num_nodes parameters of Graph.from_edge_list leads to index error

[koaladomi]

Creating a graph with the Graph.from_edge_list function with a parameter num_nodes that is higher than the number of nodes specified with the edge list, leads into an index error. But it's not the initialization that fails.
See a minimal example here:
g = pp.Graph.from_edge_list([("a","b"), ("a","c")], num_nodes=5).to_undirected()
print(f"Number of nodes: {g.N}")
for v in g.nodes:
print(v)
Number of nodes are printed out right, but referencing each node won't work anymore. This throws an IndexError:

IndexError: index 3 is out of bounds for axis 0 with size 3

[M-Lampert]

We are happy to know that you are using pathpyG and appreciate your effort in helping us improve it.

The problem is that when using from_edge_list to create a graph, we assign node_IDs to each node that are given in the list. In the example, this is a, b and c. However, the two isolated nodes that should be in the graph (according to num_nodes) don't have a node_ID, resulting in the IndexError that is mentioned.

While this is not the intended behaviour, there is no clear solution to solve this. I think we should remove the option to assign a number of nodes from the method from_edge_list so that it is not possible to assign node_IDs to only some of the nodes in the graph and ensure that either all or no nodes have an ID. Otherwise, we would need to assign a default node ID to nodes that are not mentioned in the edge_list.
If we remove the option num_nodes from from_edge_list, it would still be possible to create a graph with isolated nodes by including an IndexMap as follows:

Graph.from_edge_list(edge_list=[[0, 1], [0, 2]], mapping=IndexMap(["a", "b", "c", "d", "e"]))

@IngoScholtes what do you think?

[IngoScholtes]

I agree with this solution, i.e. different from the function Graph.from_edge_index there should not be a num_nodes parameter for the function Graph.from_edge_list.

I removed the parameter in the associated branch, which also required some changes in other functions that previously used the parameter. All tests are passing.

With the new implementatio, the suggested solution for the example above would be:

> g = pp.Graph.from_edge_list([('a', 'b'), ('a', 'c')], mapping=pp.IndexMap(list('abcde')))
> print(g)

Directed graph with 5 nodes and 2 edges