Fix edge_face_distance functions in neighbors.py. Add unit test in test_neighbors.py

[egallmeier]

Closes #1291

Overview

• Fixed _populate_edge_face_distances and _construct_edge_face_distances in neighbors.py from using node coordinates to face coordinates
• Added a simple test in test_neighbors.py to validate the _construct_edge_face_distances functionality.

Testing
Creates 5 face longitude and latitude pairs. The expected distances are:

• Face 0 to Face 1: a quarter circle, pi/2 radians
• Face 0 to Face 2: a quarter circle, pi/2 radians
• Face 1 to Face 3: both at lat=90° (north pole), same point, distance = 0
• Face 2 to Face 4: 3/8 of a circle

[philipc2]

@egallmeier

Looks like one of gradient test is failing now, which is probably due to the change in the distance. The expected values we set before we most likely incorrect.

[philipc2]

It appears that one of the tests is still failing. 3 of the values seem to be mismatched.

[egallmeier]

@philipc2 are you referring to test_gradient.py::test_quad_hex?

[philipc2]

@philipc2 are you referring to test_gradient.py::test_quad_hex?

Yeah, it seems to still be failing in the CI above.

[github-actions]

ASV Benchmarking

Benchmark Comparison Results

Benchmarks that have improved:

Change	Before [5c74b0c]	After [5c787c8]	Ratio	Benchmark (Parameter)
-	777M	346M	0.45	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
	failed	755M	n/a	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
-	380M	298M	0.79	mpas_ocean.Integrate.peakmem_integrate('480km')

Benchmarks that have stayed the same:

Change	Before [5c74b0c]	After [5c787c8]	Ratio	Benchmark (Parameter)
	345M	345M	1.00	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	376M	376M	1.00	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	19.2±0.1ms	19.2±0.2ms	1.00	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	3.34±0.02ms	3.31±0.02ms	0.99	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	17.2±0.03ms	17.2±0.01ms	1.00	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
	2.10±0ms	2.03±0.06ms	0.96	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
	2.07±0.04s	2.07±0.03s	1.00	import.Imports.timeraw_import_uxarray
	898±7μs	874±3μs	0.97	mpas_ocean.CheckNorm.time_check_norm('120km')
	701±3μs	691±2μs	0.99	mpas_ocean.CheckNorm.time_check_norm('480km')
	825±3ms	801±10ms	0.97	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('120km')
	53.4±0.7ms	52.2±1ms	0.98	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('480km')
	647±9μs	648±10μs	1.00	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('120km')
	522±20μs	532±8μs	1.02	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('480km')
	6.27±0.04ms	6.28±0.06ms	1.00	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('120km')
	4.72±0.04ms	4.69±0.03ms	0.99	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('480km')
	3.48±0.01s	3.50±0.01s	1.01	mpas_ocean.ConstructFaceLatLon.time_welzl('120km')
	220±2ms	224±1ms	1.02	mpas_ocean.ConstructFaceLatLon.time_welzl('480km')
	18.1±0.02ms	18.2±0.06ms	1.01	mpas_ocean.ConstructTreeStructures.time_ball_tree('120km')
	923±20μs	891±10μs	0.96	mpas_ocean.ConstructTreeStructures.time_ball_tree('480km')
	11.4±0.04ms	11.3±0.03ms	1.00	mpas_ocean.ConstructTreeStructures.time_kd_tree('120km')
	1.10±0.03ms	1.10±0.01ms	1.00	mpas_ocean.ConstructTreeStructures.time_kd_tree('480km')
	529±4ms	534±3ms	1.01	mpas_ocean.CrossSections.time_const_lat('120km', 1)
	272±3ms	269±2ms	0.99	mpas_ocean.CrossSections.time_const_lat('120km', 2)
	140±2ms	140±0.6ms	1.00	mpas_ocean.CrossSections.time_const_lat('120km', 4)
	426±2ms	434±4ms	1.02	mpas_ocean.CrossSections.time_const_lat('480km', 1)
	216±1ms	218±2ms	1.01	mpas_ocean.CrossSections.time_const_lat('480km', 2)
	111±0.9ms	113±0.7ms	1.02	mpas_ocean.CrossSections.time_const_lat('480km', 4)
	49.6±0.2ms	50.0±0.4ms	1.01	mpas_ocean.DualMesh.time_dual_mesh_construction('120km')
	4.92±0.05ms	4.96±0.02ms	1.01	mpas_ocean.DualMesh.time_dual_mesh_construction('480km')
	927±5ms	919±2ms	0.99	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', False)
	54.1±0.5ms	54.2±0.3ms	1.00	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', True)
	74.4±0.2ms	74.1±0.3ms	1.00	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', False)
	5.12±0.06ms	5.10±0.08ms	1.00	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', True)
	234M	235M	1.00	mpas_ocean.Gradient.peakmem_gradient('120km')
	218M	219M	1.00	mpas_ocean.Gradient.peakmem_gradient('480km')
	2.72±0ms	2.74±0.01ms	1.00	mpas_ocean.Gradient.time_gradient('120km')
	336±7μs	336±8μs	1.00	mpas_ocean.Gradient.time_gradient('480km')
	218±3μs	213±0.6μs	0.98	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('120km')
	126±2μs	126±0.7μs	1.00	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('480km')
	311M	311M	1.00	mpas_ocean.Integrate.peakmem_integrate('120km')
	150±4ms	150±1ms	1.00	mpas_ocean.Integrate.time_integrate('120km')
	18.0±0.08ms	18.3±0.4ms	1.02	mpas_ocean.Integrate.time_integrate('480km')
	349±2ms	346±0.8ms	0.99	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'exclude')
	353±7ms	349±0.9ms	0.99	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'include')
	351±3ms	349±5ms	0.99	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'split')
	22.7±0.1ms	23.0±0.2ms	1.01	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'exclude')
	22.9±0.1ms	22.7±0.3ms	0.99	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'include')
	23.1±0.2ms	22.6±0.2ms	0.98	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'split')
	failed	failed	n/a	mpas_ocean.PointInPolygon.time_face_search('120km')
	failed	failed	n/a	mpas_ocean.PointInPolygon.time_face_search('480km')
	274±5ms	267±2ms	0.98	mpas_ocean.RemapDownsample.time_bilinear_remapping
	293±2ms	291±1ms	0.99	mpas_ocean.RemapDownsample.time_inverse_distance_weighted_remapping
	28.9±0.1ms	28.8±0.1ms	1.00	mpas_ocean.RemapDownsample.time_nearest_neighbor_remapping
	1.38±0.01s	1.38±0.01s	1.00	mpas_ocean.RemapUpsample.time_bilinear_remapping
	52.1±0.4ms	51.6±0.5ms	0.99	mpas_ocean.RemapUpsample.time_inverse_distance_weighted_remapping
	26.5±0.3ms	26.3±0.4ms	1.00	mpas_ocean.RemapUpsample.time_nearest_neighbor_remapping
	27.6±0.6ms	28.0±0.05ms	1.02	mpas_ocean.ZonalAverage.time_zonal_average('120km')
	5.66±0.01ms	5.48±0.06ms	0.97	mpas_ocean.ZonalAverage.time_zonal_average('480km')
	215M	217M	1.01	quad_hexagon.QuadHexagon.peakmem_open_dataset
	214M	214M	1.00	quad_hexagon.QuadHexagon.peakmem_open_grid
	7.52±0.02ms	7.56±0.03ms	1.01	quad_hexagon.QuadHexagon.time_open_dataset
	6.52±0.02ms	6.57±0.02ms	1.01	quad_hexagon.QuadHexagon.time_open_grid

[philipc2]

Excellent work @egallmeier

[kafitzgerald]

Looks great 🎉