Failure from cfdm.write when writing identical (auxiliary) coordinates to different data variables in different groups

[davidhassell]

It should be possible to write to disk fields with identical dimension or auxiliary coordinates to different groups, but this causes a failure from cfdm.write, which complains that the netCDF data variable dimensions are not in the same group or a parent group as the data variable itself.

It is good that cfdm.write complains about this, as it is a valid restriction, but it shouldn't have ended up in that situation in the first place.

Many thanks to @ajelenak who noticed and diagnosed this problem, and provided a minimal reproducer, which I slightly adapted here to also cover auxiliary coordinates:

import numpy as np
import cfdm

# Define dimension and auxiliary coordinates
station_name = cfdm.AuxiliaryCoordinate()
station_name.set_data(["station1", "station2"])
station_name.set_properties(
    {"long_name": "sensor id", "cf_role": "timeseries_id"}
)
station_name.nc_set_variable("station_name")

times = cfdm.DimensionCoordinate()
times.set_data(range(5))
times.set_properties(
    {"standard_name": "time", "units": "days since 1967-04-01"}
)
times.nc_set_variable("time")

file_content = list()
for mt in ("Dew Point", "Wind Speed"):
    grp_name = mt.replace(" ", "_")
    var_name = mt.replace(" ", "_")

    # Define domain axes
    stations = cfdm.DomainAxis(2)
    stations.nc_set_dimension("stations")
    stations.nc_set_dimension_groups([grp_name])

    time = cfdm.DomainAxis(5)
    time.nc_set_dimension("time")
    time.nc_set_dimension_groups([grp_name])

    # Assign new groups to dimension and auxiliary coordinates
    station_name = station_name.copy()
    station_name.nc_set_variable_groups([grp_name])

    times = times.copy()
    times.nc_set_variable_groups([grp_name])

    # Define the field in the same group as the coordinates
    f = cfdm.Field()

    station_axis = f.set_construct(stations)
    time_axis = f.set_construct(time)

    f.set_construct(times, axes=time_axis)
    f.set_construct(station_name, axes=station_axis)

    f.set_data(
        np.arange(10).reshape(5, 2), axes=[time_axis, station_axis]
    )

    f.nc_set_variable(var_name)
    f.nc_set_variable_groups([grp_name])

    file_content.append(f)

# This should not raise an exception, but does at v1.9.0.2
cfdm.write(file_content, "result.nc")

produces:

Traceback (most recent call last):
  File "/home/david/alek.py", line 59, in <module>
    cfdm.write(file_content, "result.nc")
  File "/home/david/miniconda3.9/lib/python3.9/site-packages/cfdm/read_write/write.py", line 522, in write
    netcdf.write(
  File "/home/david/miniconda3.9/lib/python3.9/site-packages/cfdm/decorators.py", line 171, in verbose_override_wrapper
    return method_with_verbose_kwarg(*args, **kwargs)
  File "/home/david/miniconda3.9/lib/python3.9/site-packages/cfdm/read_write/netcdf/netcdfwrite.py", line 4809, in write
    self._file_io_iteration(
  File "/home/david/miniconda3.9/lib/python3.9/site-packages/cfdm/read_write/netcdf/netcdfwrite.py", line 5089, in _file_io_iteration
    self._write_field_or_domain(f)
  File "/home/david/miniconda3.9/lib/python3.9/site-packages/cfdm/read_write/netcdf/netcdfwrite.py", line 3972, in _write_field_or_domain
    self._write_netcdf_variable(
  File "/home/david/miniconda3.9/lib/python3.9/site-packages/cfdm/read_write/netcdf/netcdfwrite.py", line 2696, in _write_netcdf_variable
    raise ValueError(
ValueError: Can't create netCDF variable '/Wind_Speed/Wind_Speed' from <Field: ncvar%/Wind_Speed/Wind_Speed(time(5), cf_role=timeseries_id(2))> with dimension '/Dew_Point/time' that is not in the same group or a sub-group as the variable.

>>> cfdm.environment(paths=False)
Platform: Linux-5.4.0-100-generic-x86_64-with-glibc2.31
HDF5 library: 1.12.1
netcdf library: 4.8.1
Python: 3.9.5
netCDF4: 1.5.8
numpy: 1.22.2
cfdm.core: 1.9.0.2
cftime: 1.5.2
netcdf_flattener: 1.2.0
cfdm: 1.9.0.2