support writing of netfile with start_index=1 and _FillValue!=-1

[veenstrajelmer]

Unfortunately, dflowfm does not read the start_index attribute but assumes 1. When writing a newly generated meshkernelpy grid (start_index=0, _FillValue=-1) to a netcdf file, the start_index has to be converted to 1. Currently, dfm_tools uses this workaround in meshkernel_to_UgridDataset():

mesh2d_grid = mk.mesh2d_get()
xu_grid = xu.Ugrid2d.from_meshkernel(mesh2d_grid)

#convert 0-based to 1-based indices for connectivity variables like face_node_connectivity
xu_grid_ds = xu_grid.to_dataset()
xu_grid_ds = xr.decode_cf(xu_grid_ds) #decode_cf is essential since it replaces fillvalues with nans
ds_idx = xu_grid_ds.filter_by_attrs(start_index=0)
for varn_conn in ds_idx.data_vars:
    xu_grid_ds[varn_conn] += 1 #from startindex 0 to 1 (fillvalues are now nans, so this is safe to do)
    xu_grid_ds[varn_conn].attrs["start_index"] += 1
    xu_grid_ds[varn_conn].encoding["_FillValue"] = -1 #can be any value <=0, but non-zero is currently the most convenient for proper xugrid plots of node variables.

# convert to uds and add attrs and crs
xu_grid_uds = xu.UgridDataset(xu_grid_ds)

I can imagine that 1-based face_node_connectivity causes issues in 0-based Python. Could we maybe simplify the above process by for instance not changing the internal data, but instead upon writing a netcdf file with uds.ugrid.to_netcdf(), providing an argument start_index=1? Any other alternative is also fine.