def test_fixed_topology_constraints(self):
"""
Ensure that the randomizer correctly instantiates the constraints
"""
c1 = IsConnected()
rand = FixedTopology(s_pombe, constraints=[c1])
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(rand.constraints, [c1])
c2 = lambda _: True # noqa
rand = FixedTopology(s_pombe, constraints=[c2])
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(len(rand.constraints), 1)
self.assertIsInstance(rand.constraints[0], GenericTopological)
self.assertEqual(rand.constraints[0].test, c2)
with self.assertRaises(ConstraintError):
FixedTopology(s_pombe, constraints=[lambda _: False])
with self.assertRaises(TypeError):
FixedTopology(s_pombe, constraints=[IsIrreducible()])
def test_network_graph_metadata(self):
from neet.boolean.examples import s_pombe
nx_net = s_pombe.network_graph(labels='indices')
self.assertEqual(nx_net.graph['name'], 'Fission Yeast Cell Cycle')
self.assertEqual(nx_net.graph['name'], s_pombe.metadata['name'])
def test_fixed_out_degree(self):
"""
Ensure that the topologies generated by OutDegree have the same number
of nodes and edges, and the same out-degree distribution as the
original topology
"""
def out_degree(g):
return Counter(dict(g.out_degree).values())
g = nx.DiGraph([(0, 1), (1, 1), (2, 1)])
rand = OutDegree(g)
for h in islice(rand, 100):
self.assertTrue(len(h), len(g))
self.assertTrue(h.size, g.size)
try:
self.assertEqual(out_degree(h), out_degree(g))
except Exception as err:
raise Exception(h.in_degree, g.in_degree) from err
g = s_pombe.network_graph()
rand = OutDegree(g)
for h in islice(rand, 100):
self.assertTrue(len(h), len(g))
self.assertTrue(h.size, g.size)
try:
self.assertEqual(out_degree(h), out_degree(g))
except Exception as err:
raise Exception(h.in_degree, g.in_degree) from err
def test_randomizer_init_timeout(self):
"""
Ensure that the randomizer correctly sets the timeout
"""
rand = MockRandomizer(s_pombe, timeout=0)
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 0)
self.assertEqual(rand.constraints, [])
def test_network_randomizer_constraints(self):
"""
Ensure that the randomizer correctly instantiates the constraints
"""
c1, c2, c3 = IsIrreducible(), (lambda _: False), IsConnected()
rand = MockNetworkRandomizer(s_pombe, constraints=[c1])
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(rand.constraints, [c1])
self.assertEqual(rand.trand.constraints, [])
rand = MockNetworkRandomizer(s_pombe, constraints=[c2])
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(len(rand.constraints), 1)
self.assertIsInstance(rand.constraints[0], GenericDynamical)
self.assertEqual(rand.constraints[0].test, c2)
self.assertEqual(rand.trand.constraints, [])
rand = MockNetworkRandomizer(s_pombe, constraints=[c3])
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(rand.constraints, [])
self.assertEqual(rand.trand.constraints, [c3])
rand = MockNetworkRandomizer(s_pombe, constraints=[c1, c3, c2])
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(len(rand.constraints), 2)
self.assertEqual(rand.constraints[0], c1)
self.assertIsInstance(rand.constraints[1], GenericDynamical)
self.assertEqual(rand.constraints[1].test, c2)
self.assertEqual(rand.trand.constraints, [c3])
with self.assertRaises(TypeError):
MockNetworkRandomizer(s_pombe, constraints=[5])
def test_randomizer_init_constraints(self):
"""
Ensure that the randomizer correctly instantiates the constraints
"""
constraint = IsIrreducible()
rand = MockRandomizer(s_pombe, constraints=[constraint])
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(rand.constraints, [constraint])
with self.assertRaises(TypeError):
MockRandomizer(s_pombe, constraints=[lambda n: False])
def test_fixed_topology(self):
"""
Ensure that the topologies generated are isomorphic to the original topology
"""
g = nx.DiGraph([(0, 1), (1, 1), (2, 1)])
rand = FixedTopology(g)
self.assertTrue(
all(map(lambda h: nx.is_isomorphic(g, h), islice(rand, 10))))
g = s_pombe.network_graph()
rand = FixedTopology(g)
self.assertTrue(
all(map(lambda h: nx.is_isomorphic(g, h), islice(rand, 10))))
def test_default_bias(self):
"""
Ensure the generated networks have a bias of 0.5 by default
"""
rand = UniformBias(s_pombe)
s_pombe_graph = s_pombe.network_graph()
indegree = [
s_pombe_graph.in_degree(n) for n in sorted(s_pombe_graph.nodes)
]
expect = [
0.0 if s_pombe_graph.in_degree(n) == 0 else 0.5 for n in indegree
]
got = list(map(self.bias, islice(rand, 10)))
self.assertEqual(got, [expect] * len(got))
def test_other_bias(self):
"""
Ensure the generated networks have the specified
"""
p = 0.3
rand = UniformBias(s_pombe, p)
s_pombe_graph = s_pombe.network_graph()
indegree = [
s_pombe_graph.in_degree(n) for n in sorted(s_pombe_graph.nodes)
]
high = [
0.0 if k == 0 else math.ceil(p * 2**k) / 2**k for k in indegree
]
low = [
0.0 if k == 0 else math.floor(p * 2**k) / 2**k for k in indegree
]
for net in islice(rand, 10):
got = self.bias(net)
for g, l, h in zip(got, low, high):
self.assertTrue(g == l or g == h)
def test_randomizer_default_init(self):
"""
Ensure that randomizer correctly initializes with default arguments
"""
g = nx.DiGraph([(0, 1), (1, 1)])
rand = MockRandomizer(g)
self.assertIsNone(rand.network)
self.assertEqual(rand.graph, g)
self.assertEqual(rand.timeout, 1000)
self.assertEqual(rand.constraints, [])
rand = MockRandomizer(s_pombe)
self.assertEqual(rand.network, s_pombe)
self.assertTrue(nx.is_isomorphic(rand.graph, s_pombe.network_graph()))
self.assertEqual(rand.timeout, 1000)
self.assertEqual(rand.constraints, [])
with self.assertRaises(TypeError):
MockRandomizer(None)
with self.assertRaises(TypeError):
MockRandomizer(nx.Graph())
def test_network_graph_names(self):
from neet.boolean.examples import s_pombe
nx_net = s_pombe.network_graph(labels='names')
self.assertEqual(set(nx_net), set(s_pombe.names))