Devalue uxarray to make it less expensive

[cmdupuis3]

Closes #1583

Overview

This PR is to resolve suboptimal usage of .values throughout the repo, primarily by deferring to lazy xarray and dask operations. See the table of usage sites in Issue #1583.

This specific PR is for the first two tables of usage sites; dead code and bugfixes aren't really included here. Aside from simple cases, some cases were solved by branching on whether the data type was already chunked, so scalability for some parts will depend on if you're using numpy or xarray/dask arrays at those points.

PR Checklist

General

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

Testing

• Adequate tests are created if there is new functionality
• Tests cover all possible logical paths in your function
• 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/

[github-actions]

ASV Benchmarking

Benchmark Comparison Results

Benchmarks that have improved:

Change	Before [b0487c4] <v2026.07.0>	After [136177a]	Ratio	Benchmark (Parameter)
-	578M	391M	0.68	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
-	699M	390M	0.56	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
-	695±2ms	587±3ms	0.84	mpas_ocean.CrossSections.time_const_lat('120km', 1)
-	351±2ms	293±3ms	0.84	mpas_ocean.CrossSections.time_const_lat('120km', 2)
-	183±0.7ms	152±0.7ms	0.83	mpas_ocean.CrossSections.time_const_lat('120km', 4)
-	498M	383M	0.77	mpas_ocean.Gradient.peakmem_gradient('480km')

Benchmarks that have stayed the same:

Change	Before [b0487c4] <v2026.07.0>	After [136177a]	Ratio	Benchmark (Parameter)
	10.7±0.06μs	10.8±0.2μs	1.02	bench_connectivity.Connectivity.time_edge_face('120km')
	11.3±0.1μs	11.2±0.1μs	0.99	bench_connectivity.Connectivity.time_edge_face('480km')
	10.8±0.08μs	10.4±0.2μs	0.97	bench_connectivity.Connectivity.time_edge_node('120km')
	11.3±0.1μs	11.0±0.1μs	0.97	bench_connectivity.Connectivity.time_edge_node('480km')
	10.8±0.07μs	11.0±0.1μs	1.02	bench_connectivity.Connectivity.time_face_edge('120km')
	11.1±0.1μs	11.2±0.2μs	1.01	bench_connectivity.Connectivity.time_face_edge('480km')
	10.9±0.1μs	10.9±0.04μs	1	bench_connectivity.Connectivity.time_face_face('120km')
	11.1±0.1μs	11.0±0.2μs	0.99	bench_connectivity.Connectivity.time_face_face('480km')
	21.8±0.4μs	21.5±0.1μs	0.98	bench_connectivity.Connectivity.time_face_node('120km')
	22.9±0.2μs	22.3±0.3μs	0.97	bench_connectivity.Connectivity.time_face_node('480km')
	10.8±0.2μs	11.0±0.07μs	1.02	bench_connectivity.Connectivity.time_node_edge('120km')
	11.2±0.2μs	11.2±0.07μs	1	bench_connectivity.Connectivity.time_node_edge('480km')
	10.9±0.1μs	10.7±0.1μs	0.99	bench_connectivity.Connectivity.time_node_face('120km')
	11.2±0.08μs	11.1±0.2μs	0.99	bench_connectivity.Connectivity.time_node_face('480km')
	391M	389M	0.99	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	421M	421M	1	face_bounds.FaceBounds.peakmem_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	14.6±0.1ms	14.4±0.05ms	0.99	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/mpas/QU/oQU480.231010.nc'))
	3.67±0.03ms	3.64±0.03ms	0.99	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/scrip/outCSne8/outCSne8.nc'))
	18.9±0.06ms	19.1±0.04ms	1.01	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/geoflow-small/grid.nc'))
	2.20±0.04ms	2.17±0.02ms	0.99	face_bounds.FaceBounds.time_face_bounds(PosixPath('/home/runner/work/uxarray/uxarray/test/meshfiles/ugrid/quad-hexagon/grid.nc'))
	1.00±0s	1.03±0.01s	1.02	import.Imports.timeraw_import_uxarray
	899±4ns	932±3ns	1.04	mpas_ocean.CheckNorm.time_check_norm('120km')
	917±7ns	900±8ns	0.98	mpas_ocean.CheckNorm.time_check_norm('480km')
	808±4ms	832±10ms	1.03	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('120km')
	53.4±0.8ms	53.6±0.6ms	1	mpas_ocean.ConnectivityConstruction.time_face_face_connectivity('480km')
	650±9μs	677±7μs	1.04	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('120km')
	582±10μs	587±10μs	1.01	mpas_ocean.ConnectivityConstruction.time_n_nodes_per_face('480km')
	5.31±0.04ms	5.38±0.02ms	1.01	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('120km')
	3.85±0.02ms	3.91±0.02ms	1.02	mpas_ocean.ConstructFaceLatLon.time_cartesian_averaging('480km')
	3.45±0.01s	3.44±0.01s	1	mpas_ocean.ConstructFaceLatLon.time_welzl('120km')
	224±0.7ms	224±2ms	1	mpas_ocean.ConstructFaceLatLon.time_welzl('480km')
	18.1±0.01ms	18.2±0.03ms	1	mpas_ocean.ConstructTreeStructures.time_ball_tree('120km')
	1.02±0.03ms	1.05±0ms	1.02	mpas_ocean.ConstructTreeStructures.time_ball_tree('480km')
	10.6±0.01ms	10.6±0.02ms	1.01	mpas_ocean.ConstructTreeStructures.time_kd_tree('120km')
	686±20μs	740±10μs	1.08	mpas_ocean.ConstructTreeStructures.time_kd_tree('480km')
	538±2ms	524±1ms	0.97	mpas_ocean.CrossSections.time_const_lat('480km', 1)
	273±1ms	266±3ms	0.97	mpas_ocean.CrossSections.time_const_lat('480km', 2)
	141±0.7ms	137±0.7ms	0.97	mpas_ocean.CrossSections.time_const_lat('480km', 4)
	24.2±0.2ms	24.5±0.1ms	1.01	mpas_ocean.DualMesh.time_dual_mesh_construction('120km')
	3.09±0.04ms	3.12±0.05ms	1.01	mpas_ocean.DualMesh.time_dual_mesh_construction('480km')
	946±7ms	951±3ms	1.01	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', False)
	51.4±0.4ms	55.6±0.7ms	1.08	mpas_ocean.GeoDataFrame.time_to_geodataframe('120km', True)
	84.4±0.7ms	85.8±0.6ms	1.02	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', False)
	5.45±0.2ms	5.78±0.2ms	1.06	mpas_ocean.GeoDataFrame.time_to_geodataframe('480km', True)
	404M	404M	1	mpas_ocean.Gradient.peakmem_gradient('120km')
	174±0.8ms	176±0.8ms	1.01	mpas_ocean.Gradient.time_gradient('120km')
	12.2±0.09ms	12.3±0.08ms	1	mpas_ocean.Gradient.time_gradient('480km')
	223±2μs	225±1μs	1.01	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('120km')
	131±0.6μs	134±1μs	1.02	mpas_ocean.HoleEdgeIndices.time_construct_hole_edge_indices('480km')
	351M	351M	1	mpas_ocean.Integrate.peakmem_integrate('120km')
	331M	330M	1	mpas_ocean.Integrate.peakmem_integrate('480km')
	217±4μs	214±1μs	0.99	mpas_ocean.Integrate.time_integrate('120km')
	201±2μs	195±1μs	0.97	mpas_ocean.Integrate.time_integrate('480km')
	181±2ms	180±2ms	0.99	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'exclude')
	183±2ms	182±0.9ms	1	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'include')
	180±2ms	180±1ms	1	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('120km', 'split')
	13.6±0.3ms	13.8±0.08ms	1.02	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'exclude')
	13.6±0.04ms	13.6±0.08ms	1.01	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'include')
	13.5±0.3ms	13.9±0.1ms	1.03	mpas_ocean.MatplotlibConversion.time_dataarray_to_polycollection('480km', 'split')
	355±2μs	357±1μs	1.01	mpas_ocean.PointInPolygon.time_face_search_lonlat('120km')
	355±3μs	353±3μs	1	mpas_ocean.PointInPolygon.time_face_search_lonlat('480km')
	335±3μs	334±2μs	1	mpas_ocean.PointInPolygon.time_face_search_xyz('120km')
	340±0.8μs	338±2μs	0.99	mpas_ocean.PointInPolygon.time_face_search_xyz('480km')
	243±0.8ms	245±2ms	1.01	mpas_ocean.RemapDownsample.time_bilinear_remapping
	297±1ms	295±3ms	0.99	mpas_ocean.RemapDownsample.time_inverse_distance_weighted_remapping
	1.43±0.01s	1.44±0.01s	1.01	mpas_ocean.RemapUpsample.time_bilinear_remapping
	36.6±0.6ms	37.5±0.8ms	1.02	mpas_ocean.RemapUpsample.time_inverse_distance_weighted_remapping
	9.45±0.2ms	9.71±0.04ms	1.03	mpas_ocean.RemapUpsample.time_nearest_neighbor_remapping
	29.2±0.2ms	28.7±0.05ms	0.98	mpas_ocean.ZonalAverage.time_zonal_average('120km')
	6.65±0ms	6.84±0.05ms	1.03	mpas_ocean.ZonalAverage.time_zonal_average('480km')
	326M	328M	1.01	quad_hexagon.QuadHexagon.peakmem_open_dataset
	326M	326M	1	quad_hexagon.QuadHexagon.peakmem_open_grid
	7.02±0.1ms	7.09±0.1ms	1.01	quad_hexagon.QuadHexagon.time_open_dataset
	6.03±0.1ms	6.07±0.03ms	1.01	quad_hexagon.QuadHexagon.time_open_grid

Benchmarks that have got worse:

Change	Before [b0487c4] <v2026.07.0>	After [136177a]	Ratio	Benchmark (Parameter)
+	4.26±0.01ms	4.81±0.02ms	1.13	mpas_ocean.RemapDownsample.time_nearest_neighbor_remapping

[cmdupuis3]

pre-commit.ci autofix

[cmdupuis3]

There's some spurious asv results from machine variability, but the benchmarks consistenly show peak-mem reductions and some speedups for cross-sections.