added example with bounds -- fixed assign_ugrid_topology

Author: ChrisBarker-NOAA

docs/examples/example_data/tris_and_bounds.nc

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61", "wheel", "setuptools_scm[toml]>=6.2"]
+requires = ["setuptools>=72", "wheel", "setuptools_scm[toml]>=8.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -8,7 +8,7 @@ authors = [
   { name = "Matthew Iannucci", email = "[email protected]" },
   { name = "Christopher H. Barker", email = "[email protected]" },
 ]
-description = "Subset Xarray datasets in space"
+description = "Subset Xarray datasets in time and space"
 readme = "README.md"
 requires-python = ">=3.10"
 keywords = ["xarray"]
@@ -31,7 +31,7 @@ dynamic = ["version"]
 
 dependencies = [
   "numpy",
-  "xarray>=2023.10.0",
+  "xarray>=2024.6",
   "cf_xarray",
   "cftime",
   "dask[complete]",
@@ -99,7 +99,7 @@ default = { solve-group = "default" }
 dev = { features = ["dev"], solve-group = "default" }
 examples = { features = ["examples"], solve-group = "default" }
 all = { features = ["dev", "examples"], solve-group = "default" }
-test310 = ["dev", "py310"]                                        # implicit: test310 = ["dev", "py310", "default"]
+test310 = ["dev", "py310"] # implicit: test310 = ["dev", "py310", "default"]
 test311 = ["dev", "py311"]
 test312 = ["dev", "py312"]
 
@@ -109,8 +109,8 @@ test312 = ["dev", "py312"]
 [tool.pixi.dependencies]
 python = ">=3.10"
 numpy = "*"
-xarray = ">=2023.10.0"
-pandas = ">=2.2.2"
+xarray = ">=2024.6"
+pandas = "*"
 cf_xarray = "*"
 dask = "*"
 fsspec = "*"

pixi.lock

@@ -49,6 +49,7 @@
         lonc:standard_name = "longitude" ;
         lonc:long_name = "zonal longitude" ;
         lonc:units = "degree_east" ;
+
     float latc(nele) ;
         latc:standard_name = "latitude" ;
         latc:long_name = "zonal latitude" ;
@@ -60,7 +61,7 @@
 
 face_face_connectivity:
     int nbe(three, nele) ;
-        nbe:long_name = "elements surrounding anch element" ;
+        nbe:long_name = "elements surrounding each element" ;
 
 The depth coordinates (xarray is not sure what to do with these ...)
 
@@ -87,10 +88,8 @@
         time:format = "defined reference date" ;
         time:time_zone = "UTC" ;
 
-
 Data on the grid:
 
-
     float h(node) ;
         h:standard_name = "sea_floor_depth_below_geoid" ;
         h:long_name = "Bathymetry" ;
@@ -265,7 +264,11 @@ def test_assign_ugrid_topology_min():
     assert mesh["face_coordinates"] == "lonc latc"
     assert mesh["face_face_connectivity"] == "nbe"
     assert mesh["face_dimension"] == "nele"
+    assert mesh["start_index"] == 1
 
+    # There should be no empty attributes
+    for key, val in mesh.items():
+        assert val
 
 def test_assign_ugrid_topology_dict():
     """
@@ -292,6 +295,36 @@ def test_assign_ugrid_topology_dict():
     assert mesh["face_face_connectivity"] == "nbe"
     assert mesh["face_dimension"] == "nele"
 
+def test_assign_ugrid_topology_no_face_coords():
+    """
+    test for no face coords
+
+    """
+    # this example has triangles and bounds -- no face coordinates
+    ds = xr.open_dataset(EXAMPLE_DATA / "tris_and_bounds.nc")
+    with pytest.raises(KeyError):
+        ds["mesh"]
+
+    ds = ugrid.assign_ugrid_topology(ds, face_node_connectivity='tris',
+                                         node_coordinates = ('lon lat'),
+                                         boundary_node_connectivity = 'bounds'
+                                         )
+
+    # there are others, but these are the ones that really matter.
+    mesh = ds["mesh"].attrs
+    assert mesh["cf_role"] == "mesh_topology"
+    assert mesh["node_coordinates"] == "lon lat"
+    assert mesh["face_node_connectivity"] == "tris"
+    assert mesh["face_dimension"] == "tris"
+
+    assert mesh.keys() == {'cf_role',
+                         'topology_dimension',
+                         'face_node_connectivity',
+                         'boundary_node_connectivity',
+                         'node_coordinates',
+                         'face_dimension',
+                         'start_index',
+                         }
 
 def test_assign_ugrid_topology_existing_mesh_var():
     """
@@ -351,6 +384,7 @@ def test_assign_ugrid_topology_start_index_zero_infer():
     assert ds["mesh_boundary_nodes"].attrs["start_index"] == 0
 
 
+
 # NOTE: these tests are probably not complete -- but they are something.
 #       we really should have a complete UGRID example to test with.
 def test_grid_vars():

pyproject.toml

@@ -413,12 +413,11 @@ def assign_ugrid_topology(
         raise ValueError(
             "face_node_connectivity is a required parameter if it is not in the mesh_topology variable"  # noqa: E501
         )
-
     if mesh.face_coordinates is None:
         try:
-            mesh.face_coordinates = ds[mesh.face_node_connectivity].cf.coordinates
+            face_coordinates = ds[mesh.face_node_connectivity].cf.coordinates
             mesh.face_coordinates = " ".join(f"{coord[0]}"
-                                             for coord in mesh.face_coordinates.values())
+                                             for coord in face_coordinates.values())
         except AttributeError:
             mesh.face_coordinates = None
 
@@ -487,7 +486,8 @@ def assign_ugrid_topology(
 
     # push the non-None mesh attributes back into the variable
     for key, val in mesh.__dict__.items():
-        if val is not None:
+        # can't use truthiness, as 0 is false
+        if not ((val is None) or (val == "")):
             mesh_attrs[key] = val
 
     return ds