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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
1891307093 PR_kwDOAMm_X85aEMt5 8174 Exclude dimensions used in faceting from squeeze krokosik 38408316 closed 0     1 2023-09-11T21:39:54Z 2023-09-17T05:08:07Z 2023-09-17T05:08:05Z CONTRIBUTOR   0 pydata/xarray/pulls/8174
  • [x] Closes #7552
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

Implements @headtr1ck solution from the issue.

 
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     xarray 13221727 pull
1861335844 I_kwDOAMm_X85u8bsk 8096 Errors when saving PyObject coordinates krokosik 38408316 closed 0     4 2023-08-22T12:14:53Z 2023-09-06T11:44:41Z 2023-09-06T11:44:41Z CONTRIBUTOR      

What happened?

Hi, I'm trying to create a DataArray with coordinates that are tuples and potentionally even more dimensional objects. The way I did it is to create an empty numpy array with dtype=object and then insert my tuples inside. This doesn't throw an error when creating a DataArray (as opposed to using a 2D ndarray or a list of lists). However, when trying to save it to zarr or netcdf. I get an error saying ValueError: setting an array element with a sequence

What did you expect to happen?

I want to be able to save and load such coordinates without errors. Maybe there is a cleaner way to do it than the object dtype ndarray?

Minimal Complete Verifiable Example

Python n = 5 x = np.empty(n, dtype=object) for i in range(n): x[i] = (i, i) xr.DataArray(np.arange(n), dims=("x"), coords={"x": x}).to_zarr("test")

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

```Python File c:\Users\Wiktor\AppData\Local\pypoetry\Cache\virtualenvs\spin1-JGuolXDk-py3.11\Lib\site-packages\xarray\core\dataarray.py:4014, in DataArray.to_netcdf(self, path, mode, format, group, engine, encoding, unlimited_dims, compute, invalid_netcdf) 4010 else: 4011 # No problems with the name - so we're fine! 4012 dataset = self.to_dataset() -> 4014 return to_netcdf( # type: ignore # mypy cannot resolve the overloads:( 4015 dataset, 4016 path, 4017 mode=mode, 4018 format=format, 4019 group=group, 4020 engine=engine, 4021 encoding=encoding, 4022 unlimited_dims=unlimited_dims, ... 101 result = np.empty(data.shape, dtype) --> 102 result[...] = data 103 return result

ValueError: setting an array element with a sequence. ```

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.11.3 (tags/v3.11.3:f3909b8, Apr 4 2023, 23:49:59) [MSC v.1934 64 bit (AMD64)] python-bits: 64 OS: Windows OS-release: 10 machine: AMD64 processor: Intel64 Family 6 Model 183 Stepping 1, GenuineIntel byteorder: little LC_ALL: None LANG: None LOCALE: ('Polish_Poland', '1250') libhdf5: None libnetcdf: None xarray: 2023.8.0 pandas: 2.0.3 numpy: 1.25.2 scipy: 1.11.2 netCDF4: None pydap: None h5netcdf: None h5py: None Nio: None zarr: 2.16.0 cftime: None nc_time_axis: None PseudoNetCDF: None iris: None bottleneck: None dask: None distributed: None matplotlib: 3.7.2 cartopy: None seaborn: None numbagg: None fsspec: None cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 68.0.0 pip: 23.2.1 conda: None pytest: None mypy: None IPython: 8.14.0 sphinx: 7.1.2 
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   completed xarray 13221727 issue

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