issues: 762323609

What happened:

We create xarray.Dataset instances using xr.open_zarr(store) with custom chunk store instances. These will lazily fetch data chunks for data variables from the Sentinel Hub API. For coordinate variables lon, lat, time we use "static" store entries: uncompressed, bytified numpy arrays.

Since xarray 0.16.2 and Zarr 2.6.1 this approach doesnt work anymore. When we write datasets opened from such store using xr.to_zarr(dst_store), e.g. with a dst_store=s3fs.S3Map(), we get encoding errors. E.g. for a coordinate array lon we get from botocore:

Invalid type for parameter Body, value: [55.0475 55.0465 55.0455 ... 53.0025 53.0015 53.0005], type: <class 'numpy.ndarray'>, valid types: <class 'bytes'>, <class 'bytearray'>, file-like object

(Full traceback is below.) It seems that our static numpy arrays won't be encoded at all, because they are uncompressed. If we use a compressor, it works again. (That's our current workaround.)

What you expected to happen:

Before data is written into a Zarr chunk store, it must be encoded from numpy arrays to bytes. This does not seem to happen if uncompressed data is written, that is, the the Zarr encoding's compressor and filters are both None.

Minimal Complete Verifiable Example:

A minimal, self-contained example is the entire test module test_reprod_27.py of the xcube Sentinel Hub plugin xcube-sh.

Original issue in the Sentinel Hub xcube plugin is xcube-sh #27.

Environment:

Output of <tt>xr.show_versions()</tt>

INSTALLED VERSIONS ------------------ commit: None python: 3.8.6 | packaged by conda-forge | (default, Nov 27 2020, 18:58:29) [MSC v.1916 64 bit (AMD64)] python-bits: 64 OS: Windows OS-release: 10 machine: AMD64 processor: Intel64 Family 6 Model 26 Stepping 5, GenuineIntel byteorder: little LC_ALL: None LANG: None LOCALE: de_DE.cp1252 libhdf5: 1.10.6 libnetcdf: 4.7.4 xarray: 0.16.2 pandas: 1.1.5 numpy: 1.19.4 scipy: 1.5.3 netCDF4: 1.5.5 pydap: installed h5netcdf: None h5py: None Nio: None zarr: 2.6.1 cftime: 1.3.0 nc_time_axis: None PseudoNetCDF: None rasterio: 1.1.5 cfgrib: None iris: None bottleneck: None dask: 2.30.0 distributed: 2.30.1 matplotlib: 3.3.3 cartopy: None seaborn: None numbagg: None pint: None setuptools: 49.6.0.post20201009 pip: 20.3.1 conda: None pytest: 6.1.2 IPython: 7.19.0 sphinx: 3.3.1

Traceback:

traceback:

``` File "D:\Projects\xcube\xcube\cli_gen2\write.py", line 47, in write_cube data_id = writer.write_data(cube, File "D:\Projects\xcube\xcube\core\store\stores\s3.py", line 213, in write_data self._new_s3_writer(writer_id).write_data(data, data_id=path, replace=replace, write_params) File "D:\Projects\xcube\xcube\core\store\accessors\dataset.py", line 313, in write_data data.to_zarr(s3fs.S3Map(root=f'{bucket_name}/{data_id}' if bucket_name else data_id, File "D:\Miniconda3\envs\xcube\lib\site-packages\xarray\core\dataset.py", line 1745, in to_zarr return to_zarr( File "D:\Miniconda3\envs\xcube\lib\site-packages\xarray\backends\api.py", line 1481, in to_zarr dump_to_store(dataset, zstore, writer, encoding=encoding) File "D:\Miniconda3\envs\xcube\lib\site-packages\xarray\backends\api.py", line 1158, in dump_to_store store.store(variables, attrs, check_encoding, writer, unlimited_dims=unlimited_dims) File "D:\Miniconda3\envs\xcube\lib\site-packages\xarray\backends\zarr.py", line 473, in store self.set_variables( File "D:\Miniconda3\envs\xcube\lib\site-packages\xarray\backends\zarr.py", line 549, in set_variables writer.add(v.data, zarr_array, region) File "D:\Miniconda3\envs\xcube\lib\site-packages\xarray\backends\common.py", line 143, in add target[region] = source File "D:\Miniconda3\envs\xcube\lib\site-packages\zarr\core.py", line 1122, in setitem self.set_basic_selection(selection, value, fields=fields) File "D:\Miniconda3\envs\xcube\lib\site-packages\zarr\core.py", line 1217, in set_basic_selection return self._set_basic_selection_nd(selection, value, fields=fields) File "D:\Miniconda3\envs\xcube\lib\site-packages\zarr\core.py", line 1508, in _set_basic_selection_nd self._set_selection(indexer, value, fields=fields) File "D:\Miniconda3\envs\xcube\lib\site-packages\zarr\core.py", line 1580, in _set_selection self._chunk_setitems(lchunk_coords, lchunk_selection, chunk_values, File "D:\Miniconda3\envs\xcube\lib\site-packages\zarr\core.py", line 1709, in _chunk_setitems self.chunk_store.setitems({k: v for k, v in zip(ckeys, cdatas)}) File "D:\Miniconda3\envs\xcube\lib\site-packages\fsspec\mapping.py", line 110, in setitems self.fs.pipe(values) File "D:\Miniconda3\envs\xcube\lib\site-packages\fsspec\asyn.py", line 121, in wrapper return maybe_sync(func, self, args, kwargs) File "D:\Miniconda3\envs\xcube\lib\site-packages\fsspec\asyn.py", line 100, in maybe_sync return sync(loop, func, args, kwargs) File "D:\Miniconda3\envs\xcube\lib\site-packages\fsspec\asyn.py", line 71, in sync raise exc.with_traceback(tb) File "D:\Miniconda3\envs\xcube\lib\site-packages\fsspec\asyn.py", line 55, in f result[0] = await future File "D:\Miniconda3\envs\xcube\lib\site-packages\fsspec\asyn.py", line 211, in _pipe await asyncio.gather( File "D:\Miniconda3\envs\xcube\lib\site-packages\s3fs\core.py", line 608, in _pipe_file return await self._call_s3( File "D:\Miniconda3\envs\xcube\lib\site-packages\s3fs\core.py", line 225, in _call_s3 raise translate_boto_error(err) from err File "D:\Miniconda3\envs\xcube\lib\site-packages\s3fs\core.py", line 207, in _call_s3 return await method(additional_kwargs) File "D:\Miniconda3\envs\xcube\lib\site-packages\aiobotocore\client.py", line 123, in _make_api_call request_dict = await self._convert_to_request_dict( File "D:\Miniconda3\envs\xcube\lib\site-packages\aiobotocore\client.py", line 171, in _convert_to_request_dict request_dict = self._serializer.serialize_to_request( File "D:\Miniconda3\envs\xcube\lib\site-packages\botocore\validate.py", line 297, in serialize_to_request raise ParamValidationError(report=report.generate_report())

Invalid type for parameter Body, value: [55.0475 55.0465 55.0455 ... 53.0025 53.0015 53.0005], type: <class 'numpy.ndarray'>, valid types: <class 'bytes'>, <class 'bytearray'>, file-like object ```