How to not write empty chunks when appending to a Zarr store

[maxrjones]

Does anyone have any recommendations for how to write to a zarr store without including empty chunks when using the append_dim or region parameters? An example of the desired behavior is given below for the case in which the data are written immediately, along with an example in which the data are written afterwards.

Write data immediately (doesn't write empty chunks)

import xarray as xr
import numpy as np

# Create dataset
store = "test0.zarr"
ds = xr.Dataset({"x": (("d1"), np.arange(2))}).chunk({"d1": 1})
ds = ds.where(ds.x>0)
# Write data
ds.to_zarr(store, encoding={'x': {'write_empty_chunks': False}}, mode='w')
# Check number of chunks stored
root = zarr.open_consolidated(store)
print(f'nchunks: {root["x"].nchunks}')
print(f'nchunks_initiliazed: {root["x"].nchunks_initialized}')

nchunks: 2
nchunks_initiliazed: 1

Write metadata first and fill in later (writes empty chunks)

import xarray as xr
import numpy as np

# Create dataset
store = "test1.zarr"
ds = xr.Dataset({"x": (("d1"), np.arange(2))}).chunk({"d1": 1})
ds = ds.where(ds.x>0)
# Write metadata
ds.to_zarr(store, encoding={'x': {'write_empty_chunks': False}}, mode='w', compute=False)
# Fill in data
ds.to_zarr(store, region={'d1': slice(0,2)})
# Check number of chunks stored
root = zarr.open_consolidated(store)
print(f'nchunks: {root["x"].nchunks}')
print(f'nchunks_initiliazed: {root["x"].nchunks_initialized}')

nchunks: 2
nchunks_initiliazed: 2