Error converting graphs - cannot add edges, Invalid vertex id

Describe the bug I have received the “InternalError: Error at type_indexededgelist.c:272: cannot add edges, Invalid vertex id” error trying to use the method algorithms.angel. I have a nx undirected weighted graph, created from a pandas data frame, and think that the error is in __from_nx_to_igraph at utils.py

To Reproduce my graph: g = nx.from_pandas_edgelist(df, 'source', 'target', 'weight') When I try to see my edges: list(g.edges()) I receive: [(21198069, 28883519), (21198069, 28667573), (21198069, 26440037), ... ] To see the weight of an edge: g.edges[21198069, 28883519] Output: {'weight': 9} When I try to get the communities with the command: coms = algorithms.angel(g, min_community_size=4, threshold=0.25) I get the error:

InternalError                             Traceback (most recent call last)
<ipython-input-132-44b171f02346> in <module>
      1 #coms = algorithms.big_clam(g, 5)
----> 2 coms = algorithms.angel(g, min_community_size=4, threshold=0.25)

/opt/conda/lib/python3.6/site-packages/cdlib/algorithms/overlapping_partition.py in angel(g, threshold, min_community_size)
    120         raise ModuleNotFoundError("Optional dependency not satisfied: install igraph to use the selected feature.")
    121 
--> 122     g = convert_graph_formats(g, ig.Graph)
    123     with suppress_stdout():
    124         a = Angel(graph=g, min_comsize=min_community_size, threshold=threshold, save=False)

/opt/conda/lib/python3.6/site-packages/cdlib/utils.py in convert_graph_formats(graph, desired_format, directed)
    122         return __from_igraph_to_nx(graph, directed)
    123     elif ig is not None and desired_format is ig.Graph:
--> 124         return __from_nx_to_igraph(graph, directed)
    125     else:
    126         raise TypeError("The graph object should be either a networkx or an igraph one.")

/opt/conda/lib/python3.6/site-packages/cdlib/utils.py in __from_nx_to_igraph(g, directed)
     79     gi = ig.Graph(directed=directed)
     80     gi.add_vertices(list(g.nodes()))
---> 81     gi.add_edges(list(g.edges()))
     82     return gi
     83 

/opt/conda/lib/python3.6/site-packages/igraph/__init__.py in add_edges(self, es)
    253           endpoints. Vertices are enumerated from zero.
    254         """
--> 255         return GraphBase.add_edges(self, es)
    256 
    257     def add_vertex(self, name=None, kwds):

InternalError: Error at type_indexededgelist.c:272: cannot add edges, Invalid vertex id

• CDlib version cdlib-0.1.7
• Operating System mac os 10.12.5
• Python version 3.6
• Version(s) of CDlib required libraries

Additional context I’m using jupyter notebook

[Yquetzal]

Got it! (I think) Playing around with a colab notebook I realized that you need to reload the cdlib library after installing angel, because a variable is set at None in cdlib for Angel if it is not available when you import it. So you would only have to restart your notebook kernel, or, in your docker installation process, to install angel before importing cdlib. It that is the explanation, we could solve the problem by checking if the library can be imported again at each angel run… (Giulio, would it break something else ?)

[oiwilliam]

Yes!!! \0/ \0/ You’ve solved it! CONGRATULATIONS! An issue really hard to find and you got it.