G wants to be symmetric?

[wolfiex]

 line 110, in force_atlas2_layout
    assert numpy.all(G.T == G), "G is not symmetric."
AssertionError: G is not symmetric

[NMertsch]

Maybe a bit late, but Force Atlas 2 is a algorithm for undirected graphs. This means that every edge from node1 to node2 has a equal edge from node2 to node1 (-> edges have no direction).

This implies that G, the weight matrix of the graph, is symmetric: The entry G[node1, node2] of that matrix contains the weight for the edge node1->node2. For undirected graphs this implies that the edge node2->node1 has the same weight, so G[node1, node2] == G[node2, node1] has to be True for every entry in G (0 means "no edge").

The line of code you mentions means exactly that: It checks if G is symmetric and raises the AssertionError if the check fails.

In short: The weight matrix of your graph is not symmetric, so your graph is not undirected, so Force Atlas 2 can not help you here.

If you are sure that the graph is undirected, maybe it is a floating point precision error (like 1 != 1.000000000001).

[wolfiex]

A good compromise of the code would then be to take the abs net edge weight in creation of a symmetric graph. That would replace the assertion error with a simple warning, allowing the code to run for all usercases.