cluster to cluster edge fails

[GoogleCodeExporter]

What steps will reproduce the problem?
To see if I'm it's possible to get the dependency graph from VCL/Delphi
project, I'm trying to reproduce this example
http://www.graphviz.org/content/fdpclust (directed)

everything works well, until it come to add edges on clusters then it fail.
(e-> clusterB and clusterC -> clusterD)

What version of the product are you using? On what operating system?
pydot 1.0.28 (patched so it find Graphviz in "Program Files (x86), python 3.3,
Windows 7 64 bits.

Joined : the function I use to produce the graph,

Original issue reported on code.google.com by [email protected] on 7 Mar 2014 at 10:41

Attachments:

• clusterExample.py

def GraphDirectedCluster():
    graph = pydot.Dot(graph_type='digraph')

    e = pydot.Node("e")
    graph.add_node(e)

    clusterA = pydot.Cluster("A")
    a = pydot.Node("a")
    b = pydot.Node("b")
    clusterA.add_node(a)
    clusterA.add_node(b)
    clusterA.add_edge(pydot.Edge(a,b))
    graph.add_subgraph(clusterA)`
    clusterC = pydot.Cluster("C")
    C = pydot.Node("C")
    D = pydot.Node("D")
    clusterC.add_node(C)
    clusterC.add_node(D)
    clusterC.add_edge(pydot.Edge(C,D))
    clusterA.add_subgraph(clusterC)

    clusterB = pydot.Cluster("B")
    d = pydot.Node("d")
    f = pydot.Node("f")
    clusterB.add_node(d)
    clusterB.add_node(f)
    clusterB.add_edge(pydot.Edge(d,f))
    graph.add_subgraph(clusterB)
    graph.add_edge(pydot.Edge(d,D))

    graph.add_edge(pydot.Edge(e,clusterB))
    graph.add_edge(pydot.Edge(clusterC,clusterB))

    print(graph.to_string())
    graph.write_png('directedGraphCluster.png')

[peternowee]

I ran the example code, which gave me the following error in Python 3:

Traceback (most recent call last):
  File "mre01a.py", line 35, in <module>
    print(graph.to_string())
  File "pydot.py", line 1564, in to_string
    graph.append( edge.to_string() + '\n' )
  File "pydot.py", line 875, in to_string
    return ' '.join(edge) + ';'
TypeError: sequence item 2: expected str instance, Cluster found

In Python 2, the error is:

TypeError: sequence item 2: expected string, Cluster found

The error complains about one of the edge points being a Cluster object instead of a string. Stepping through the code using pdb, I found the reason to be in the Edge constructor, where for Node object edge points the name string is looked up and stored, while for Subgraph and Cluster objects this is not done and they are just stored as-is, leading to the error.

I did not find any explanation for this difference. The DOT Language definition defines that both nodes and subgraphs can be points of an edge. A cluster is just a specific kind of subgraph, as also described there.

The reason this bug does not seem to get run into very often is, I think, twofold:

1. Edges are probably more commonly set between nodes than between subgraphs or clusters. Notice that the pydot docstring for Edge also only mentions nodes as possible end points.
2. Edges may be more often instantiated using the name strings of the edge points rather than the edge point objects. The OP's example code works when using name strings to refer to the edge points: graph.add_edge(pydot.Edge('e','cluster_B')).

Anyway, I have prepared PR #238 to remove this difference by always storing Subgraph and Cluster edge points as name strings, just like we do with Node edge points. I checked that it allows the example code of the OP to run successfully.

Some further remarks about the example code:

• New link to the Graphviz example the OP mentioned: https://www.graphviz.org/Gallery/undirected/fdpclust.html
• The Graphviz example shows an undirected graph, so start with graph = pydot.Dot(graph_type='graph') instead of graph = pydot.Dot(graph_type='digraph').
• Also, you need to render using Graphviz fdp, not dot, to easily get edges between clusters: graph.write_png('undirectedGraphCluster_fdp.png', prog='fdp'). You would have to do some very hacky tricks to accomplish something similar with dot. See this Graphviz FAQ entry, this SO question, Graphviz issue 745 and other issues linked to from there.

Then finally, when all the fixes in pydot and the example code are in place, the end result will look the same as in the Graphviz example:

Versions: pydot 1.4.1, python 3.7.3. Mentioning same issue in earlier fork pydot-ng: pydot/pydot-ng#25.

[peternowee]

I just rebased #238 on master, no merge conflicts or changes. With regard to the failing AppVeyor tests, see #213, help there would be appreciated.

For the rest, all tests pass and no comments were received, so I will merge it to master.