Zarr v3 fill_value #10064
Description
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", goodMVCE 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