After doing ```python

!wget https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/dev/xarray-issue/source.nc

ds = xr.open_dataset('source.nc') ds = ds.rename({'number': 'n'}) ds = ds.set_coords('valid_time') print(ds) ds.to_netcdf('out.nc') ds = xr.open_dataset('out.nc') print(ds) ``'valid_time'` is not a coordinate in the netcdf file coordinate is turned into a variable.

<xarray.Dataset> Dimensions: (heightAboveGround: 1, latitude: 121, longitude: 240, n: 2, step: 3, time: 1) Coordinates: * n (n) int64 0 1 * time (time) datetime64[ns] 2020-01-02 * step (step) timedelta64[ns] 1 days 2 days 3 days * heightAboveGround (heightAboveGround) int64 2 * latitude (latitude) float64 90.0 88.5 87.0 ... -87.0 -88.5 -90.0 * longitude (longitude) float64 0.0 1.5 3.0 4.5 ... 355.5 357.0 358.5 valid_time (time, step) datetime64[ns] ... Data variables: t2m (n, time, step, heightAboveGround, latitude, longitude) float32 ... Attributes: GRIB_edition: 2 GRIB_centre: ecmf GRIB_centreDescription: European Centre for Medium-Range Weather Forecasts GRIB_subCentre: 0 Conventions: CF-1.7 institution: European Centre for Medium-Range Weather Forecasts history: 2021-04-15T12:08:59 GRIB to CDM+CF via cfgrib-0....

<xarray.Dataset> Dimensions: (heightAboveGround: 1, latitude: 121, longitude: 240, n: 2, step: 3, time: 1) Coordinates: * n (n) int64 0 1 * time (time) datetime64[ns] 2020-01-02 * step (step) timedelta64[ns] 1 days 2 days 3 days * heightAboveGround (heightAboveGround) int64 2 * latitude (latitude) float64 90.0 88.5 87.0 ... -87.0 -88.5 -90.0 * longitude (longitude) float64 0.0 1.5 3.0 4.5 ... 355.5 357.0 358.5 Data variables: valid_time (time, step) datetime64[ns] ... t2m (n, time, step, heightAboveGround, latitude, longitude) float32 ... Attributes: GRIB_edition: 2 GRIB_centre: ecmf GRIB_centreDescription: European Centre for Medium-Range Weather Forecasts GRIB_subCentre: 0 Conventions: CF-1.7 institution: European Centre for Medium-Range Weather Forecasts history: 2021-04-15T12:08:59 GRIB to CDM+CF via cfgrib-0....

What happened: Output of the MCVE is : Coords written in copy.1.nc: ['number', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time'] Reread and check copy.1.nc: ['number', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time']

Coords written in copy.2.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time'] Reread and check copy.2.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude']

Coords written in copy.4.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time'] Reread and check copy.4.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time']

What you expected to happen Output of the MCVE should be :

Coords written in copy.1.nc: ['number', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time'] Reread and check copy.1.nc: ['number', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time']

Coords written in copy.2.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time'] Reread and check copy.2.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time']

Coords written in copy.4.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time'] Reread and check copy.4.nc: ['n', 'time', 'step', 'heightAboveGround', 'latitude', 'longitude', 'valid_time']

Minimal Complete Verifiable Example:

```python

import xarray as xr import numpy as np

xr.show_versions() print(xr.file)

FILE1 = 'copy.1.nc' FILE2 = 'copy.2.nc' FILE3 = 'copy.3.nc' FILE4 = 'copy.4.nc'

ds = xr.open_dataset('source.nc')

Initial dataset is ok

print(f'Coords written in {FILE1}: {list(ds.coords)}') ds.to_netcdf(FILE1) print(f'Reread and check {FILE1}: {list(xr.open_dataset(FILE1).coords)}')

print(xr.open_dataset(FILE1))

print()

No round trip

ds = ds.rename({'number': 'n'}) ds = ds.set_coords('valid_time') print(f'Coords written in {FILE2}: {list(ds.coords)}') ds.to_netcdf(FILE2) print(f'Reread and check {FILE2}: {list(xr.open_dataset(FILE2).coords)}')

print(xr.open_dataset(FILE2))

print()

Doing a round trip solves the issue :

ds = xr.open_dataset('source.nc') ds = ds.rename({'number': 'n'}) ds.to_netcdf(FILE3) ds = xr.open_dataset(FILE3) ds = ds.set_coords('valid_time') print(f'Coords written in {FILE4}: {list(ds.coords)}') ds.to_netcdf(FILE4) print(f'Reread and check {FILE4}: {list(xr.open_dataset(FILE4).coords)}')

print(xr.open_dataset(FILE4))

```

Anything else we need to know?: The initial source.nc file is available at wget https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/dev/xarray-issue/source.nc

Environment:

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

INSTALLED VERSIONS ------------------ commit: None python: 3.8.6 | packaged by conda-forge | (default, Jan 25 2021, 23:21:18) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 3.10.0-1160.15.2.el7.x86_64 machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.12.0 libnetcdf: 4.7.4 xarray: 0.17.0 pandas: 1.2.2 numpy: 1.19.5 scipy: None netCDF4: 1.5.6 pydap: None h5netcdf: None h5py: 2.10.0 Nio: None zarr: 2.6.1 cftime: 1.4.1 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: 0.9.8.5 iris: None bottleneck: None dask: 2021.02.0 distributed: 2021.02.0 matplotlib: 3.3.4 cartopy: None seaborn: None numbagg: None pint: None setuptools: 49.6.0.post20210108 pip: 21.0.1 conda: 4.9.2 pytest: 5.3.1 IPython: 7.20.0 sphinx: 3.4.3

It may be related/duplicate of #4512 and linked to https://github.com/pydata/xarray/pull/4108