Zarr v3 fill_value

[aldenks]

What happened?

I'm attempting to set a nan fill value in the encoding of a zarr v3 format array created with xarray and seeing 0.0 in the fill value metadata instead. Not sure if this is user error or a bug.

What did you expect to happen?

see "fill_value": "NaN" in the variable's encoding in the array's zarr.json.

Minimal Complete Verifiable Example

import json

import numpy as np
import xarray as xr

variable_data = np.full((4, 3), np.nan, dtype="float32")

ds = xr.Dataset({"example_var": (("x", "y"), variable_data)})

ds["example_var"].encoding["_FillValue"] = "NaN"
ds["example_var"].encoding["fill_value"] = "NaN"
# Also tried this but got the same 0.0 float value
# xr_dataset["example_var"].encoding["_FillValue"] = np.nan
# xr_dataset["example_var"].encoding["fill_value"] = np.nan

ds.to_zarr("xarray_fill_value_test.zarr", mode="w", zarr_version=3)

with open("xarray_fill_value_test.zarr/zarr.json") as f:
    metadata = json.load(f)
    # prints 0.0 instead of NaN
    print(
        f"{metadata['consolidated_metadata']['metadata']['example_var']['fill_value'] =}"
    )

Note this doesn't appear to be a zarr-python issue, I'm seeing behavior I expect there:

import json

import numpy as np
import zarr

data = np.full((4, 3), np.nan, dtype="float32")

array = zarr.create_array("zarr_fill_value_test.zarr", data=data, fill_value=np.nan)

with open("zarr_fill_value_test.zarr/zarr.json") as f:
    metadata = json.load(f)
    print(f"{metadata['fill_value']=}")  # prints "NaN", good

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==2025.1.2
zarr==3.0.3

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[aldenks]

If this is indeed a bug I'd be happy to work on it if someone would confirm it's not user error and point me in the right direction.