Fix gradient returning all NaN on SCRIP-derived grids

[rajeeja]

Skip edges with incomplete edge_face_connectivity in the gradient stencil instead of NaN-ing the entire face. Fixes #1452.

The ne120np4 grid in #1452 is a spectral element cubed-sphere mesh read through SCRIP format. UXarray's SCRIP reader deduplicates corner coordinates with exact floating-point comparison, but SE grids compute shared boundary nodes independently per element, so coordinates at element junctions can differ by machine epsilon. This prevents node merging and produces edges that only one face claims, leaving INT_FILL_VALUE in edge_face_connectivity for most edges. The boundary check then falsely flags nearly every face and sets the gradient to NaN — exactly what @jpan84 observed (1 non-NaN value out of 777,602 faces).

This fix skips those incomplete edges per-edge rather than rejecting the whole face, which is sufficient for exploratory analysis of smooth fields. The proper long-term fix is tolerance-based node deduplication in the SCRIP reader or native SE grid support (#1402).

[jpan84]

Thank you for the quick workaround @rajeeja! These changes appear to fix #1452. Using the MVCE I provided there, the output of _compute_gradient() is global array of numerical values (zero NaNs), and the values of d(U200)/dy in units of s^-1 look reasonable:

[<xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(-0.00528834)
Coordinates:
quantile float64 8B 0.0, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(-0.00030125)
Coordinates:
quantile float64 8B 0.1, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(-0.00017363)
Coordinates:
quantile float64 8B 0.2, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(-0.00010098)
Coordinates:
quantile float64 8B 0.3, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(-4.57090395e-05)
Coordinates:
quantile float64 8B 0.4, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(3.17519363e-06)
Coordinates:
quantile float64 8B 0.5, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(5.10507316e-05)
Coordinates:
quantile float64 8B 0.6, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(0.00010479)
Coordinates:
quantile float64 8B 0.7, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(0.00017359)
Coordinates:
quantile float64 8B 0.8, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(0.00029627)
Coordinates:
quantile float64 8B 0.9, <xarray.UxDataArray 'meridional_gradient' ()> Size: 8B
array(0.01029345)
Coordinates:
quantile float64 8B 1.0]