Merge pull request #168 from csiro-coasts/165-connectivity-fill-value-validation

Added additional validation for connectivity checks.

Author: david-sh-csiro

docs/releases/development.rst

@@ -2,5 +2,7 @@
 Next release (in development)
 =============================
 
+* Added additional validation for ugrid
+  connectivity(:issue:`165`, :pr:`168`).
 * Fix datasets hash_key generation when geometry encoding
   is missing a dtype (:issue:`166`, :pr:`167`).

src/emsarray/conventions/ugrid.py

@@ -748,6 +748,20 @@ def has_valid_face_edge_connectivity(self) -> bool:
             )
             return False
 
+        if '_FillValue' in data_array.encoding:
+            fill_value = data_array.encoding['_FillValue']
+
+            lower_bound = _get_start_index(data_array)
+            upper_bound = self.edge_count + lower_bound
+
+            if lower_bound <= fill_value <= upper_bound:
+                warnings.warn(
+                    f"Got a face_edge_connectivity variable {data_array.name!r} with "
+                    f"a _FillValue inside the actual index range",
+                    ConventionViolationWarning,
+                )
+                return False
+
         return True
 
     @cached_property

tests/conventions/test_ugrid.py

@@ -924,3 +924,60 @@ def da(attrs: dict) -> xarray.DataArray:
 
     with pytest.raises(ConventionViolationError):
         _get_start_index(da({'start_index': 2}))
+
+
+def test_has_valid_face_edge_connectivity():
+    # Create dataset with face_edges
+    dataset = make_dataset(width=3, make_edges=True, make_face_coordinates=True)
+    topology = dataset.ems.topology
+    topology.mesh_variable.attrs.update({
+        'face_edge_connectivity': 'Mesh2_face_edges',
+    })
+
+    mesh2_face_edges_array = topology.face_edge_array
+
+    mesh2_face_edges = xarray.DataArray(
+        mesh2_face_edges_array,
+        dims=[topology.face_dimension, topology.max_node_dimension],
+    )
+
+    dataset = dataset.assign({
+        'Mesh2_face_edges': mesh2_face_edges,
+    })
+
+    dataset_fill_value_below_range = dataset.copy()
+
+    dataset_fill_value_in_range_on_lower_boundary = dataset.copy()
+
+    dataset_fill_value_in_range = dataset.copy()
+
+    dataset_fill_value_in_range_on_upper_boundary = dataset.copy()
+
+    dataset_fill_value_above_range = dataset.copy()
+
+    # Make sure original dataset is valid
+    assert dataset.ems.topology.has_valid_face_edge_connectivity is True
+
+    # Test valid and invalid fill values
+    dataset_fill_value_below_range['Mesh2_face_edges'].encoding['_FillValue'] = -1
+
+    assert dataset_fill_value_below_range.ems.topology.has_valid_face_edge_connectivity is True
+
+    dataset_fill_value_in_range_on_lower_boundary['Mesh2_face_edges'].encoding['_FillValue'] = 0
+
+    with pytest.warns(ConventionViolationWarning):
+        assert dataset_fill_value_in_range_on_lower_boundary.ems.topology.has_valid_face_edge_connectivity is not True
+
+    dataset_fill_value_in_range['Mesh2_face_edges'].encoding['_FillValue'] = 44
+
+    with pytest.warns(ConventionViolationWarning):
+        assert dataset_fill_value_in_range.ems.topology.has_valid_face_edge_connectivity is not True
+
+    dataset_fill_value_in_range_on_upper_boundary['Mesh2_face_edges'].encoding['_FillValue'] = 88
+
+    with pytest.warns(ConventionViolationWarning):
+        assert dataset_fill_value_in_range_on_upper_boundary.ems.topology.has_valid_face_edge_connectivity is not True
+
+    dataset_fill_value_above_range['Mesh2_face_edges'].encoding['_FillValue'] = 89
+
+    assert dataset_fill_value_above_range.ems.topology.has_valid_face_edge_connectivity is True