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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
1466586967 I_kwDOAMm_X85XaldX 7328 Zarr store array dtype changes for empty object string tomwhite 85085 closed 0     2 2022-11-28T15:05:14Z 2023-06-16T03:56:16Z 2023-06-16T03:56:16Z CONTRIBUTOR      

What happened?

Saving a dataset with an empty object (string) variable to zarr changes the dtype to float64.

What did you expect to happen?

The dtype should remain as O, just as it does for non-empty object variables.

Minimal Complete Verifiable Example

```Python import numpy as np import xarray as xr ds = xr.Dataset({"a": np.array([], dtype="O")}) ds["a"].dtype

prints: dtype('O')

ds.to_zarr("a.zarr") ds = xr.open_dataset("a.zarr") ds["a"].dtype

prints: dtype('float64')

```

MVCE confirmation

  • [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [X] Complete example — the example is self-contained, including all data and the text of any traceback.
  • [X] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • [X] New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

No response

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.8.13 (default, Mar 28 2022, 06:16:26) [Clang 12.0.0 ] python-bits: 64 OS: Darwin OS-release: 21.6.0 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: 2022.11.0 pandas: 1.5.0 numpy: 1.23.4 scipy: 1.9.2 netCDF4: None pydap: None h5netcdf: None h5py: None Nio: None zarr: 2.13.3 cftime: None nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2022.10.0 distributed: 2022.10.0 matplotlib: 3.6.1 cartopy: None seaborn: 0.12.0 numbagg: None fsspec: 2022.8.2 cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 63.4.1 pip: 22.2.2 conda: None pytest: 7.1.3 IPython: 8.5.0 sphinx: 4.2.0 
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   completed xarray 13221727 issue
1429920838 I_kwDOAMm_X85VOtxG 7243 Some aggregate operations using the array API fail tomwhite 85085 open 0     0 2022-10-31T14:15:00Z 2023-01-15T16:02:00Z   CONTRIBUTOR      

What happened?

Here are some tests demonstrating the problem https://github.com/pydata/xarray/commit/9d6269de9fec4c66aeade2fdf9829c6e066a6eac:

FAILED xarray/tests/test_array_api.py::test_aggregation[max] - assert False FAILED xarray/tests/test_array_api.py::test_aggregation[min] - assert False FAILED xarray/tests/test_array_api.py::test_aggregation[mean] - assert False FAILED xarray/tests/test_array_api.py::test_aggregation[prod] - assert False FAILED xarray/tests/test_array_api.py::test_aggregation[std] - assert False FAILED xarray/tests/test_array_api.py::test_aggregation[var] - assert False FAILED xarray/tests/test_array_api.py::test_aggregation_skipna[std] - TypeError: std() got an unexpected keyword argument 'ddof' FAILED xarray/tests/test_array_api.py::test_aggregation_skipna[var] - TypeError: var() got an unexpected keyword argument 'ddof'

What did you expect to happen?

No response

Minimal Complete Verifiable Example

No response

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.

Relevant log output

No response

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: 9d6269de9fec4c66aeade2fdf9829c6e066a6eac python: 3.8.13 (default, Mar 28 2022, 06:16:26) [Clang 12.0.0 ] python-bits: 64 OS: Darwin OS-release: 21.6.0 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: 2022.6.1.dev63+ge6791852a pandas: 1.5.0 numpy: 1.23.3 scipy: None netCDF4: None pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: None nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: None distributed: None matplotlib: None cartopy: None seaborn: None numbagg: None fsspec: None cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 63.4.1 pip: 22.1.2 conda: None pytest: 7.1.3 IPython: None sphinx: None 
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     xarray 13221727 issue
1165277802 I_kwDOAMm_X85FdLpq 6347 Can't set write_empty_chunks in Zarr encoding tomwhite 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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   completed xarray 13221727 issue

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