Fix 224 inconsistent bounds

clisops/ops/base_operation.py

@@ -71,13 +71,15 @@ def _remove_redundant_fill_values(self, ds):
         """
         Get coordinate variables and remove fill values added by xarray (CF conventions say that coordinate variables cannot have missing values).
         Get bounds variables and remove fill values added by xarray.
+
+        See issue: https://github.com/roocs/clisops/issues/224
         """
         if isinstance(ds, xr.Dataset):
             main_var = get_main_variable(ds)
             for coord_id in ds[main_var].coords:
                 # remove fill value from coordinate variables
-                if ds.coords[coord_id].dims == (coord_id,):
-                    ds[coord_id].encoding["_FillValue"] = None
+                # if ds.coords[coord_id].dims == (coord_id,):
+                ds[coord_id].encoding["_FillValue"] = None
                 # remove fill value from bounds variables if they exist
                 try:
                     bnd = ds.cf.get_bounds(coord_id).name
@@ -86,6 +88,29 @@ def _remove_redundant_fill_values(self, ds):
                     continue
         return ds
 
+    def _remove_redundant_coordinates_from_bounds(self, ds):
+        """
+        This method removes redundant coordinates from bounds, example:
+
+            double time_bnds(time, bnds) ;
+                time_bnds:coordinates = "height" ;
+
+        Programs like cdo will complain about this:
+
+            Warning (cdf_set_var): Inconsistent variable definition for time_bnds!
+
+        See issue: https://github.com/roocs/clisops/issues/224
+        """
+        if isinstance(ds, xr.Dataset):
+            main_var = get_main_variable(ds)
+            for coord_id in ds[main_var].coords:
+                try:
+                    bnd = ds.cf.get_bounds(coord_id).name
+                    ds[bnd].encoding["coordinates"] = None
+                except KeyError:
+                    continue
+        return ds
+
     def process(self):
         """
         Main processing method used by all sub-classes.
@@ -108,6 +133,8 @@ def process(self):
 
         # remove fill values from lat/lon/time if required
         processed_ds = self._remove_redundant_fill_values(processed_ds)
+        # remove redundant coordinates from bounds
+        processed_ds = self._remove_redundant_coordinates_from_bounds(processed_ds)
 
         # Work out how many outputs should be created based on the size
         # of the array. Manage this as a list of time slices.

tests/ops/test_subset.py

@@ -1604,18 +1604,47 @@ def test_subset_nc_no_fill_value(cmip5_tas_file, tmpdir):
     ds.to_netcdf(f"{tmpdir}/test_fill_values.nc")
     ds = _load_ds(f"{tmpdir}/test_fill_values.nc")
 
+    # assert np.isnan(float(ds.time.encoding.get("_FillValue")))
     assert np.isnan(float(ds.lat.encoding.get("_FillValue")))
     assert np.isnan(float(ds.lon.encoding.get("_FillValue")))
+    assert np.isnan(float(ds.height.encoding.get("_FillValue")))
 
     assert np.isnan(float(ds.lat_bnds.encoding.get("_FillValue")))
     assert np.isnan(float(ds.lon_bnds.encoding.get("_FillValue")))
     assert np.isnan(float(ds.time_bnds.encoding.get("_FillValue")))
 
     # check that there is no fill value in encoding for coordinate variables and bounds
     res = _load_ds(result)
+    assert "_FillValue" not in res.time.encoding
     assert "_FillValue" not in res.lat.encoding
     assert "_FillValue" not in res.lon.encoding
+    assert "_FillValue" not in res.height.encoding
 
     assert "_FillValue" not in res.lat_bnds.encoding
     assert "_FillValue" not in res.lon_bnds.encoding
     assert "_FillValue" not in res.time_bnds.encoding
+
+
+def test_subset_nc_consistent_bounds(cmip5_tas_file, tmpdir):
+    """Tests clisops subset function with a time subset."""
+    result = subset(
+        ds=CMIP5_TAS,
+        time=time_interval("2005-01-01T00:00:00", "2020-12-30T00:00:00"),
+        output_dir=tmpdir,
+        output_type="nc",
+        file_namer="simple",
+    )
+    res = _load_ds(result)
+    # check fill value in bounds
+    assert "_FillValue" not in res.lat_bnds.encoding
+    assert "_FillValue" not in res.lon_bnds.encoding
+    assert "_FillValue" not in res.time_bnds.encoding
+    # check fill value in coordinates
+    assert "_FillValue" not in res.time.encoding
+    assert "_FillValue" not in res.lat.encoding
+    assert "_FillValue" not in res.lon.encoding
+    assert "_FillValue" not in res.height.encoding
+    # check coordinates in bounds
+    assert "coordinates" not in res.lat_bnds.encoding
+    assert "coordinates" not in res.lon_bnds.encoding
+    assert "coordinates" not in res.time_bnds.encoding