Python 3 networkx draw_graphviz() does not work

Question

I just want to draw a simple graph with Python 3 networkx & graphviz:

import networkx as nx

G = nx.complete_graph(3)
nx.draw_graphviz(G)

I'm using ubuntu14.04 and IPython3 and as usual I did pip3 install networkx and running the code gave me:

ImportError: pydot could not be loaded: http://code.google.com/p/pydot/

And I tried installing pydotplus and running the code:

/usr/local/lib/python3.4/dist-packages/networkx/drawing/nx_pydot.py in pydot_layout(G, prog, root, **kwds)
    294 
    295         if isinstance(node,list):
--> 296             node=node[0]
    297         pos=node.get_pos()[1:-1] # strip leading and trailing double quotes
    298         if pos != None:

IndexError: list index out of range

and pydot2 also:

/usr/local/lib/python3.4/dist-packages/pydot.py in write(self, path, prog, format)
   1893             prog = self.prog
   1894 
-> 1895         dot_fd = file(path, "w+b")
   1896         if format == 'raw':
   1897             data = self.to_string()

NameError: name 'file' is not defined

I spent quite some time searching and installing other pydots and pygraphviz combinations already but still no luck.

While this may be related: pydot and graphviz error: Couldn't import dot_parser, loading of dot files will not be possible, that doesn't solve the problem in Python 3.

Does this groups.google.com/forum/#!topic/pygraphviz-discuss/mbK5voZ9-hs explain some of the issue? — Joel
– Joel, Commented Aug 24, 2015 at 22:21
I think pygraphviz depends on parsing of the DOT language which is the job of pydot? And now somehow it is pydot that is incompatible with Python3 rather than pygraphviz. — pterodragon
– pterodragon, Commented Aug 25, 2015 at 0:57
FWIW, I achieved the desired result by outputting a .dot file using networkx.write_dot(G, 'graph.dot') and then do the appropriate graphviz output command like neato -T png graph.dot > graph.png. (graphviz has to be installed beforehand; see the man page for more) — pterodragon
– pterodragon, Commented Sep 1, 2015 at 13:02
You might add that as an answer. Others with the same problem may not check the comments. — Joel
– Joel, Commented Sep 2, 2015 at 4:14
Some additional information: pygraphviz now claims to work with Python 3 right now but as of this moment I install it using the source by running python3 setup.py install, and import pygraphviz in Python3 gives me ImportError: No module named '_graphviz'. — pterodragon
– pterodragon, Commented Sep 2, 2015 at 15:31

mfitzp · Accepted Answer · 2015-11-06 09:29:12Z

2

You can fix this by editing the line #292 from:

    pydot_node = pydot.Node(make_str(n)).get_name().encode('utf-8')

to remove the encode at the end:

    pydot_node = pydot.Node(make_str(n)).get_name() #.encode('utf-8')

I've reported this bug/fix here.

answered Nov 6, 2015 at 9:29

mfitzp

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3 Comments

pterodragon Over a year ago

It does resolve the error when using pydotplus in this case :). But I still can't see the matplotlib window popup?

mfitzp Over a year ago

@pterodragon Is matplotlib in interactive mode? You might need to do a plt.show() to get the window to appear.

pterodragon Over a year ago

I thought it will show automatically. Thanks for your help! :)

Log0 · Accepted Answer · 2016-01-25 05:36:21Z

2

This seems to be the same issue as that the pydot you're using is a version incompatible with Python 3, which uses file(...). file(...) is removed in Python 3 already.

I noticed this issue and setup a Python 3 compatible version on PyPi.

For Linux systems for Python 3.x, try:

pip3 install pydot3

Or in general for Python 2.x, try:

pip install pydot3

answered Jan 25, 2016 at 5:36

Log0

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Comments

pterodragon · Accepted Answer · 2015-09-02 15:26:54Z

1

Not a very great answer but it acts as a workaround.

First output the .dot file by networkx.write_dot(G, 'graph.dot') using Python

and then do the appropriate graphviz output command like neato -T png graph.dot > graph.png on the command line.

answered Sep 2, 2015 at 15:26

pterodragon

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