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# coding=utf-8
"""
Test for community package
"""
import unittest
import random
import networkx as nx
import community as co
def girvan_graphs(zout):
"""
Create a graph of 128 vertices, 4 communities, like in
Community Structure in social and biological networks.
Girvan newman, 2002. PNAS June, vol 99 n 12
community is node_1 modulo 4
"""
pout = float(zout) / 96.
pin = (16. - pout * 96.) / 31.
graph = nx.Graph()
graph.add_nodes_from(range(128))
for node_1 in graph.nodes():
for node_2 in graph.nodes():
if node_1 < node_2:
val = random.random()
if node_1 % 4 == node_2 % 4:
# nodes belong to the same community
if val < pin:
graph.add_edge(node_1, node_2)
else:
if val < pout:
graph.add_edge(node_1, node_2)
return graph
class ModularityTest(unittest.TestCase):
"""
Tests for modularity function
"""
number_of_tests = 10
def test_allin_is_zero(self):
"""it test that everyone in one community has a modularity of 0"""
for _ in range(self.number_of_tests):
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph:
part[node] = 0
self.assertEqual(co.modularity(part, graph), 0)
def test_range(self):
"""test that modularity is always between -1 and 1"""
for _ in range(self.number_of_tests):
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph:
part[node] = random.randint(0, self.number_of_tests / 10)
mod = co.modularity(part, graph)
self.assertGreaterEqual(mod, -1)
self.assertLessEqual(mod, 1)
def test_bad_graph_input(self):
"""modularity is only defined with undirected graph"""
graph = nx.erdos_renyi_graph(50, 0.1, directed=True)
part = dict([])
for node in graph:
part[node] = 0
self.assertRaises(TypeError, co.modularity, part, graph)
def test_empty_graph_input(self):
"""modularity of a graph without links is undefined"""
graph = nx.Graph()
graph.add_nodes_from(range(10))
part = dict([])
for node in graph:
part[node] = 0
self.assertRaises(ValueError, co.modularity, part, graph)
def test_bad_partition_input(self):
"""modularity is undefined when some nodes are not in a community"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for count, node in enumerate(graph):
part[node] = 0
if count == 40:
break
self.assertRaises(KeyError, co.modularity, part, graph)
# These are known values taken from the paper
# 1. Bartheemy, M. & Fortunato, S. Resolution limit in community detection.
# Proceedings of the National Academy of Sciences of the United States of
# America 104, 36-41(2007).
def test_disjoint_clique(self):
""""
A group of num_clique of size size_clique disjoint, should maximize
the modularity and have a modularity of 1 - 1/ num_clique
"""
for _ in range(self.number_of_tests):
size_clique = random.randint(5, 20)
num_clique = random.randint(5, 20)
graph = nx.Graph()
for i in range(num_clique):
clique_i = nx.complete_graph(size_clique)
graph = nx.union(graph, clique_i, rename=("", str(i) + "_"))
part = dict([])
for node in graph:
part[node] = node.split("_")[0].strip()
mod = co.modularity(part, graph)
self.assertAlmostEqual(mod, 1. - 1. / float(num_clique))
def test_ring_clique(self):
""""
then, a group of num_clique of size size_clique connected with only
two links to other in a ring have a modularity of
1 - 1/ num_clique - num_clique / num_links
"""
for _ in range(self.number_of_tests):
size_clique = random.randint(5, 20)
num_clique = random.randint(5, 20)
graph = nx.Graph()
for i in range(num_clique):
clique_i = nx.complete_graph(size_clique)
graph = nx.union(graph, clique_i, rename=("", str(i) + "_"))
if i > 0:
graph.add_edge(str(i) + "_0", str(i - 1) + "_1")
graph.add_edge("0_0", str(num_clique - 1) + "_1")
part = dict([])
for node in graph:
part[node] = node.split("_")[0].strip()
mod = co.modularity(part, graph)
self.assertAlmostEqual(mod, 1. - 1. / float(num_clique) - float(
num_clique) / float(graph.number_of_edges()))
class BestPartitionTest(unittest.TestCase):
"""
Test for best_partition function
"""
number_of_tests = 10
def test_bad_graph_input(self):
"""best_partition is only defined with undirected graph"""
graph = nx.erdos_renyi_graph(50, 0.1, directed=True)
self.assertRaises(TypeError, co.best_partition, graph)
def test_girvan(self):
"""
Test that community found are good using Girvan & Newman benchmark
"""
graph = girvan_graphs(3) # use small zout otherwise results may change
part = co.best_partition(graph)
for node, com in part.items():
self.assertEqual(com, part[node % 4])
def test_ring(self):
"""
Test that community found are good using a ring of cliques
"""
for _ in range(self.number_of_tests):
size_clique = random.randint(5, 20)
num_clique = random.randint(5, 20)
graph = nx.Graph()
for i in range(num_clique):
clique_i = nx.complete_graph(size_clique)
graph = nx.union(graph, clique_i, rename=("", str(i) + "_"))
if i > 0:
graph.add_edge(str(i) + "_0", str(i - 1) + "_1")
graph.add_edge("0_0", str(num_clique - 1) + "_1")
part = co.best_partition(graph)
for clique in range(num_clique):
part_name = part[str(clique) + "_0"]
for node in range(size_clique):
expected = part[str(clique) + "_" + str(node)]
self.assertEqual(part_name, expected)
def test_all_nodes(self):
"""
Test that all nodes are in a community
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = co.best_partition(graph)
for node in graph.nodes():
self.assertTrue(node in part)
def test_karate(self):
""""test modularity on Zachary's karate club"""
graph = nx.karate_club_graph()
part = co.best_partition(graph)
self.assertTrue(co.modularity(part, graph) > 0.41)
for e1, e2 in graph.edges():
graph[e1][e2]["test_weight"] = 1.
part_weight = co.best_partition(graph, weight="test_weight")
self.assertAlmostEqual(co.modularity(part, graph),
co.modularity(part_weight,
graph,
"test_weight"))
part_res_low = co.best_partition(graph, resolution=0.1)
self.assertTrue(
len(set(part.values())) < len(set(part_res_low.values())))
class InducedGraphTest(unittest.TestCase):
"""
Test the induce graph
"""
def test_nodes(self):
"""
Test that result nodes are the communities
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node % 5
self.assertSetEqual(set(part.values()),
set(co.induced_graph(part, graph).nodes()))
def test_weight(self):
"""
Test that total edge weight does not change
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node % 5
self.assertEqual(graph.size(weight='weight'),
co.induced_graph(part, graph).size(weight='weight'))
for e1, e2 in graph.edges():
graph[e1][e2]["test_weight"] = 1.
induced = co.induced_graph(part, graph, "test_weight")
self.assertEqual(graph.size(weight='test_weight'),
induced.size(weight='test_weight'))
def test_unique(self):
"""
Test that the induced graph is the same when all nodes are alone
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node
ind = co.induced_graph(part, graph)
self.assertTrue(nx.is_isomorphic(graph, ind))
def test_clique(self):
"""
Test that a complete graph of size 2*graph_size has the right behavior
when split in two
"""
graph_size = 5
graph = nx.complete_graph(2 * graph_size)
part = dict([])
for node in graph.nodes():
part[node] = node % 2
ind = co.induced_graph(part, graph)
goal = nx.Graph()
edges = [(0, 1, graph_size ** 2),
(0, 0, graph_size * (graph_size - 1) / 2),
(1, 1, graph_size * (graph_size - 1) / 2)]
goal.add_weighted_edges_from(edges)
self.assertTrue(nx.is_isomorphic(ind, goal))
class GenerateDendrogramTest(unittest.TestCase):
"""
Test dendogram generation
"""
def test_bad_graph_input(self):
"""generate_dendrogram is only defined with undirected graph"""
graph = nx.erdos_renyi_graph(50, 0.1, directed=True)
self.assertRaises(TypeError, co.best_partition, graph)
def test_modularity_increase(self):
"""
Generate a dendrogram and test that modularity is always increasing
"""
graph = nx.erdos_renyi_graph(1000, 0.01)
dendo = co.generate_dendrogram(graph)
mods = [co.modularity(co.partition_at_level(dendo, level), graph)
for level in range(len(dendo))]
self.assertListEqual(mods, sorted(mods))
def test_nodes_stay_together(self):
"""
Test that two nodes in the same community at one level stay in the
same at higher level
"""
graph = nx.erdos_renyi_graph(500, 0.01)
dendo = co.generate_dendrogram(graph)
parts = dict([])
for level in range(len(dendo)):
parts[level] = co.partition_at_level(dendo, level)
for level in range(len(dendo) - 1):
part_1 = parts[level]
part_2 = parts[level + 1]
coms = set(part_1.values())
for com in coms:
comhigher = [part_2[node]
for node, comnode in part_1.items()
if comnode == com]
self.assertEqual(len(set(comhigher)), 1)
if __name__ == '__main__':
unittest.main()
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