Errors due to networkx changes

[ccasar]

Hi,

it seems due to changes to the networkx pacakge, GraphEmbed no longer works.
I'm on Python 2.7.17 and networkx 2.1.
I used the provided example files and first ran into this error (I've edited out some parts of the file paths):

Traceback (most recent call last):
  File "./graph_embed.py", line 405, in <module>
    main(args)
  File "./graph_embed.py", line 354, in main
    data_matrix_2d = ge.transform(data_matrix=data_matrix, target=y)
  File "../GraphEmbed/graph_layout_embedder.py", line 114, in transform
    random_state=self.random_state)
  File "../miniconda3/envs/py27/lib/python2.7/site-packages/toolz/functoolz.py", line 440, in memof
    cache[k] = result = func(*args, **kwargs)
  File "../GraphEmbed/graph_layout_embedder.py", line 324, in annotate_graph_with_graphviz_layout
    layout_pos = nx.graphviz_layout(graph)
AttributeError: 'module' object has no attribute 'graphviz_layout'

This can be solved by editing graph_layout_embedder.py:

1. Add an addtional import: from networkx.drawing.nx_agraph import graphviz_layout
2. Change line 323 from:
   layout_pos = nx.graphviz_layout(graph)
   to
   layout_pos = nx.drawing.nx_agraph.graphviz_layout(graph)

After that, a second error popped up:

Traceback (most recent call last):
  File "./graph_embed.py", line 405, in <module>
    main(args)
  File "./graph_embed.py", line 377, in main
    figure_size=figure_size)
  File "../GraphEmbed/graph_layout_embedder.py", line 447, in display_hull
    save_figure=save_figure)
  File "../GraphEmbed/graph_layout_embedder.py", line 616, in display_graph
    cmap=cmap)
  File "../GraphEmbed/graph_layout_embedder.py", line 668, in _display_class
    for i, j in average_graph.edges()]
AttributeError: 'Graph' object has no attribute 'edge'

Changing line 667 in graph_layout_embedder.py from
widths = [average_graph.edge[i][j]['width'] * 20
to
widths = [average_graph[i][j]['width'] * 20

fixed this.
I'm not too well versed in Python, so I don't know if these are the best fixes for the errors.