issues: 1416709246

What is your issue?

This seems to be an issue only with netcdf files that I have first opened altered and then saved with xarray. Also, this could be related to: https://github.com/pydata/xarray/issues/997 but seems to have different bug characteristics. However, I am unable to save to netcdf due to apparent conflicts in the masking attribute variables, which don't exist in the file.

xarray package version: python print(xr.__version__) ##2022.10.0 print(dask.__version__) ##2022.03.0

I am unable to save to netcdf due to error: python ValueError: Variable 'uwnd' has conflicting _FillValue (nan) and missing_value (-9.969209968386869e+36). Cannot encode data. Though variable uwnd has neither attrs "_FillValue" or "missing_value".

```python DS_cera0_full.to_netcdf('/Users/wchapman/Downloads/uvwndNOAA/tester.nc')

---

ValueError Traceback (most recent call last) Cell In [35], line 1 ----> 1 DS_cera0_full.to_netcdf('/Users/wchapman/Downloads/uvwndNOAA/tester.nc')

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/core/dataset.py:1899, in Dataset.to_netcdf(self, path, mode, format, group, engine, encoding, unlimited_dims, compute, invalid_netcdf) 1896 encoding = {} 1897 from ..backends.api import to_netcdf -> 1899 return to_netcdf( # type: ignore # mypy cannot resolve the overloads:( 1900 self, 1901 path, 1902 mode=mode, 1903 format=format, 1904 group=group, 1905 engine=engine, 1906 encoding=encoding, 1907 unlimited_dims=unlimited_dims, 1908 compute=compute, 1909 multifile=False, 1910 invalid_netcdf=invalid_netcdf, 1911 )

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/backends/api.py:1230, in to_netcdf(dataset, path_or_file, mode, format, group, engine, encoding, unlimited_dims, compute, multifile, invalid_netcdf) 1225 # TODO: figure out how to refactor this logic (here and in save_mfdataset) 1226 # to avoid this mess of conditionals 1227 try: 1228 # TODO: allow this work (setting up the file for writing array data) 1229 # to be parallelized with dask -> 1230 dump_to_store( 1231 dataset, store, writer, encoding=encoding, unlimited_dims=unlimited_dims 1232 ) 1233 if autoclose: 1234 store.close()

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/backends/api.py:1277, in dump_to_store(dataset, store, writer, encoder, encoding, unlimited_dims) 1274 if encoder: 1275 variables, attrs = encoder(variables, attrs) -> 1277 store.store(variables, attrs, check_encoding, writer, unlimited_dims=unlimited_dims)

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/backends/common.py:266, in AbstractWritableDataStore.store(self, variables, attributes, check_encoding_set, writer, unlimited_dims) 263 if writer is None: 264 writer = ArrayWriter() --> 266 variables, attributes = self.encode(variables, attributes) 268 self.set_attributes(attributes) 269 self.set_dimensions(variables, unlimited_dims=unlimited_dims)

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/backends/common.py:355, in WritableCFDataStore.encode(self, variables, attributes) 352 def encode(self, variables, attributes): 353 # All NetCDF files get CF encoded by default, without this attempting 354 # to write times, for example, would fail. --> 355 variables, attributes = cf_encoder(variables, attributes) 356 variables = {k: self.encode_variable(v) for k, v in variables.items()} 357 attributes = {k: self.encode_attribute(v) for k, v in attributes.items()}

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/conventions.py:868, in cf_encoder(variables, attributes) 865 # add encoding for time bounds variables if present. 866 _update_bounds_encoding(variables) --> 868 new_vars = {k: encode_cf_variable(v, name=k) for k, v in variables.items()} 870 # Remove attrs from bounds variables (issue #2921) 871 for var in new_vars.values():

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/conventions.py:868, in <dictcomp>(.0) 865 # add encoding for time bounds variables if present. 866 _update_bounds_encoding(variables) --> 868 new_vars = {k: encode_cf_variable(v, name=k) for k, v in variables.items()} 870 # Remove attrs from bounds variables (issue #2921) 871 for var in new_vars.values():

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/conventions.py:273, in encode_cf_variable(var, needs_copy, name) 264 ensure_not_multiindex(var, name=name) 266 for coder in [ 267 times.CFDatetimeCoder(), 268 times.CFTimedeltaCoder(), (...) 271 variables.UnsignedIntegerCoder(), 272 ]: --> 273 var = coder.encode(var, name=name) 275 # TODO(shoyer): convert all of these to use coders, too: 276 var = maybe_encode_nonstring_dtype(var, name=name)

File ~/opt/miniconda3/envs/windypharm/lib/python3.10/site-packages/xarray/coding/variables.py:161, in CFMaskCoder.encode(self, variable, name) 154 mv = encoding.get("missing_value") 156 if ( 157 fv is not None 158 and mv is not None 159 and not duck_array_ops.allclose_or_equiv(fv, mv) 160 ): --> 161 raise ValueError( 162 f"Variable {name!r} has conflicting _FillValue ({fv}) and missing_value ({mv}). Cannot encode data." 163 ) 165 if fv is not None: 166 # Ensure _FillValue is cast to same dtype as data's 167 encoding["_FillValue"] = dtype.type(fv)

ValueError: Variable 'uwnd' has conflicting _FillValue (nan) and missing_value (-9.969209968386869e+36). Cannot encode data.

```

Manually setting those variables does not remove the error.

```python DS_cera0_full.uwnd.attrs['_FillValue']=np.nan DS_cera0_full.uwnd.attrs['missing_value']=np.nan DS_cera0_full.to_netcdf('/Users/wchapman/Downloads/uvwndNOAA/tester.nc')

ValueError: Variable 'uwnd' has conflicting _FillValue (nan) and missing_value (-9.969209968386869e+36). Cannot encode data. ```

h5netcdf engine shows the same behavior.

python DS_cera0_full.to_netcdf('/Users/wchapman/Downloads/uvwndNOAA/tester.nc',engine='h5netcdf') ValueError: Variable 'uwnd' has conflicting _FillValue (nan) and missing_value (-9.969209968386869e+36). Cannot encode data.