Error when writing string coordinate variables to zarr

I saved an xarray dataset to zarr using to_zarr. I then later tried to read that dataset from the original zarr, re-chunk it, and then write to a new zarr. When I did that I get a strange error. I attached a zip of minimal version of the zarr dataset that I am using. test_sm_zarr.zip

MCVE Code Sample

import xarray as xr

sm_from_zarr = xr.open_zarr('test_sm_zarr')
sm_from_zarr.to_zarr('test_sm_zarr_from', mode='w')

Expected Output

No error

Problem Description

I get this error:

C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\core\merge.py:18: FutureWarning: The Panel class is removed from pandas. Accessing it from the top-level namespace will also be removed in the next version
  PANDAS_TYPES = (pd.Series, pd.DataFrame, pd.Panel)
C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\core\dataarray.py:1829: FutureWarning: The Panel class is removed from pandas. Accessing it from the top-level namespace will also be removed in the next version
  'DataArray', pd.Series, pd.DataFrame, pd.Panel]:
Traceback (most recent call last):
  File "rechunk_test.py", line 38, in <module>
    sm_from_zarr.to_zarr('test_sm_zarr_from', mode='w')
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\core\dataset.py", line 1414, in to_zarr
    consolidated=consolidated, append_dim=append_dim)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\backends\api.py", line 1101, in to_zarr
    dump_to_store(dataset, zstore, writer, encoding=encoding)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\backends\api.py", line 929, in dump_to_store
    unlimited_dims=unlimited_dims)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\backends\zarr.py", line 366, in store
    unlimited_dims=unlimited_dims)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\backends\zarr.py", line 432, in set_variables
    writer.add(v.data, zarr_array)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\xarray\backends\common.py", line 173, in add
    target[...] = source
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\zarr\core.py", line 1115, in __setitem__
    self.set_basic_selection(selection, value, fields=fields)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\zarr\core.py", line 1210, in set_basic_selection
    return self._set_basic_selection_nd(selection, value, fields=fields)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\zarr\core.py", line 1501, in _set_basic_selection_nd
    self._set_selection(indexer, value, fields=fields)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\zarr\core.py", line 1550, in _set_selection
    self._chunk_setitem(chunk_coords, chunk_selection, chunk_value, fields=fields)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\zarr\core.py", line 1659, in _chunk_setitem
    fields=fields)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\zarr\core.py", line 1723, in _chunk_setitem_nosync
    cdata = self._encode_chunk(chunk)
  File "C:\Users\jsadler\AppData\Local\Continuum\anaconda3\envs\nwm\lib\site-packages\zarr\core.py", line 1769, in _encode_chunk
    chunk = f.encode(chunk)
  File "numcodecs/vlen.pyx", line 108, in numcodecs.vlen.VLenUTF8.encode
TypeError: expected unicode string, found 20

BUT I think it has something to do with the datatype of one of my coordinates, site_code. Because, if it do this I get no error:

import xarray as xr

sm_from_zarr = xr.open_zarr('test_sm_zarr')
sm_from_zarr['site_code'] = sm_from_zarr.site_code.astype('str')
sm_from_zarr.to_zarr('test_sm_zarr_from', mode='w')

Before converting the datatype of the site_code coordinate is object

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.7.4 (default, Aug 9 2019, 18:34:13) [MSC v.1915 64 bit (AMD64)] python-bits: 64 OS: Windows OS-release: 10 machine: AMD64 processor: Intel64 Family 6 Model 158 Stepping 10, GenuineIntel byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: None.None libhdf5: 1.10.4 libnetcdf: 4.6.2

xarray: 0.12.2 pandas: 0.25.1 numpy: 1.17.1 scipy: 1.3.1 netCDF4: 1.5.1.2 pydap: installed h5netcdf: None h5py: None Nio: None zarr: 2.3.2 cftime: 1.0.3.4 nc_time_axis: None PseudonetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2.3.0 distributed: 2.5.1 matplotlib: 3.1.1 cartopy: None seaborn: None numbagg: None setuptools: 41.2.0 pip: 19.2.3 conda: None pytest: 5.1.2 IPython: 7.8.0 sphinx: None

[Hoeze]

Hi, I also keep running into this issue all the time. Right now, there is no way of round-tripping xr.open_zarr().to_zarr(), also because of https://github.com/pydata/xarray/issues/5219.

The only workaround that seems to help is the following:

to_store = xrds.copy()
for var in to_store.variables:
    to_store[var].encoding.clear()

[dnerini]

I’m experiencing the same issue, which seems to be also related to one of my coordinates having object as datatype. Luckily, the workaround proposed by @jsadler2 works in my case, too.