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:

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

INSTALLED VERSIONS ------------------ commit: None python: 3.7.3 (default, Mar 27 2019, 16:54:48) [Clang 4.0.1 (tags/RELEASE_401/final)] python-bits: 64 OS: Darwin OS-release: 18.7.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: ('en_GB', 'UTF-8') libhdf5: 1.10.5 libnetcdf: 4.6.3 xarray: 0.18.2 pandas: 1.1.3 numpy: 1.19.2 scipy: None netCDF4: 1.5.4 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.4.1 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: 1.3.2 dask: 2.30.0 distributed: 2.30.0 matplotlib: None cartopy: None seaborn: None numbagg: None pint: None setuptools: 54.1.1 pip: 21.0.1 conda: None pytest: 6.2.2 IPython: 7.21.0 sphinx: 1.8.1