KeyError triggered by model.run()

[mihaibanciu]

This has happened after migrating from 0.14 to 1.0.x on code that ran without issues on the older version. This is a basic SEIR model on a network (no quarantine/tracing/social distancing), after instantiating the network. I'll do more investigating to see what the exact context is, but in the meantime I thought I would flag it. If it matters, the network I am using has roughly 4,000 nodes and 100,000 edges.

The error message is as follows:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-6-4d6a510161ce> in <module>
    104                                        gamma = 1/15,
    105                                        initI = 5)
--> 106         model.run(T=100, print_interval=10)

seirsplus\models.py in run(self, T, checkpoints, print_interval, verbose)
   1336         while running:
   1337 
-> 1338             running = self.run_iteration()
   1339 
   1340             #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

seirsplus\models.py in run_iteration(self)
   1224             # Save information about infection events when they occur:
   1225             if(transitionType == 'StoE'):
-> 1226                 transitionNode_GNbrs  = list(self.G[transitionNode].keys())
   1227                 transitionNode_GQNbrs = list(self.G_Q[transitionNode].keys())
   1228                 self.infectionsLog.append({ 't':                            self.t,

networkx\classes\graph.py in __getitem__(self, n)
    473         AtlasView({1: {}})
    474         """
--> 475         return self.adj[n]
    476 
    477     def add_node(self, node_for_adding, **attr):

networkx\classes\coreviews.py in __getitem__(self, name)
     79 
     80     def __getitem__(self, name):
---> 81         return AtlasView(self._atlas[name])
     82 
     83     def copy(self):

KeyError: 3047

[mihaibanciu]

@ryansmcgee I believe the problem is that the routine run_iteration in module.py expects both G and G_Q to be indexed sequentially, e.g. G[0] is the first node and so on. However, if the graph built in networkx has labels attached to the nodes, e.g. G['Hello'] is the first node, then the KeyError mentioned above occurs.

Edit: Here's a minimal working example that triggers the error:

from seirsplus.models import *
from seirsplus.networks import *
import networkx as nx
import random

graph = nx.erdos_renyi_graph(100, 0.1)
nlist = ["{:02}".format(n) for n in range(100)] # generate node ids as strings '00' through '99'
random.shuffle(nlist) # assign the node ids randomly
mapping = dict(zip(list(graph.nodes), nlist))
graph = nx.relabel_nodes(graph, mapping)

model = SEIRSNetworkModel(G     = graph, 
                          beta  = 0.25 
                          sigma = 1 / 5, 
                          gamma = 1 / 15,
                          initI = 5)
model.run(T=100, print_interval=10)
model.figure_infections(ylim=0.5)

Commenting out lines 8-11 (node relabeling) removes the error.

[chrisvander]

In the meantime, I suggest trying out nx.relabel.convert_node_labels_to_integers