forceatlas2 networkx gephi comparison

import networkx as nx, numpy as np, matplotlib.pyplot as plt

np.random.seed(0)
g = nx.florentine_families_graph()
# g = nx.krackhardt_kite_graph()
pos = nx.random_layout(g)

x = {node: p[0] for node, p in pos.items()}
y = {node: p[1] for node, p in pos.items()}
l = {node: node for node in g.nodes()}
s = {node: 4 for node in g.nodes()}
nx.set_node_attributes(g, x, "x")
nx.set_node_attributes(g, y, "y")
nx.set_node_attributes(g, l, "label")
nx.set_node_attributes(g, s, "size")

for r in "rgb":
    nx.set_node_attributes(g, 0, r)

nx.write_graphml(g, "f.graphml", named_key_ids=1)


import inspect
from subprocess import call


def get_pos(g):
    pos = {}
    p = np.zeros(2)
    for node in g.nodes():
        for idx, i in enumerate("x y".split()):
            p[idx] = g.nodes[node][i]
        pos[node] = p.copy()
    return pos


base = "java -jar gephi-cli.jar force-atlas-2"
tmp = inspect.getargspec(nx.forceatlas2_layout)
print(tmp)
assert len(tmp.defaults) == len(tmp.args) - 1, len(tmp.defaults)

for default, arg in zip(tmp.defaults, tmp.args[1:]):
    print(f"Checking {arg=}")
    if arg not in "pos".split():
        gephi_arg = arg.replace("_", "-")
        # reverse flag
        if arg in "dissuade_hubs distributed_action gravity".split():
            continue
        if type(default) is bool:
            print(arg)
            if arg == "edge_weight_influence":
                t = 1.0
            else:
                default = not default
                t = "true" if default else "false"
            name = arg
            command = f"{base} --max-iters=1000 --{gephi_arg}={t} -i f.graphml -o {name}.graphml"
            print(arg, command)
            call(command.split())
            # gephi graph
            gg = nx.read_graphml(f"{name}.graphml")
            tmp = {arg: default, "scaling_ratio": 10.0, "n_iter": 1000}
            nx_pos = nx.forceatlas2_layout(g, pos=pos, **tmp)
            g_pos = get_pos(gg)

            fig, ax = plt.subplots(1, 2)
            nx.draw(g, nx_pos, ax=ax[0])
            nx.draw(gg, g_pos, ax=ax[1])
            ax[0].set_title("networkx")
            ax[1].set_title("gephi")
            fig.suptitle(arg)
            for node in g.nodes():
                d = ((g_pos[str(node)] - nx_pos[node]) ** 2).sum()
                # this currently fails because gephi disregards input positions
                try:
                    assert np.allclose(d, 0)  # , (g_pos[node], nx_pos[node])
                except Exception as e:
                    continue
                    # print(e)

plt.show(block=1)