Update node_link_data to networkx 3.6 compatibility

[myxie]

The following deprecation warning appears when running SHADOW:

    nx.node_link_graph(data, edges="links") to preserve current behavior, or
    nx.node_link_graph(data, edges="edges") for forward compatibility.
    warnings.warn(

We should use the explicit "links" approach to preserve existing behaviour.

Potentially, we can also look at what the results are for moving towards "edges".