zarr: None
cftime: None
nc_time_axis: None
iris: None
bottleneck: 1.4.2
dask: 2024.12.1
distributed: 2024.12.1
matplotlib: 3.10.0
cartopy: None
seaborn: 0.13.2
numbagg: None
fsspec: 2025.3.2
cupy: 13.3.0
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 75.2.0
pip: 24.1.2
conda: None
pytest: 8.3.5
mypy: None
IPython: 7.34.0
sphinx: 8.2.3

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  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 by reproducing the failure with the provided xarray.DataArray example and trace the interaction between xr.open_zarr and Dataset.to_zarr when changing from format 3 to format 2. Done means the conversion completes without the serializer error and the resulting Zarr v2 dataset can be opened successfully.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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