to_zarr: can't extend null coordinate (error on subsequent read)

What happened?

When attempting to extend an on-disk (Zarr-backed) xarray by extending a time dimension, .to_zarr(<name>,mode='a',append_dim='t') fails upon subsequently loading the array if the time dimension was initially null.

This means that the initial write to the on-disk zarr must be special-cased, since it is impossible to initialize the array with a size-zero dimension for later expansion.

What did you expect to happen?

I expected the 0→1 case to function in the same way as the 1→2 case, which does work.

Minimal Complete Verifiable Example

import xarray as xr
import numpy as np
ds0 = xr.Dataset(coords={'t' : np.array([],dtype=np.int64)})
print('ds0', ds0)
ds0.to_zarr('foo.zarr',mode='w'); # Works
ds1 = xr.Dataset({'foo' : ('t',np.array([0]))},
                 coords={'t' : np.array([0],dtype=np.int64)})
print('ds1',ds1)
ds1.to_zarr('foo.zarr',mode='a',append_dim='t'); # Completes successfully, but...
ds_load = xr.open_zarr('foo.zarr') # Errors

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

ds0 <xarray.Dataset>
Dimensions:  (t: 0)
Coordinates:
  * t        (t) int64 
Data variables:
    *empty*
ds1 <xarray.Dataset>
Dimensions:  (t: 1)
Coordinates:
  * t        (t) int64 0
Data variables:
    foo      (t) int64 0

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[2], line 10
      8 print('ds1',ds1)
      9 ds1.to_zarr('foo.zarr',mode='a',append_dim='t'); # Completes successfully, but...
---> 10 ds_load = xr.open_zarr('foo.zarr') # Errors

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/backends/zarr.py:900, in open_zarr(store, group, synchronizer, chunks, decode_cf, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, consolidated, overwrite_encoded_chunks, chunk_store, storage_options, decode_timedelta, use_cftime, zarr_version, chunked_array_type, from_array_kwargs, **kwargs)
    886     raise TypeError(
    887         "open_zarr() got unexpected keyword arguments " + ",".join(kwargs.keys())
    888     )
    890 backend_kwargs = {
    891     "synchronizer": synchronizer,
    892     "consolidated": consolidated,
   (...)
    897     "zarr_version": zarr_version,
    898 }
--> 900 ds = open_dataset(
    901     filename_or_obj=store,
    902     group=group,
    903     decode_cf=decode_cf,
    904     mask_and_scale=mask_and_scale,
    905     decode_times=decode_times,
    906     concat_characters=concat_characters,
    907     decode_coords=decode_coords,
    908     engine="zarr",
    909     chunks=chunks,
    910     drop_variables=drop_variables,
    911     chunked_array_type=chunked_array_type,
    912     from_array_kwargs=from_array_kwargs,
    913     backend_kwargs=backend_kwargs,
    914     decode_timedelta=decode_timedelta,
    915     use_cftime=use_cftime,
    916     zarr_version=zarr_version,
    917 )
    918 return ds

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/backends/api.py:573, in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)
    561 decoders = _resolve_decoders_kwargs(
    562     decode_cf,
    563     open_backend_dataset_parameters=backend.open_dataset_parameters,
   (...)
    569     decode_coords=decode_coords,
    570 )
    572 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 573 backend_ds = backend.open_dataset(
    574     filename_or_obj,
    575     drop_variables=drop_variables,
    576     **decoders,
    577     **kwargs,
    578 )
    579 ds = _dataset_from_backend_dataset(
    580     backend_ds,
    581     filename_or_obj,
   (...)
    591     **kwargs,
    592 )
    593 return ds

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/backends/zarr.py:982, in ZarrBackendEntrypoint.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, group, mode, synchronizer, consolidated, chunk_store, storage_options, stacklevel, zarr_version)
    980 store_entrypoint = StoreBackendEntrypoint()
    981 with close_on_error(store):
--> 982     ds = store_entrypoint.open_dataset(
    983         store,
    984         mask_and_scale=mask_and_scale,
    985         decode_times=decode_times,
    986         concat_characters=concat_characters,
    987         decode_coords=decode_coords,
    988         drop_variables=drop_variables,
    989         use_cftime=use_cftime,
    990         decode_timedelta=decode_timedelta,
    991     )
    992 return ds

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/backends/store.py:58, in StoreBackendEntrypoint.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta)
     44 encoding = filename_or_obj.get_encoding()
     46 vars, attrs, coord_names = conventions.decode_cf_variables(
     47     vars,
     48     attrs,
   (...)
     55     decode_timedelta=decode_timedelta,
     56 )
---> 58 ds = Dataset(vars, attrs=attrs)
     59 ds = ds.set_coords(coord_names.intersection(vars))
     60 ds.set_close(filename_or_obj.close)

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/core/dataset.py:696, in Dataset.__init__(self, data_vars, coords, attrs)
    693 if isinstance(coords, Dataset):
    694     coords = coords._variables
--> 696 variables, coord_names, dims, indexes, _ = merge_data_and_coords(
    697     data_vars, coords
    698 )
    700 self._attrs = dict(attrs) if attrs is not None else None
    701 self._close = None

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/core/dataset.py:425, in merge_data_and_coords(data_vars, coords)
    421     coords = create_coords_with_default_indexes(coords, data_vars)
    423 # exclude coords from alignment (all variables in a Coordinates object should
    424 # already be aligned together) and use coordinates' indexes to align data_vars
--> 425 return merge_core(
    426     [data_vars, coords],
    427     compat="broadcast_equals",
    428     join="outer",
    429     explicit_coords=tuple(coords),
    430     indexes=coords.xindexes,
    431     priority_arg=1,
    432     skip_align_args=[1],
    433 )

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/core/merge.py:724, in merge_core(objects, compat, join, combine_attrs, priority_arg, explicit_coords, indexes, fill_value, skip_align_args)
    719 prioritized = _get_priority_vars_and_indexes(aligned, priority_arg, compat=compat)
    720 variables, out_indexes = merge_collected(
    721     collected, prioritized, compat=compat, combine_attrs=combine_attrs
    722 )
--> 724 dims = calculate_dimensions(variables)
    726 coord_names, noncoord_names = determine_coords(coerced)
    727 if compat == "minimal":
    728     # coordinates may be dropped in merged results

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/core/variable.py:2997, in calculate_dimensions(variables)
   2995             last_used[dim] = k
   2996         elif dims[dim] != size:
-> 2997             raise ValueError(
   2998                 f"conflicting sizes for dimension {dim!r}: "
   2999                 f"length {size} on {k!r} and length {dims[dim]} on {last_used!r}"
   3000             )
   3001 return dims

ValueError: conflicting sizes for dimension 't': length 1 on 't' and length 2 on {'t': 'foo'}

Anything else we need to know?

No response

Environment

Start with xarray/backends/zarr.py, especially the to_zarr and open_zarr entry points, and reproduce the 0→1 append case from the issue. Trace how the dimension sizes are written and loaded; done means the example opens successfully after appending to an initially null coordinate, with a regression test covering that case.