issue_comments

I can't seem recreate this with a minimal example, xarray roundtrips a NetCDF file with a coordinates attribute correctly:

```python from netCDF4 import Dataset import xarray as xr

with Dataset('test.nc', format='NETCDF4', mode='w') as nc: nc.createDimension('dim1', size=0) var = nc.createVariable('var1', 'f8', dimensions=('dim1')) var[:] = [1., 2., 3.] var.setncattr('coordinates', 'dim1')

xr.open_dataset('test.nc').to_netcdf('test2.nc') ```

There is something peculiar about how WRF handles the coordinates attribute, but I can't see anything off about it yet.

Interestingly, I can workaround the WRF coordinates issue by setting decode_coords=False in xarray.open_dataset(), for example, this works:

python xr.open_dataset('wrfout_d01_2019-04-16_15_00_00', decode_coords=False).to_netcdf('test.nc')

while this doesn't:

python xr.open_dataset('wrfout_d01_2019-04-16_15_00_00').to_netcdf('test.nc')

I ran into this issue trying to roundtrip a WRF output file. It looks like xarray raises an error for any NetCDF file that has variables with a coordinates attribute:

python # These coordinates are saved according to CF conventions for var_name, coord_names in variable_coordinates.items(): attrs = variables[var_name].attrs if 'coordinates' in attrs: raise ValueError('cannot serialize coordinates because variable ' "%s already has an attribute 'coordinates'" % var_name) attrs['coordinates'] = ' '.join(map(str, coord_names))

~~Both this choice, and the proposed solution in this issue (delete all coordinates attributes), I don't understand.~~ Variables with a coordinates attribute are CF conforming, so xarray should be able to play along with this.

~~The solution that makes more sense to me is to raise a warning and overwrite or ignore the coordinates attribute, if the attribute is already present. Later step of the fix could even be a keyword argument to allow the user to choose whether to overwrite or ignore "conflicting" attributes.~~

Or perhaps I'm missing something obvious here... Let me know either way. I'd be happy to make a PR to patch this.

That's perfect. Thank you!

@gbromley The best option is probably a loop, e.g., python def remove_problematic_attrs(ds): for variable in ds.variables.values(): if 'coordinates' in variable.attrs: del variable.attrs['coordinates']

Hello, I realized I never followed up with this but am again running into issues. The real problem for me is that deleting coordinates on 30+ variables isn't really feasible. Is it possible to delete the coordinates attribute for all variables?

Thanks for the solution (that was my SO post as well). Deleting the attrs.['coordinates'] was a clean workaround. Here's the requested WRF meta. It was concatenated with NCO, but meta should be consistent.

WRF_meta.txt

See https://stackoverflow.com/questions/50475453/xarray-cannot-serialize-coordinates/50475925.

It seems like WRF may often produce netCDF files that lead to this issue. If the problem can be reproduced by simply opening and resaving a netCDF file then we may want to revisit our logic in xarray, because we always want xarray.open_dataset(input_path).to_netcdf(output_path) to work. If this is the case, it would be great if someone could share metadata for such a problematic netCDF file (e.g., from ncdump -h).

Did you ever find a solution to this?

It looks like your variable has an attribute coordinates: try deleting it before writing the data.

Would you mind printing md first to show what it looks like?