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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
1959816045 I_kwDOAMm_X8500Gtt 8368 to_netcdf: Unexpected drop of "units" attribute of attached "bounds" leonfoks 15173535 open 0     4 2023-10-24T18:15:05Z 2024-04-09T11:11:20Z   NONE      

What happened?

When writing a Dataset to netcdf, any DataArrays that are linked as bounds through another variables attrs['bounds'] entry, have their (specifically) 'units' attribute dropped inside the written netcdf file.

See example

What did you expect to happen?

Units attribute to be written to the netcdf file.

Minimal Complete Verifiable Example

```Python import numpy as np import xarray as xr

Create a new Dataset

ds = xr.Dataset()

Add the x variable, Specify 'x_bnds' as bounds, defined later.

ds['x'] = xr.DataArray(np.arange(10), dims='x', attrs={'units':'m', 'bounds':'x_bnds'})

Bounds require an extra dimension equal to number of vertices.

ds['nv'] = xr.DataArray(np.r_[0, 1], dims='nv')

Add the actual bounding values for variable x.

ds['x_bnds'] = xr.DataArray(np.squeeze(np.dstack([np.arange(10)-0.5, np.arange(10)+0.5])),
dims=['x', 'nv'], attrs={'test':4, 'units':'m', })

print('Units is attached to the bounds in the dataset before writing', 'units' in ds['x_bnds'].attrs)

Write to netcdf file

ds.to_netcdf('tmp.nc', format='netcdf4', engine='netcdf4')

Open the dataset and check x_bnds attrs. units is dropped.

new = xr.open_dataset('tmp.nc') print(new['x_bnds'].attrs)

Confirm that units were never written to the file.

!h5dump -d /x_bnds tmp.nc ```

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.
  • [X] Recent environment — the issue occurs with the latest version of xarray and its dependencies.

Relevant log output

No response

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.11.5 (main, Sep 11 2023, 08:19:27) [Clang 14.0.6 ] python-bits: 64 OS: Darwin OS-release: 21.6.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.12.2 libnetcdf: 4.9.3-development xarray: 2023.10.1 pandas: 2.1.1 numpy: 1.26.1 scipy: 1.11.3 netCDF4: 1.6.4 pydap: None h5netcdf: None h5py: 3.10.0 Nio: None zarr: None cftime: 1.6.3 nc_time_axis: None PseudoNetCDF: None iris: None bottleneck: None dask: None distributed: None matplotlib: 3.8.0 cartopy: None seaborn: None numbagg: None fsspec: None cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 68.0.0 pip: 23.3 conda: None pytest: None mypy: None IPython: 8.16.1 sphinx: 7.2.6 
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     xarray 13221727 issue

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