I'm also not sure why _FillValue and missing_value should be required to have the same value.

Xarray has only one way to represent both concepts: np.nan. So when you decode you lose information on whether a value was a missing_value or _FillValue. Then when you encode, you have to pick either _FillValue or missing_value to represent the np.nan

to_netcdf will assign '_FillValue': nan.

This seems like a bug. Can you open a new issue with a minimum reproducible example that uses random data please?

@kmuehlbauer So it looks like uwnd.encoding does contain _FillVale and missing_value which are contrasting. Setting them to equal values enables a save.

However, these variables were set to contrasting values after an xarray subset or save. See workflow below. It appears that to_netcdf will assign '_FillValue': nan. I don't know if this is behavior that requires a change, or if it is just a quirk that folks will have to work through.

python fn_E20c_VP=sorted(glob.glob('/Users/wchapman/Downloads/uvwndNOAA/uwnd*.nc')) DSorig = xr.open_dataset(fn_E20c_VP[0]) DSorig.uwnd.encoding {'zlib': True, 'szip': False, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': True, 'complevel': 2, 'fletcher32': False, 'contiguous': False, 'chunksizes': (1, 1, 73, 144), 'least_significant_digit': 1, 'source': '/Users/wchapman/Downloads/uvwndNOAA/uwnd.1950.nc', 'original_shape': (365, 17, 73, 144), 'dtype': dtype('float32'), 'missing_value': -9.96921e+36} Subset and Save: python fn_E20c_VP=sorted(glob.glob('/Users/wchapman/Downloads/uvwndNOAA/uwnd*.nc')) DS_subset = DSorig.sel(level=300) DS_subset.to_netcdf('/Users/wchapman/Downloads/test_behavior.nc') DS_subset.uwnd.encoding {'zlib': True, 'szip': False, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': True, 'complevel': 2, 'fletcher32': False, 'contiguous': False, 'chunksizes': (1, 1, 73, 144), 'least_significant_digit': 1, 'source': '/Users/wchapman/Downloads/uvwndNOAA/uwnd.1950.nc', 'original_shape': (365, 17, 73, 144), 'dtype': dtype('float32'), 'missing_value': -9.96921e+36} Re-open newly saved file and inspect :

python DS_subset_aftersave = xr.open_dataset('/Users/wchapman/Downloads/test_behavior.nc') DS_subset_aftersave.uwnd.encoding {'zlib': True, 'szip': False, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': True, 'complevel': 2, 'fletcher32': False, 'contiguous': False, 'chunksizes': (1, 73, 144), 'least_significant_digit': 1, 'source': '/Users/wchapman/Downloads/test_behavior.nc', 'original_shape': (365, 73, 144), 'dtype': dtype('float32'), 'missing_value': -9.96921e+36, '_FillValue': nan, 'coordinates': 'level'}

@dopplershift equivalence is checked here, there is also the error origination from.

https://github.com/pydata/xarray/blob/3c98ec7d96cc4b46664850cc7a40af2bc184fea0/xarray/coding/variables.py#L153-L163

And on the variable? Please also have a look at the docs on to_netcdf regarding encoding-kwarg.

@kmuehlbauer it looks like encoding is empty.

```python print(DS_cera0.encoding)

{}

```

I'm also not sure why _FillValue and missing_value should be required to have the same value.

@WillyChap Could you inspect the contents of .encoding. IIRC that values are located there. Or you would need to specify the encoding kwarg in to_netcdf.

Disclaimer: This is from the top of my head, so mistakes are likely.