issues: 1165277802

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id node_id number title user state locked assignee milestone comments created_at updated_at closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
1165277802 I_kwDOAMm_X85FdLpq 6347 Can't set write_empty_chunks in Zarr encoding 85085 closed 0     0 2022-03-10T14:11:36Z 2022-03-17T04:52:10Z 2022-03-17T04:52:10Z CONTRIBUTOR      

What happened?

Zarr 2.11.0 made a change where chunks with data equal to the fill value are no longer written to disk by default. I would like to override the default, but this isn't possible using xarray's to_zarr.

What did you expect to happen?

No response

Minimal Complete Verifiable Example

Python import numpy as np import xarray as xr ds = xr.Dataset({"x": (("d1"), np.full((2,), np.nan))}) ds.to_zarr("/tmp/ds.zarr", encoding={"x": {"write_empty_chunks":True}})

Relevant log output

Python Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/tom/miniconda/envs/sgkit-3.8/lib/python3.8/site-packages/xarray/core/dataset.py", line 2036, in to_zarr return to_zarr( File "/Users/tom/miniconda/envs/sgkit-3.8/lib/python3.8/site-packages/xarray/backends/api.py", line 1431, in to_zarr dump_to_store(dataset, zstore, writer, encoding=encoding) File "/Users/tom/miniconda/envs/sgkit-3.8/lib/python3.8/site-packages/xarray/backends/api.py", line 1119, in dump_to_store store.store(variables, attrs, check_encoding, writer, unlimited_dims=unlimited_dims) File "/Users/tom/miniconda/envs/sgkit-3.8/lib/python3.8/site-packages/xarray/backends/zarr.py", line 534, in store self.set_variables( File "/Users/tom/miniconda/envs/sgkit-3.8/lib/python3.8/site-packages/xarray/backends/zarr.py", line 581, in set_variables encoding = extract_zarr_variable_encoding( File "/Users/tom/miniconda/envs/sgkit-3.8/lib/python3.8/site-packages/xarray/backends/zarr.py", line 220, in extract_zarr_variable_encoding raise ValueError( ValueError: unexpected encoding parameters for zarr backend: ['write_empty_chunks']

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS

commit: None python: 3.8.12 (default, Oct 12 2021, 06:23:56) [Clang 10.0.0 ] python-bits: 64 OS: Darwin OS-release: 19.6.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: ('en_GB', 'UTF-8') libhdf5: None libnetcdf: None

xarray: 2022.3.0 pandas: 1.3.5 numpy: 1.21.5 scipy: 1.7.3 netCDF4: None pydap: None h5netcdf: None h5py: None Nio: None zarr: 2.11.0 cftime: None nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2022.01.0 distributed: 2022.01.0 matplotlib: 3.5.1 cartopy: None seaborn: 0.11.2 numbagg: None fsspec: 2022.01.0 cupy: None pint: None sparse: None setuptools: 58.0.4 pip: 21.2.4 conda: None pytest: 6.2.5 IPython: 8.0.1 sphinx: 4.2.0

 
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