Connectivity benchmarks: gate larger files

[cmdupuis3]

This PR is to fix an issue with the connectivity benchmarks. The current github runner doesn't seem to have access to the larger dyamond files, so those benchmarks fail and spam up the benchmark logs.

Continuation of #1549.

Overview

I naively copied the file paths from the dyamond benchmarks without the gate, not realizing that the github runner wouldn't have access to them. The gate there basically pings for file access, which will fail for github's runner, but would succeed for someone running somewhere with transparent access to the data on Glade.

PR Checklist

General

• An issue is linked created and linked
• Add appropriate labels
• Filled out Overview and Expected Usage (if applicable) sections

Testing

• [N/A] Adequate tests are created if there is new functionality
• [N/A] Tests cover all possible logical paths in your function
• [N/A] Tests are not too basic (such as simply calling a function and nothing else)

Documentation

• Docstrings have been added to all new functions
• Docstrings have updated with any function changes
• Internal functions have a preceding underscore (_) and have been added to docs/internal_api/index.rst
• User functions have been added to docs/user_api/index.rst

Examples

• Any new notebook examples added to docs/examples/ folder
• Clear the output of all cells before committing
• New notebook files added to docs/examples.rst toctree
• New notebook files added to new entry in docs/gallery.yml with appropriate thumbnail photo in docs/_static/thumbnails/

[Sevans711]

Note, looks like benchmarks seem to be "failing" here for the reason discussed in issue #1547 (also affecting PR #1541).

[github-actions]

ASV Benchmarking

Benchmark Comparison Results

Benchmarks that have improved:

Change	Before [7c9b487]	After [b85be3a]	Ratio	Benchmark (Parameter)
-	630M	441M	0.7	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
-	751M	440M	0.59	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
-	550M	433M	0.79	mpas_ocean.Gradient.peakmem_gradient('480km')

Benchmarks that have stayed the same:

Change	Before [7c9b487]	After [b85be3a]	Ratio	Benchmark (Parameter)
	10.8±0.07μs	10.7±0.3μs	0.99	bench_connectivity.Connectivity.time_edge_face('120km')
	11.0±0.2μs	11.1±0.1μs	1.01	bench_connectivity.Connectivity.time_edge_face('480km')
	10.7±0.2μs	10.8±0.06μs	1.01	bench_connectivity.Connectivity.time_edge_node('120km')
	11.0±0.09μs	11.0±0.1μs	1.00	bench_connectivity.Connectivity.time_edge_node('480km')
	10.7±0.05μs	11.0±0.1μs	1.03	bench_connectivity.Connectivity.time_face_edge('120km')
	11.0±0.1μs	11.0±0.04μs	1.00	bench_connectivity.Connectivity.time_face_edge('480km')
	10.8±0.1μs	11.0±0.1μs	1.02	bench_connectivity.Connectivity.time_face_face('120km')
	11.2±0.1μs	10.9±0.1μs	0.97	bench_connectivity.Connectivity.time_face_face('480km')
	22.0±0.7μs	21.8±0.3μs	0.99	bench_connectivity.Connectivity.time_face_node('120km')
	22.2±0.3μs	22.0±0.1μs	0.99	bench_connectivity.Connectivity.time_face_node('480km')
	11.0±0.07μs	10.6±0.2μs	0.96	bench_connectivity.Connectivity.time_node_edge('120km')
	11.0±0.1μs	10.9±0.2μs	0.99	bench_connectivity.Connectivity.time_node_edge('480km')
	10.8±0.3μs	10.7±0.07μs	0.99	bench_connectivity.Connectivity.time_node_face('120km')
	11.0±0.2μs	11.2±0.08μs	1.02	bench_connectivity.Connectivity.time_node_face('480km')
	439M	439M	1.00	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	469M	469M	1.00	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	14.8±0.07ms	15.1±0.1ms	1.02	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	3.76±0.04ms	3.76±0.05ms	1.00	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	19.1±0.3ms	19.0±0.04ms	1.00	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
	2.21±0.02ms	2.21±0.05ms	1.00	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
	4.85±0.01s	4.98±0.02s	1.03	import.Imports.timeraw_import_uxarray
	943±9ns	960±5ns	1.02	mpas_ocean.CheckNorm.time_check_norm('120km')
	907±5ns	893±4ns	0.98	mpas_ocean.CheckNorm.time_check_norm('480km')
	839±3ms	872±20ms	1.04	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('120km')
	53.7±0.8ms	55.1±0.5ms	1.03	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('480km')
	703±10μs	679±7μs	0.97	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('120km')
	605±10μs	641±10μs	1.06	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('480km')
	5.43±0.02ms	5.46±0.02ms	1.01	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('120km')
	3.94±0.02ms	4.01±0.05ms	1.02	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('480km')
	3.42±0.01s	3.44±0.01s	1.01	mpas_ocean.ConstructFaceLatLon.time_welzl('120km')
	225±0.5ms	224±0.6ms	0.99	mpas_ocean.ConstructFaceLatLon.time_welzl('480km')
	18.2±0.04ms	18.2±0.03ms	1.00	mpas_ocean.ConstructTreeStructures.time_ball_tree('120km')
	1.04±0.02ms	1.07±0.02ms	1.03	mpas_ocean.ConstructTreeStructures.time_ball_tree('480km')
	10.6±0.03ms	10.7±0.04ms	1.02	mpas_ocean.ConstructTreeStructures.time_kd_tree('120km')
	690±4ms	733±4ms	1.06	mpas_ocean.CrossSections.time_const_lat('120km', 1)
	351±0.9ms	371±4ms	1.06	mpas_ocean.CrossSections.time_const_lat('120km', 2)
	184±0.3ms	191±3ms	1.04	mpas_ocean.CrossSections.time_const_lat('120km', 4)
	543±5ms	564±4ms	1.04	mpas_ocean.CrossSections.time_const_lat('480km', 1)
	275±2ms	286±2ms	1.04	mpas_ocean.CrossSections.time_const_lat('480km', 2)
	142±0.7ms	146±2ms	1.02	mpas_ocean.CrossSections.time_const_lat('480km', 4)
	24.5±0.1ms	25.1±0.2ms	1.02	mpas_ocean.DualMesh.time_dual_mesh_construction('120km')
	3.42±0.07ms	3.37±0.07ms	0.99	mpas_ocean.DualMesh.time_dual_mesh_construction('480km')
	954±6ms	963±8ms	1.01	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', False)
	50.4±0.8ms	54.8±0.8ms	1.09	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', True)
	83.5±0.7ms	84.9±0.4ms	1.02	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', False)
	5.41±0.1ms	5.92±0.1ms	1.09	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', True)
	454M	454M	1.00	mpas_ocean.Gradient.peakmem_gradient('120km')
	173±0.6ms	177±1ms	1.02	mpas_ocean.Gradient.time_gradient('120km')
	12.6±0.08ms	12.5±0.1ms	0.99	mpas_ocean.Gradient.time_gradient('480km')
	224±0.6μs	225±2μs	1.01	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('120km')
	132±0.3μs	133±0.6μs	1.01	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('480km')
	403M	403M	1.00	mpas_ocean.Integrate.peakmem_integrate('120km')
	382M	383M	1.00	mpas_ocean.Integrate.peakmem_integrate('480km')
	214±2μs	218±2μs	1.02	mpas_ocean.Integrate.time_integrate('120km')
	197±2μs	202±2μs	1.02	mpas_ocean.Integrate.time_integrate('480km')
	132±1ms	135±0.8ms	1.02	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'exclude')
	127±1ms	132±2ms	1.05	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'include')
	129±1ms	131±1ms	1.01	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'split')
	10.2±0.2ms	11.1±0.6ms	1.09	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'exclude')
	10.2±0.1ms	10.6±0.1ms	1.04	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'include')
	10.1±0.2ms	10.6±0.1ms	1.06	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'split')
	351±1μs	355±1μs	1.01	mpas_ocean.PointInPolygon.time_face_search_lonlat('120km')
	355±2μs	357±2μs	1.00	mpas_ocean.PointInPolygon.time_face_search_lonlat('480km')
	334±1μs	336±2μs	1.01	mpas_ocean.PointInPolygon.time_face_search_xyz('120km')
	338±1μs	341±2μs	1.01	mpas_ocean.PointInPolygon.time_face_search_xyz('480km')
	240±1ms	248±0.8ms	1.03	mpas_ocean.RemapDownsample.time_bilinear_remapping
	296±2ms	302±2ms	1.02	mpas_ocean.RemapDownsample.time_inverse_distance_weighted_remapping
	4.74±0.03ms	4.94±0.2ms	1.04	mpas_ocean.RemapDownsample.time_nearest_neighbor_remapping
	1.43±0s	1.45±0.01s	1.02	mpas_ocean.RemapUpsample.time_bilinear_remapping
	36.1±0.5ms	37.7±0.5ms	1.05	mpas_ocean.RemapUpsample.time_inverse_distance_weighted_remapping
	9.45±0.2ms	9.70±0.2ms	1.03	mpas_ocean.RemapUpsample.time_nearest_neighbor_remapping
	29.3±0.5ms	29.9±1ms	1.02	mpas_ocean.ZonalAverage.time_zonal_average('120km')
	6.51±0.02ms	7.10±0.2ms	1.09	mpas_ocean.ZonalAverage.time_zonal_average('480km')
	379M	378M	1.00	quad_hexagon.QuadHexagon.peakmem_open_dataset
	377M	377M	1.00	quad_hexagon.QuadHexagon.peakmem_open_grid
	7.00±0.2ms	7.40±0.3ms	1.06	quad_hexagon.QuadHexagon.time_open_dataset
	5.87±0.1ms	6.59±0.3ms	~1.12	quad_hexagon.QuadHexagon.time_open_grid

Benchmarks that have got worse:

Change	Before [7c9b487]	After [b85be3a]	Ratio	Benchmark (Parameter)
+	703±20μs	817±40μs	1.16	mpas_ocean.ConstructTreeStructures.time_kd_tree('480km')

[Sevans711]

Looks good, though I would maybe suggest tiny changes for readability:

• rename all_paths_exist to all_dyamond_paths_exist or something that suggests only glade/dyamond paths are being checked.
• (less important) instead of looping with something like: flag = flag and check, might be more readable to do, e.g.: all(os.path.exists(file_path) for file_path in dyamond_path_dict.values())

[cmdupuis3]

Maybe, I was trying to mirror what's in the dyamond benchmarks since it's a copy-paste job, so If we change one we should maybe change both.

Only requested style changes, and those changes deviate from the existing style in other dyamond tests.

[Sevans711]

Looks good, my only previous comments were about style, but this style actually matches the existing style from benchmarks/mpas_dyamond.py