solve edge_node_connectivity in xugrid 0.6.0

[veenstrajelmer]

Reading a ugrid file with triangles and squares results in several errors in xugrid==0.6.0:
"ValueError: Invalid edge_node_connectivity"
"ValueError: triangles are indices into the points and must be in the range 0 <= i < 3101 but found value -2"

This probably has to do with the fact that the dflowfm connectivities are 1-based instead of the default 0-based and a testcase must be missing for this situation:

Attributes:
    cf_role:      edge_node_connectivity
    start_index:  1
    _FillValue:   0

MWE:

import xugrid as xu
file_nc = 'Grevelingen-FM_0002_map.nc' #dflowfm map output with 1-based connectivity and mix of triangles/squares
uds = xu.open_dataset(file_nc)

uds.isel({uds.grid.face_dimension:[1]}) # raises "ValueError: Invalid edge_node_connectivity"
uds.mesh2d_node_z.ugrid.plot() # raises "ValueError: triangles are indices into the points and must be in the range 0 <= i < 3101 but found value -2"

Additional info
All connectivity vars have start_index 1 in this file, when printing

uds_grid_ds = uds.grid.to_dataset()
ds_startidx1 = uds_grid_ds.filter_by_attrs(start_index=1)
for varn_conn in ds_startidx1.data_vars:
    mesh2d_attrs = uds_grid_ds.mesh2d.attrs
    connect_name = list(filter(lambda x: mesh2d_attrs[x] == varn_conn, mesh2d_attrs))[0]
    print(f'connectivity in {varn_conn} ({connect_name})')
    print('start_index', ds_startidx1[varn_conn].attrs["start_index"])
    print('min()', ds_startidx1[varn_conn].min().to_numpy())

in xugrid 0.5.0 this gives:

connectivity in mesh2d_face_nodes (face_node_connectivity)
start_index 1
min() 1.0
connectivity in mesh2d_edge_nodes (edge_node_connectivity)
start_index 1
min() 1.0
connectivity in mesh2d_edge_faces (edge_face_connectivity)
start_index 1
min() 0.0

in xugrid 0.6.0 this gives:

connectivity in mesh2d_face_nodes (face_node_connectivity)
start_index 1
min() -1.0
connectivity in mesh2d_edge_nodes (edge_node_connectivity)
start_index 1
min() 1.0
connectivity in mesh2d_edge_faces (edge_face_connectivity)
start_index 1
min() 0.0

The face_node_connectivity is messed up here, with a start_index of 1 the minimum value should be 1 or 0 (missing value). Could it be that there was a minus-to-plus-1 (or the other way round) introduced somewhere in the code? I cannot find a lot about face_node_connectivity in the diff though. Also interesting, when opening a partition with only triangles, the minimum of face_node_connectivity is 1 (so correct).

This issue was introduced by fixing #101

testcase suggestion
Suggestion to add a testcase with e.g. the sandiego dataset, regridding it to a mesh with triangles+squares. And with these edits to the grid before putting it in a new UgridDataset and plotting it:

ds_idx = xu_grid_ds.filter_by_attrs(start_index=0)
for varn_conn in ds_idx.data_vars:
    xu_grid_ds[varn_conn] += 1
    xu_grid_ds[varn_conn].attrs["_FillValue"] += 1
    xu_grid_ds[varn_conn].attrs["start_index"] += 1