What happened: Coordinates added to some variables unexpectedly.

I noticed this after outputting to netCDF. What I have: variables: double time(time) ; time:bounds = "time_bnds" ; time:axis = "T" ; time:long_name = "valid_time" ; time:standard_name = "time" ; time:units = "days since 1850-01-01" ; time:calendar = "gregorian" ; double time_bnds(time, bnds) ; time_bnds:_FillValue = NaN ; time_bnds:coordinates = "reftime leadtime height" ; double lat(lat) ; lat:bounds = "lat_bnds" ; lat:units = "degrees_north" ; lat:axis = "Y" ; lat:long_name = "latitude" ; lat:standard_name = "latitude" ; double lat_bnds(lat, bnds) ; lat_bnds:_FillValue = NaN ; lat_bnds:coordinates = "reftime height" ; double lon(lon) ; lon:bounds = "lon_bnds" ; lon:units = "degrees_east" ; lon:axis = "X" ; lon:long_name = "Longitude" ; lon:standard_name = "longitude" ; double lon_bnds(lon, bnds) ; lon_bnds:_FillValue = NaN ; lon_bnds:coordinates = "reftime height" ; double height ; height:_FillValue = NaN ; height:units = "m" ; height:axis = "Z" ; height:positive = "up" ; height:long_name = "height" ; height:standard_name = "height" ; float tas(time, lat, lon) ; tas:_FillValue = 1.e+20f ; tas:standard_name = "air_temperature" ; tas:long_name = "Near-Surface Air Temperature" ; tas:comment = "near-surface (usually, 2 meter) air temperature" ; tas:units = "K" ; tas:cell_methods = "area: time: mean" ; tas:cell_measures = "area: areacella" ; tas:history = "2019-05-11T15:53:32Z altered by CMOR: Treated scalar dimension: \'height\'. 2019-05-11T15:53:32Z altered by CMOR: Reordered dimensions, original order: lat lon time." ; tas:coordinates = "height reftime leadtime" ; tas:missing_value = 1.e+20f ; int reftime ; reftime:long_name = "Start date of the forecast" ; reftime:standard_name = "forecast_reference_time" ; reftime:units = "days since 1850-01-01" ; reftime:calendar = "gregorian" ; double leadtime(time) ; leadtime:_FillValue = NaN ; leadtime:long_name = "Time elapsed since the start of the forecast" ; leadtime:standard_name = "forecast_period" ; leadtime:units = "days" ; int realization ; realization:long_name = "realization" ; realization:comment = "For more information on the ripf, refer to the variant_label, initialization_description, physics_description and forcing_description global attributes" ; realization:coordinates = "reftime height" ;

On time_bnds, lon_bnds, lat_bnds and realization there is coordinates that I wouldn't expect to be there.

What you expected to happen: Looking only at the coordinates attribute, I expected my ncdump to show:

variables: int reftime ; reftime:long_name = "Start date of the forecast" ; reftime:standard_name = "forecast_reference_time" ; reftime:units = "days since 1850-01-01" ; reftime:calendar = "gregorian" ; double leadtime(time) ; leadtime:long_name = "Time elapsed since the start of the forecast" ; leadtime:standard_name = "forecast_period" ; leadtime:units = "days" ; int realization ; realization:long_name = "realization" ; realization:comment = "For more information on the ripf, refer to the variant_label, initialization_description, physics_description and forcing_description global attributes" ; double time(time) ; time:bounds = "time_bnds" ; time:axis = "T" ; time:standard_name = "time" ; time:units = "days since 1850-01-01" ; time:calendar = "gregorian" ; time:long_name = "valid_time" ; double time_bnds(time, bnds) ; time_bnds:units = "days since 1850-01-01" ; double lat(lat) ; lat:bounds = "lat_bnds" ; lat:units = "degrees_north" ; lat:axis = "Y" ; lat:long_name = "latitude" ; lat:standard_name = "latitude" ; double lat_bnds(lat, bnds) ; double lon(lon) ; lon:bounds = "lon_bnds" ; lon:units = "degrees_east" ; lon:axis = "X" ; lon:long_name = "Longitude" ; lon:standard_name = "longitude" ; double lon_bnds(lon, bnds) ; double height ; height:units = "m" ; height:axis = "Z" ; height:positive = "up" ; height:long_name = "height" ; height:standard_name = "height" ; float tas(time, lat, lon) ; tas:standard_name = "air_temperature" ; tas:long_name = "Near-Surface Air Temperature" ; tas:comment = "near-surface (usually, 2 meter) air temperature" ; tas:units = "K" ; tas:cell_methods = "area: time: mean" ; tas:cell_measures = "area: areacella" ; tas:history = "2019-05-11T15:53:32Z altered by CMOR: Treated scalar dimension: \'height\'. 2019-05-11T15:53:32Z altered by CMOR: Reordered dimensions, original order: lat lon time." ; tas:missing_value = 1.e+20f ; tas:_FillValue = 1.e+20f ; tas:coordinates = "height reftime leadtime" ;

I tried to remove this in the xarray dataset, but whatever I tried they always ended up back in there:

```

import xarray as xr ds = xr.open_dataset("file.nc", use_cftime=True)

show coords on realization

ds.realization <xarray.DataArray 'realization' ()> array(1, dtype=int32) Coordinates: height float64 ... reftime object ... Attributes: long_name: realization comment: For more information on the ripf, refer to the variant_label,...

try reset_coords - removes the coords

ds.realization.reset_coords(names=["height", "reftime"], drop=True) <xarray.DataArray 'realization' ()> array(1, dtype=int32) Attributes: long_name: realization comment: For more information on the ripf, refer to the variant_label,...

set realization with result of reset_coords

ds["realization"] = ds.realization.reset_coords(names=["height", "reftime"], drop=True)

coords back in

ds.realization <xarray.DataArray 'realization' ()> array(1, dtype=int32) Coordinates: height float64 ... reftime object ... Attributes: long_name: realization comment: For more information on the ripf, refer to the variant_label,...

try drop_vars - same thing happens

ds.realization.drop_vars(("height", "reftime")) <xarray.DataArray 'realization' ()> array(1, dtype=int32) Attributes: long_name: realization comment: For more information on the ripf, refer to the variant_label,...

ds["realization"] = ds.realization.drop_vars(("height", "reftime"))

ds.realization <xarray.DataArray 'realization' ()> array(1, dtype=int32) Coordinates: height float64 ... reftime object ... Attributes: long_name: realization comment: For more information on the ripf, refer to the variant_label,...

tried creating a new variable to see if the same thing happens - it does

ds["test"] = ds.realization.drop_vars(("height", "reftime")) ds.test <xarray.DataArray 'test' ()> array(1, dtype=int32) Coordinates: height float64 ... reftime object ... Attributes: long_name: realization comment: For more information on the ripf, refer to the variant_label,... ```

This seems like incorrect behaviour, but perhaps it is expected?

Minimal Complete Verifiable Example:

```python

data = xr.DataArray(np.random.randn(2, 3), dims=("x", "y"), coords={"x": [10, 20]}) ds = xr.Dataset({"foo": data, "bar": ("x", [1, 2]), "fake": 10}) ds = ds.assign_coords({"reftime":np.array("2004-11-01T00:00:00", dtype=np.datetime64)}) ds = ds.assign({"test": 1})

ds.test <xarray.DataArray 'test' ()> array(1) Coordinates: reftime datetime64[ns] 2004-11-01

ds.test.reset_coords(names=["reftime"], drop=True) <xarray.DataArray 'test' ()> array(1)

ds["test"] = ds.test.reset_coords(names=["reftime"], drop=True) ds.test <xarray.DataArray 'test' ()> array(1) Coordinates: reftime datetime64[ns] 2004-11-01

ds.to_netcdf("file.nc") ```

ncdump -h file.nc netcdf file { dimensions: x = 2 ; y = 3 ; variables: int64 x(x) ; double foo(x, y) ; foo:_FillValue = NaN ; foo:coordinates = "reftime" ; int64 bar(x) ; bar:coordinates = "reftime" ; int64 fake ; fake:coordinates = "reftime" ; int64 reftime ; reftime:units = "days since 2004-11-01 00:00:00" ; reftime:calendar = "proleptic_gregorian" ; int64 test ; test:coordinates = "reftime" ; }

Environment:

• [x] Closes #5510
• [x] Tests added - added one test - not sure if it should be somewhere else
• [x] Passes pre-commit run --all-files
• [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

What happened: When opening a netCDF file with xarray, then outputting to netCDF, _FillValue is added. This is an issue for coordinate variables time, lat and lon as CF conventions say that coordinate variables cannot have missing values, so we don't want this added _FillValue in this case.

e.g.

Before working with xarray: double lat(lat) ; lat:bounds = "lat_bnds" ; lat:units = "degrees_north" ; lat:axis = "Y" ; lat:long_name = "latitude" ; lat:standard_name = "latitude" ;

After working with xarray: double lat(lat) ; lat:_FillValue = NaN ; lat:bounds = "lat_bnds" ; lat:units = "degrees_north" ; lat:axis = "Y" ; lat:long_name = "latitude" ; lat:standard_name = "latitude" ;

_FIllValue is also added to the netCDF file for other variables but the main issue is the coordinate variables.

By setting ds.lat.encoding['_FillValue'] = None before outputting to NetCDF, the lat:_FillValue = NaN ; can be removed, but I don't think it should be there in the first place?

What you expected to happen: Output in file after to_netcdf to be the same as the input file.

Minimal Complete Verifiable Example:

```python import xarray as xr

my_file = xr.open_dataset("ts_Amon_HadGEM3-GC31-LL_ssp126_r1i1p1f3_gn_201501-204912.nc", use_cftime=True) my_file.to_netcdf("my_file_output.nc") ``` The file I used can be retrieved using https://dap.ceda.ac.uk/badc/cmip6/data/CMIP6/ScenarioMIP/MOHC/HadGEM3-GC31-LL/ssp126/r1i1p1f3/Amon/ts/gn/v20200114/ts_Amon_HadGEM3-GC31-LL_ssp126_r1i1p1f3_gn_201501-204912.nc, but this happens with any file.

Then comparing the ncdumps:

ncdump -h ts_Amon_HadGEM3-GC31-LL_ssp126_r1i1p1f3_gn_201501-204912.nc netcdf ts_Amon_HadGEM3-GC31-LL_ssp126_r1i1p1f3_gn_201501-204912 { dimensions: time = UNLIMITED ; // (420 currently) bnds = 2 ; lat = 144 ; lon = 192 ; variables: double time(time) ; time:bounds = "time_bnds" ; time:units = "days since 1850-01-01" ; time:calendar = "360_day" ; time:axis = "T" ; time:long_name = "time" ; time:standard_name = "time" ; double time_bnds(time, bnds) ; double lat(lat) ; lat:bounds = "lat_bnds" ; lat:units = "degrees_north" ; lat:axis = "Y" ; lat:long_name = "Latitude" ; lat:standard_name = "latitude" ; double lat_bnds(lat, bnds) ; double lon(lon) ; lon:bounds = "lon_bnds" ; lon:units = "degrees_east" ; lon:axis = "X" ; lon:long_name = "Longitude" ; lon:standard_name = "longitude" ; double lon_bnds(lon, bnds) ; float ts(time, lat, lon) ; ts:standard_name = "surface_temperature" ; ts:long_name = "Surface Temperature" ; ts:comment = "Temperature of the lower boundary of the atmosphere" ; ts:units = "K" ; ts:original_name = "mo: (stash: m01s00i024, lbproc: 128)" ; ts:cell_methods = "area: time: mean" ; ts:cell_measures = "area: areacella" ; ts:history = "2020-01-13T10:05:19Z altered by CMOR: replaced missing value flag (-1.07374e+09) with standard missing value (1e+20)." ; ts:missing_value = 1.e+20f ; ts:_FillValue = 1.e+20f ;
and

ncdump -h my_file_output.nc netcdf my_file_output { dimensions: time = UNLIMITED ; // (420 currently) bnds = 2 ; lat = 144 ; lon = 192 ; variables: double time(time) ; time:_FillValue = NaN ; time:bounds = "time_bnds" ; time:axis = "T" ; time:long_name = "time" ; time:standard_name = "time" ; time:units = "days since 1850-01-01" ; time:calendar = "360_day" ; double time_bnds(time, bnds) ; time_bnds:_FillValue = NaN ; double lat(lat) ; lat:_FillValue = NaN ; lat:bounds = "lat_bnds" ; lat:units = "degrees_north" ; lat:axis = "Y" ; lat:long_name = "Latitude" ; lat:standard_name = "latitude" ; double lat_bnds(lat, bnds) ; lat_bnds:_FillValue = NaN ; double lon(lon) ; lon:_FillValue = NaN ; lon:bounds = "lon_bnds" ; lon:units = "degrees_east" ; lon:axis = "X" ; lon:long_name = "Longitude" ; lon:standard_name = "longitude" ; double lon_bnds(lon, bnds) ; lon_bnds:_FillValue = NaN ; float ts(time, lat, lon) ; ts:_FillValue = 1.e+20f ; ts:standard_name = "surface_temperature" ; ts:long_name = "Surface Temperature" ; ts:comment = "Temperature of the lower boundary of the atmosphere" ; ts:units = "K" ; ts:original_name = "mo: (stash: m01s00i024, lbproc: 128)" ; ts:cell_methods = "area: time: mean" ; ts:cell_measures = "area: areacella" ; ts:history = "2020-01-13T10:05:19Z altered by CMOR: replaced missing value flag (-1.07374e+09) with standard missing value (1e+20)." ; ts:missing_value = 1.e+20f ;

shows that _FillValue has been added to time, time_bnds, lat, lat_bnds, lon and lon_bnds

Environment: