def test_add_node():
"""Test the node assignment."""
# add string and create new node in the network
net = Network()
net.add_node('v', color='red')
assert len(net.nodes) == 1
assert 'v' in net.nodes.uids
assert net.nodes['v']['color'] == 'red'
assert net.nodes.index['v'] == 0
assert net.number_of_nodes() == 1
assert isinstance(net.nodes['v'], Node)
assert net.nodes['v'].uid == 'v'
w = Node('w', color='green')
net.add_node(w)
assert net.number_of_nodes() == 2
assert isinstance(net.nodes['w'], Node)
assert net.nodes['w'].uid == 'w'
assert net.nodes['w']['color'] == 'green'
v = Node('v', color='blue')
with pytest.raises(Exception):
net.add_node(v)
def test_network_degrees():
"""Test node degrees of a network"""
a = Node('a')
net = Network(directed=False)
net.add_edges((a, 'b'), ('b', 'c'), ('c', 'a'))
assert isinstance(list(net.nodes.keys())[0], (str, int))
def test_properties():
"""Test network properties."""
net = Network(directed=False)
net.add_edge('a', 'b', uid='a-b')
net.edges['a-b']['color'] = 'red'
assert net.edges['a-b']['color'] == 'red'
def test_network_plot():
"""Test the plot function on a network."""
net = Network()
net.add_node('a', color='red')
net.add_node('b', size=40)
net.add_edge('a', 'b', uid='a-b', color='blue')
net.plot(filename='simple_plot.html', node_color={'a': 'green'})
def test_mean_degree():
"""Test the mean degree calculation."""
# net = pp.generators.Molloy_Reed([2]*500)
net = Network(directed=False)
net.add_edges(('a', 'b'), ('b', 'c'), ('c', 'a'))
mean_degree = pp.statistics.mean_degree(net)
assert mean_degree == 2.0
def test_add_nodes():
"""Test assigning notes form a list."""
net = Network()
u = Node('u', color='blue')
net.add_nodes(u, 'v', 'w', color='green')
assert net.number_of_nodes() == 3
assert net.nodes['u']['color'] == 'green'
assert net.nodes['v']['color'] == 'green'
assert net.nodes['w']['color'] == 'green'
def test_directed():
"""Test if a network is directed."""
net = Network()
assert net.directed is True
net = Network(directed=False)
assert net.directed is False
def test_update():
"""Test update network attributes."""
net = Network(city='London')
assert net['city'] == 'London'
net.update(city='Vienna', year='1850')
assert net['city'] == 'Vienna'
assert net['year'] == '1850'
def test_network_edges():
"""Test the edges of a network"""
net = Network(directed=False)
net.add_edges(('a', 'b'), ('b', 'c'), ('c', 'd'))
assert net.number_of_edges() == 3
assert isinstance(list(net.edges), list)
# np does not allow to sample from iterables
# edge = np.random.choice(list(net.edges.values()))
edge = random.choice(list(net.edges))
assert edge in net.edges
def test_adjacency_matrix():
"""Test the adjacency matrix of a network."""
net = Network()
net.add_edges(('a', 'b'), ('b', 'c'))
A1 = net.adjacency_matrix()
assert A1[0, 1] == 1.0
assert A1[1, 2] == 1.0
A2 = pp.algorithms.matrices.adjacency_matrix(net)
assert A2[0, 1] == 1.0
assert A2[1, 2] == 1.0
def test_uid():
"""Test the uid assignment."""
net = Network(uid='test')
assert isinstance(net, Network)
assert isinstance(net.uid, str)
assert net.uid == 'test'
net = Network()
assert isinstance(net, Network)
assert isinstance(net.uid, str)
def test_adjacency_matrix():
"""Test the adjacency matrix of a network."""
net = Network()
net.add_edges(('a', 'b'), ('b', 'c'))
n = net.nodes.index
A1 = net.adjacency_matrix()
assert A1[n['a'], n['b']] == 1.0
assert A1[n['b'], n['c']] == 1.0
A2 = pp.algorithms.matrices.adjacency_matrix(net)
assert A2[n['a'], n['b']] == 1.0
assert A2[n['b'], n['c']] == 1.0
def test_getitem():
"""Test the extraction of attributes."""
net = Network(city='London')
assert net['city'] == 'London'
assert net['attribute not in dict'] == None
def test_setitem():
"""Test the assignment of attributes."""
net = Network()
net['city'] = 'Zurich'
assert net['city'] == 'Zurich'
def __init__(self, paths, max_order=1, model_selection=True):
"""Initialise MOGen."""
self.paths = {tuple(x.uid for x in p.nodes): paths[p]['frequency'] for p in paths}
self.network = Network()
for e in paths.edges:
self.network.add_edge(e)
self.max_order = max_order
self.model_selection = model_selection
# initialise variables
self.optimal_maximum_order = None
self.A = None
self.T = None
self.log_L = None
self.dof = None
self.AIC = None
self.models = collections.defaultdict(lambda: {})
self.log_L_offset = None
def test_largest_connected_component():
"""Test to find the largest connected component."""
net = Network(directed=False)
net.add_edge('a', 'b')
net.add_edge('b', 'c')
net.add_edge('x', 'y')
lcc = pp.algorithms.components.largest_connected_component(net)
def test_find_connected_components():
"""Test to find the connected components."""
net = Network(directed=False)
net.add_edge('a', 'b')
net.add_edge('b', 'c')
net.add_edge('x', 'y')
cn = pp.algorithms.components.find_connected_components(net)
def test_network_properties():
"""Test network properties."""
net = Network()
net.add_edge('a', 'b', uid='a-b')
net.add_edge('b', 'c', uid='b-c')
net.add_edge('c', 'a', uid='c-a')
assert net.successors['c'] == {net.nodes['a']}
assert net.incoming['a'] == {net.edges['c-a']}
net.remove_edge('c-a')
assert net.successors['c'] == set()
assert net.incoming['a'] == set()
def test_network_undirected():
"""Test undirected networks"""
net = Network(directed=False)
net.add_edge('a', 'b', timestamp=1, color='red', size=4)
net.add_edge('b', 'a', timestamp=3, color='blue', frequency=30)
assert net.number_of_edges() == 1
assert net.edges['a', 'b']['color'] == 'blue'
assert net.edges['b', 'a']['size'] == 4
assert net.edges['a', 'b']['timestamp'] == 3
def get_metric(network: pp.Network, metric: str):
switcher = {
'num_vertices':
network.number_of_nodes(),
'num_edges':
network.number_of_edges(),
'is_directed':
network.directed,
'average_degree':
pp.statistics.mean_degree(network),
'degree_assortativity':
pp.statistics.degree_assortativity(network),
'global_clustering_coefficient':
pp.statistics.avg_clustering_coefficient(network),
'diameter':
pp.algorithms.diameter(network),
'edge_reciprocity':
pp.statistics.edge_reciprocity(network),
'largest_component_fraction':
pp.algorithms.largest_component_size(network) /
network.number_of_nodes()
}
return switcher.get(metric, None)
def test_get_edge():
"""Test to get edges."""
net = Network(directed=False)
net.add_edge('a', 'b')
assert (('a', 'b') in net.edges) is True
assert (('b', 'a') in net.edges) is True
assert (('a', 'c') in net.edges) is False
a = Node('a')
b = Node('b')
e = Edge(a, b)
net = Network(directed=True)
net.add_edge(e)
assert ((a, b) in net.edges) is True
assert (e in net.edges) is True
assert (('a', b) in net.edges) is True
assert ((b, a) in net.edges) is False
def test_sql_write_network():
"""Write network to sql database."""
net = Network()
net.add_edges(('a', 'b'), ('a', 'c'))
pp.io.sql.write(net,
filename='network.db',
table='test',
if_exists='replace')
net = pp.io.sql.read_network(db_file='network.db', table='test')
assert isinstance(net, Network)
assert net.number_of_nodes() == 3
assert net.number_of_edges() == 2
def test_remove_edge():
"""Test to remove an edge from the network."""
net = Network()
a = Node('a')
b = Node('b')
c = Node('c')
e = Edge(a, b, uid='e')
f = Edge(b, a, uid='f')
g = Edge(b, c, uid='g')
net.add_edge(e)
net.add_edge(f)
net.remove_edge(g)
assert net.number_of_edges() == 2
assert isinstance(net.edges['e'], Edge)
assert g not in net.edges
assert net.edges['a', 'b'] in net.edges
assert net.successors['a'] == {b}
assert net.outgoing['a'] == {e}
assert net.incident_edges['a'] == {e, f}
net.remove_edge(e)
assert net.number_of_edges() == 1
assert net.successors['a'] == set()
assert net.outgoing['a'] == set()
assert net.incident_edges['a'] == {f}
net.remove_edge('f')
assert net.number_of_edges() == 0
assert net.incident_edges['a'] == set()
a = Node('a')
b = Node('b')
e = Edge(a, b, uid='e')
f = Edge(a, b, uid='f')
g = Edge(a, b, uid='g')
net = Network(multiedges=True)
net.add_edges(e, f, g)
assert net.number_of_edges() == 3
assert e and f and g in net.edges['a', 'b']
net.remove_edge('a', 'b', uid='g')
assert net.number_of_edges() == 2
assert g not in net.edges['a', 'b']
net.remove_edge('a', 'b')
assert net.number_of_edges() == 0
assert len(net.edges['a', 'b']) == 0
def test_plot_empty_network_plot():
"""Test the plot function on a network."""
net = Network()
net.plot()
def test_shape():
"""Test the shape of the network."""
net = Network()
assert net.shape == (0, 0)
def test_remove_node():
"""Test to remove a node from the network."""
net = Network(directed=True)
net.add_edge('a', 'b')
net.add_edge('a', 'c')
net.add_edge('b', 'd')
net.add_edge('b', 'e')
net.add_edge('d', 'b')
net.add_edge('d', 'e')
net.add_edge('e', 'd')
assert net.shape == (5, 7)
net.remove_node('b')
assert net.shape == (4, 3)
def test_isub_networks():
"""Test to remove a network with isub"""
net_1 = Network()
net_2 = Network()
net_1.add_edge('a', 'b', uid='a-b')
net_2.add_edge('c', 'd', uid='c-d')
net_1 += net_2
net_2.add_edge('d', 'e', uid='d-e')
net_1 -= net_2
assert net_1.number_of_nodes() == 2
assert net_1.number_of_edges() == 1
assert 'a' and 'b' in net_1.nodes
assert 'a-b' in net_1.edges
assert net_2.number_of_nodes() == 3
assert net_2.number_of_edges() == 2
def test_sub_networks():
"""Test to remove a network"""
net_1 = Network()
net_2 = Network()
net_1.add_edge('a', 'b', uid='a-b')
net_2.add_edge('c', 'd', uid='c-d')
net_1 += net_2
net_2.add_edge('d', 'e', uid='d-e')
net_3 = net_1 - net_2
assert net_3.number_of_nodes() == 2
assert net_3.number_of_edges() == 1
assert 'a' and 'b' in net_3.nodes
assert 'a-b' in net_3.edges
assert net_1.number_of_nodes() == 4
assert net_1.number_of_edges() == 2
assert net_2.number_of_nodes() == 3
assert net_2.number_of_edges() == 2
net_4 = Network()
net_4.add_edge('x', 'y', uid='x-y')
net_5 = net_3 - net_4
assert net_5.number_of_nodes() == 2
assert net_5.number_of_edges() == 1
assert 'a' and 'b' in net_5.nodes
assert 'a-b' in net_5.edges
def test_iadd_networks():
"""Test to add networks together"""
net_1 = Network()
net_1.add_edges(('a', 'b'), ('b', 'c'))
net_2 = Network()
net_2.add_edges(('x', 'y'), ('y', 'z'))
net_1 += net_2
assert net_1.number_of_nodes() == 6
assert net_1.number_of_edges() == 4
assert net_2.number_of_nodes() == 3
assert net_2.number_of_edges() == 2
# test same node objects
a = Node('a')
b = Node('b')
c = Node('c')
net_1 = Network()
net_2 = Network()
net_1.add_edge(a, b)
net_2.add_edge(b, c)
net_1 += net_2
assert net_1.number_of_nodes() == 3
assert net_1.number_of_edges() == 2
assert net_2.number_of_nodes() == 2
assert net_2.number_of_edges() == 1
# nodes with same uids but different objects
net_1 = Network()
net_2 = Network()
net_1.add_edge(a, b)
net_2.add_edge('b', c)
with pytest.raises(Exception):
net_1 += net_2
# test same edge objects
a = Node('a')
b = Node('b')
c = Node('c')
net_1 = Network()
net_2 = Network()
net_1.add_edge(a, b, uid='e1')
net_2.add_edge(a, b, uid='e2')
with pytest.raises(Exception):
net_1 += net_2
# assert net_1.number_of_edges() == 2
# assert net_1.number_of_nodes() == 2
# assert 'e1' in net_1.edges and 'e2' in net_1.edges
# edges with same uids but different objects
net_1 = Network()
net_2 = Network()
net_1.add_edge(a, b, uid='e1')
net_2.add_edge(a, b, uid='e1')
with pytest.raises(Exception):
net_1 += net_2
# add multiple networks
net_1 = Network()
net_2 = Network()
net_3 = Network()
net_1.add_edge('a', 'b')
net_2.add_edge('c', 'd')
net_3.add_edge('e', 'f')
net_1 += net_2 + net_3
assert net_1.number_of_edges() == 3
assert net_1.number_of_nodes() == 6
def test_str():
"""Test string representations of the network."""
net = Network()
assert isinstance(net.summary(), str)