TypeError: Object of type 'int64' is not JSON serializable

[j6k4m8]

When you try to render a graph derived from a numpy adjacency matrix, you get this error.

G = nx.from_numpy_matrix(mymatrix)
nx2d3.embed_networkx(G)

This can be solved by converting node IDs to strings (G = nx.relabel_nodes(G, lambda x: str(x))) but it seems like a more general solution is to handle this in the embed_networkx call, since any non-JSON-serializable ID type will fail with this error.

(Traceback suggests that this is a failure of the node_link_data(graph) call on line 99 of embed.py)

[EDIT]: This still fails even if I verify that the data are JSON-serializable with

G =  json_graph.node_link_graph(json_graph.node_link_data(G))

So this is a function of the nx2d3 library, not of the networkx JSON serializer, I believe.

[cthoyt]

First, sorry for the late reply.

Could you give an example of a real matrix for which this is a problem?

Also, do you think that it's a good idea to try and bake more logic into the embed_networkx function? There could be lots of edge cases. A previous pull request added the ability to specify a JSONEncoder that can be made custom for any kinds of classes, so that might be able to fit more general needs without having to write more code in this library.

[j6k4m8]

My main concern here is that the serialization error appears to be internal to nx2d3 rather than an issue with the data; using the python standard json library for serialization seems to work.

Definitely agree about not bloating this library though! Maybe a good middle ground is to throw a more readable error if serialization fails (for this or any other reason)?