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pythonnetworkx

Save networkx DiGraph preserving nodes attributes

I'm trying to save networkx DiGraph by preserving nodes' attributes.

I have tried with nx.write_weighted_edgelist, nx.write_edgelist and nx.write_weighted_edgelist , and after trying (and also looking at https://networkx.org/documentation/networkx-1.10/reference/readwrite.html) I know that both adjacency and edge lists does not preserve nodes' attributes.

Now I have seen also the other options in the networkx link, but I don't understand if other commands preserve attributes, and I need to be sure that it works (my code need to create and save more than 5000 graphs and it takes almost a day to run).

So which is the best way to save a graph and preserve nodes' attributes?

Solution

  • First, note that you are using an outdated version of the NetworkX docs; you should always use the stable version.

    One format which is guaranteed to preserve node data is the pickle (although this is deprecated in NetworkX 2.6, it is currently usable):

    In [1]: import networkx as nx

In [2]: G = nx.Graph()

In [3]: G.add_node("A", weight=10)

In [4]: nx.write_gpickle(G, "test.gpickle")

In [5]: H = nx.read_gpickle("test.gpickle")

In [6]: H.nodes(data=True)
Out[6]: NodeDataView({'A': {'weight': 10}})

    The GML format should also work for most datatypes:

    In [8]: nx.write_gml(G, "test.gml")

In [9]: H = nx.read_gml("test.gml")

In [10]: H.nodes(data=True)
Out[10]: NodeDataView({'A': {'weight': 10}})

    GEXF works as well:

    In [12]: nx.write_gexf(G, "test.gexf")

In [13]: H = nx.read_gexf("test.gexf")

In [14]: H.nodes(data=True)
Out[14]: NodeDataView({'A': {'weight': 10, 'label': 'A'}})

    So you have several options and can decide based on performance and support for the specific attribute data you are trying to save.