def test_state_space(self):
net = bnet.WTNetwork([[1]])
self.assertEqual(2, len(list(net.state_space())))
net = bnet.WTNetwork([[1, 0], [1, 1]])
self.assertEqual(4, len(list(net.state_space())))
net = bnet.WTNetwork([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
self.assertEqual(8, len(list(net.state_space())))
def test_init_weights(self):
net = bnet.WTNetwork([[1]])
self.assertEqual(1, net.size)
self.assertTrue(np.array_equal([[1]], net.weights))
self.assertTrue(np.array_equal([0], net.thresholds))
self.assertIsNone(net.names)
net = bnet.WTNetwork([[1, 0], [0, 1]])
self.assertEqual(2, net.size)
self.assertTrue(np.array_equal([[1, 0], [0, 1]], net.weights))
self.assertTrue(np.array_equal([0, 0], net.thresholds))
self.assertIsNone(net.names)
net = bnet.WTNetwork([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
self.assertEqual(3, net.size)
self.assertTrue(
np.array_equal([[1, 0, 0], [0, 1, 0], [0, 0, 1]], net.weights))
self.assertTrue(np.array_equal([0, 0, 0], net.thresholds))
self.assertIsNone(net.names)
net = bnet.WTNetwork(1)
self.assertEqual(1, net.size)
self.assertTrue(np.array_equal([[0]], net.weights))
self.assertTrue(np.array_equal([0], net.thresholds))
self.assertIsNone(net.names)
net = bnet.WTNetwork(2)
self.assertEqual(2, net.size)
self.assertTrue(np.array_equal([[0, 0], [0, 0]], net.weights))
self.assertTrue(np.array_equal([0, 0], net.thresholds))
self.assertIsNone(net.names)
def test_init_thresholds(self):
with self.assertRaises(TypeError):
bnet.WTNetwork([[1]], theta=5)
net = bnet.WTNetwork([[1]])
self.assertEqual(bnet.WTNetwork.split_threshold, net.theta)
net = bnet.WTNetwork([[1]], theta=bnet.WTNetwork.negative_threshold)
self.assertEqual(bnet.WTNetwork.negative_threshold, net.theta)
net = bnet.WTNetwork([[1]], theta=bnet.WTNetwork.positive_threshold)
self.assertEqual(bnet.WTNetwork.positive_threshold, net.theta)
def test_update_values_none(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=bnet.WTNetwork.positive_threshold)
xs = [0, 0]
self.assertEqual([0, 1], net.update(xs, values=None))
xs = [0, 0]
self.assertEqual([0, 1], net.update(xs, values={}))
def test_update_invalid_values(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=bnet.WTNetwork.positive_threshold)
with self.assertRaises(ValueError):
net.update([0, 0], values={0: 2})
with self.assertRaises(ValueError):
net.update([0, 0], values={0: -1})
def test_update_pin_invalid_indicies(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=bnet.WTNetwork.positive_threshold)
with self.assertRaises(IndexError):
net.update([0, 0], values={-3: 0})
with self.assertRaises(IndexError):
net.update([0, 0], values={2: 0})
def test_complex(self):
net = nb.WTNetwork([
[0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, -1, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
[1, 0, -1, -1, 1, 1, 0, 0, 0, 0],
[0, -1, 0, -1, 1, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, -1, 1, 0, 0],
[0, 0, 0, 0, 1, 0, -1, 1, 0, 0],
[0, 0, 0, 0, 0, 1, 0, 0, -1, -1],
[0, 0, 0, 0, -1, 0, 0, 0, 1, 0],
])
g = net.to_networkx_graph()
self.assertEqual([[8, 9], [6, 7], [4, 5], [0, 1], [2, 3]],
list(map(list, nx.strongly_connected_components(g))))
self.assertEqual([(2, 1), (2, 0), (3, 2), (4, 2)],
list(nx.condensation(g).edges))
expect = ns.attractors(net)
got = main.attractors(net)
self.assertUnorderedEqual(expect, got)
def test_neighbors_WTNetwork(self):
net = bnet.WTNetwork([[1, 0], [1, 1]])
with self.assertRaises(ValueError):
neighbors(net, 0, direction='')
self.assertTrue(neighbors(net, 0), [set([0])])
def test_fission_yeast_numpy(self):
net = bnet.WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0])
self.assertEqual(9, net.size)
self.assertEqual(512, len(list(net.state_space())))
init = np.asarray([1, 0, 1, 1, 0, 0, 1, 0, 0])
bio_sequence = np.asarray([[0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 1, 0, 1, 0],
[0, 1, 0, 0, 1, 1, 0, 1, 0],
[0, 0, 0, 0, 1, 0, 0, 1, 1],
[0, 0, 1, 1, 0, 0, 1, 0, 1],
[0, 0, 1, 1, 0, 0, 1, 0, 0]])
for expected in bio_sequence:
self.assertTrue(np.array_equal(expected, net.update(init)))
def test_update_pin_index_clash(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=bnet.WTNetwork.positive_threshold)
with self.assertRaises(ValueError):
net.update([0, 0], index=0, pin=[1])
with self.assertRaises(ValueError):
net.update([0, 0], index=1, pin=[1])
with self.assertRaises(ValueError):
net.update([0, 0], index=1, pin=[0, 1])
def test_update_values_index_clash(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=bnet.WTNetwork.positive_threshold)
with self.assertRaises(ValueError):
net.update([0, 0], index=0, values={0: 1})
with self.assertRaises(ValueError):
net.update([0, 0], index=1, values={1: 0})
with self.assertRaises(ValueError):
net.update([0, 0], index=1, values={0: 0, 1: 0})
def test_update(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0])
self.assertEqual(bnet.WTNetwork.split_threshold, net.theta)
xs = [0, 0]
self.assertEqual([0, 0], net.update(xs))
self.assertEqual([0, 0], xs)
xs = [1, 0]
self.assertEqual([1, 0], net.update(xs))
self.assertEqual([1, 0], xs)
xs = [0, 1]
self.assertEqual([0, 1], net.update(xs))
self.assertEqual([0, 1], xs)
xs = [1, 1]
self.assertEqual([1, 1], net.update(xs))
self.assertEqual([1, 1], xs)
net.theta = bnet.WTNetwork.negative_threshold
xs = [0, 0]
self.assertEqual([0, 0], net.update(xs))
self.assertEqual([0, 0], xs)
xs = [1, 0]
self.assertEqual([1, 0], net.update(xs))
self.assertEqual([1, 0], xs)
xs = [0, 1]
self.assertEqual([0, 1], net.update(xs))
self.assertEqual([0, 1], xs)
xs = [1, 1]
self.assertEqual([1, 0], net.update(xs))
self.assertEqual([1, 0], xs)
net.theta = bnet.WTNetwork.positive_threshold
xs = [0, 0]
self.assertEqual([0, 1], net.update(xs))
self.assertEqual([0, 1], xs)
xs = [1, 0]
self.assertEqual([1, 0], net.update(xs))
self.assertEqual([1, 0], xs)
xs = [0, 1]
self.assertEqual([0, 1], net.update(xs))
self.assertEqual([0, 1], xs)
xs = [1, 1]
self.assertEqual([1, 1], net.update(xs))
self.assertEqual([1, 1], xs)
def test_update_pin(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0])
net.theta = bnet.WTNetwork.negative_threshold
xs = [1, 1]
self.assertEqual([1, 0], net.update(xs, pin=[0]))
net.theta = bnet.WTNetwork.positive_threshold
xs = [0, 0]
self.assertEqual([0, 0], net.update(xs, pin=[1]))
def test_update_values(self):
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=bnet.WTNetwork.negative_threshold)
xs = [1, 1]
self.assertEqual([1, 1], net.update(xs, values={1: 1}))
net.theta = bnet.WTNetwork.positive_threshold
xs = [0, 0]
self.assertEqual([1, 1], net.update(xs, values={0: 1}))
def test_neighbors_both_split_threshold(self):
net = bnet.WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0])
self.assertEqual(net.neighbors(2), set([0, 1, 2, 5, 8]))
def test_neighbors_out_negative_threshold(self):
net = bnet.WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0],
theta=bnet.WTNetwork.negative_threshold)
self.assertEqual(net.neighbors_out(2), set([1, 5]))
def test_update_invalid_states(self):
net = bnet.WTNetwork([[1, 0], [1, 1]])
with self.assertRaises(ValueError):
net.update([-1, 0])
with self.assertRaises(ValueError):
net.update([1, -1])
with self.assertRaises(ValueError):
net.update([2, 0])
with self.assertRaises(ValueError):
net.update([1, 2])
with self.assertRaises(ValueError):
net.update([[1], [0]])
with self.assertRaises(ValueError):
net.update("101")
def test_neighbors_in_split_threshold(self):
net = bnet.WTNetwork(
[[-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[-1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 0.0, -1.0, 1.0, 0.0],
[0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]],
[0.0, -0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0])
self.assertEqual(net.neighbors_in(2), set([0, 1, 2, 5, 8]))
with self.assertRaises(IndexError):
self.assertEqual(net.neighbors_in(2.0))
with self.assertRaises(IndexError):
self.assertEqual(net.neighbors_in('2'))
def test_init_names(self):
with self.assertRaises(TypeError):
bnet.WTNetwork([[1]], names=5)
with self.assertRaises(ValueError):
bnet.WTNetwork([[1]], names=["A", "B"])
with self.assertRaises(ValueError):
bnet.WTNetwork([[1]], names=["A", "B"])
net = bnet.WTNetwork([[1]], names=["A"])
self.assertEqual(['A'], net.names)
net = bnet.WTNetwork([[1, 0], [1, 1]], names=['A', 'B'])
self.assertEqual(['A', 'B'], net.names)
net = bnet.WTNetwork([[1]], names="A")
self.assertEqual(['A'], net.names)
net = bnet.WTNetwork([[1, 0], [1, 1]], names="AB")
self.assertEqual(['A', 'B'], net.names)
def test_user_defined_threshold(self):
def reverse_negative(values, states):
if isinstance(values, list) or isinstance(values, np.ndarray):
for i, x in enumerate(values):
if x <= 0:
states[i] = 1
else:
states[i] = 0
return states
else:
if values <= 0:
return 1
else:
return 0
net = bnet.WTNetwork([[1, 0], [-1, 1]], [0.5, 0.0],
theta=reverse_negative)
xs = [0, 0]
self.assertEqual([1, 1], net.update(xs))
self.assertEqual([1, 1], xs)
xs = [0, 0]
self.assertEqual([1, 0], net.update(xs, 0))
self.assertEqual([1, 0], xs)
xs = [0, 0]
self.assertEqual([0, 1], net.update(xs, 1))
self.assertEqual([0, 1], xs)
xs = [1, 0]
self.assertEqual([0, 1], net.update(xs))
self.assertEqual([0, 1], xs)
xs = [1, 0]
self.assertEqual([0, 0], net.update(xs, 0))
self.assertEqual([0, 0], xs)
xs = [1, 0]
self.assertEqual([1, 1], net.update(xs, 1))
self.assertEqual([1, 1], xs)
xs = [0, 1]
self.assertEqual([1, 0], net.update(xs))
self.assertEqual([1, 0], xs)
xs = [0, 1]
self.assertEqual([1, 1], net.update(xs, 0))
self.assertEqual([1, 1], xs)
xs = [0, 1]
self.assertEqual([0, 0], net.update(xs, 1))
self.assertEqual([0, 0], xs)
xs = [1, 1]
self.assertEqual([0, 1], net.update(xs))
self.assertEqual([0, 1], xs)
xs = [1, 1]
self.assertEqual([0, 1], net.update(xs, 0))
self.assertEqual([0, 1], xs)
xs = [1, 1]
self.assertEqual([1, 1], net.update(xs, 1))
self.assertEqual([1, 1], xs)
def test_has_metadata(self):
net = bnet.WTNetwork([[1]])
self.assertTrue(hasattr(net, 'metadata'))
self.assertEqual(type(net.metadata), dict)
def test_is_network(self):
from neet.interfaces import is_network
self.assertTrue(is_network(bnet.WTNetwork))
self.assertTrue(is_network(bnet.WTNetwork([[1]])))
def test_is_fixed_sized(self):
from neet.interfaces import is_fixed_sized
self.assertTrue(is_fixed_sized(bnet.WTNetwork))
self.assertTrue(is_fixed_sized(bnet.WTNetwork([[1]])))
def test_update_empty_states(self):
net = bnet.WTNetwork([[1, 0], [1, 1]])
with self.assertRaises(ValueError):
net.update([])
def test_init_failed(self):
with self.assertRaises(ValueError):
bnet.WTNetwork(None)
with self.assertRaises(ValueError):
bnet.WTNetwork('a')
with self.assertRaises(ValueError):
bnet.WTNetwork(0)
with self.assertRaises(ValueError):
bnet.WTNetwork(-1)
with self.assertRaises(ValueError):
bnet.WTNetwork([[1]], 'a')
with self.assertRaises(ValueError):
bnet.WTNetwork([[1]], 0)
with self.assertRaises(ValueError):
bnet.WTNetwork([[1]], -1)
with self.assertRaises(ValueError):
bnet.WTNetwork([])
with self.assertRaises(ValueError):
bnet.WTNetwork([[]])
with self.assertRaises(ValueError):
bnet.WTNetwork([[1]], [])
with self.assertRaises(ValueError):
bnet.WTNetwork([[1]], [1, 2])
def test_update_invalid_index(self):
net = bnet.WTNetwork([[1, 0], [1, 1]])
with self.assertRaises(IndexError):
net.update([0, 0], 2)
def test_average_sensitivity(self):
net = NB.WTNetwork([[1, -1], [0, 1]], [0.5, 0])
self.assertEqual(1.0, average_sensitivity(net))
def test_to_networkx_graph_names_fail(self):
net = bnet.WTNetwork([[1, 0], [0, 1]])
with self.assertRaises(ValueError):
net.to_networkx_graph(labels='names')
def test_average_sensitivity_lengths(self):
net = NB.WTNetwork([[1, -1], [0, 1]], [0.5, 0])
with self.assertRaises(ValueError):
average_sensitivity(
net, states=[[0, 0], [0, 1]], weights=[0, 1, 2])
