Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
282 lines
11 KiB
282 lines
11 KiB
4 years ago
|
import pytest
|
||
|
|
|
||
|
|
import networkx as nx
|
||
|
|
from networkx.testing import assert_nodes_equal, assert_edges_equal, assert_graphs_equal
|
||
|
|
from networkx.convert import (
|
||
|
|
to_networkx_graph,
|
||
|
|
to_dict_of_dicts,
|
||
|
|
from_dict_of_dicts,
|
||
|
|
to_dict_of_lists,
|
||
|
|
from_dict_of_lists,
|
||
|
|
)
|
||
|
|
from networkx.generators.classic import barbell_graph, cycle_graph
|
||
|
|
|
||
|
|
|
||
|
|
class TestConvert:
|
||
|
|
def edgelists_equal(self, e1, e2):
|
||
|
|
return sorted(sorted(e) for e in e1) == sorted(sorted(e) for e in e2)
|
||
|
|
|
||
|
|
def test_simple_graphs(self):
|
||
|
|
for dest, source in [
|
||
|
|
(to_dict_of_dicts, from_dict_of_dicts),
|
||
|
|
(to_dict_of_lists, from_dict_of_lists),
|
||
|
|
]:
|
||
|
|
G = barbell_graph(10, 3)
|
||
|
|
G.graph = {}
|
||
|
|
dod = dest(G)
|
||
|
|
|
||
|
|
# Dict of [dicts, lists]
|
||
|
|
GG = source(dod)
|
||
|
|
assert_graphs_equal(G, GG)
|
||
|
|
GW = to_networkx_graph(dod)
|
||
|
|
assert_graphs_equal(G, GW)
|
||
|
|
GI = nx.Graph(dod)
|
||
|
|
assert_graphs_equal(G, GI)
|
||
|
|
|
||
|
|
# With nodelist keyword
|
||
|
|
P4 = nx.path_graph(4)
|
||
|
|
P3 = nx.path_graph(3)
|
||
|
|
P4.graph = {}
|
||
|
|
P3.graph = {}
|
||
|
|
dod = dest(P4, nodelist=[0, 1, 2])
|
||
|
|
Gdod = nx.Graph(dod)
|
||
|
|
assert_graphs_equal(Gdod, P3)
|
||
|
|
|
||
|
|
def test_exceptions(self):
|
||
|
|
# NX graph
|
||
|
|
class G:
|
||
|
|
adj = None
|
||
|
|
|
||
|
|
pytest.raises(nx.NetworkXError, to_networkx_graph, G)
|
||
|
|
|
||
|
|
# pygraphviz agraph
|
||
|
|
class G:
|
||
|
|
is_strict = None
|
||
|
|
|
||
|
|
pytest.raises(nx.NetworkXError, to_networkx_graph, G)
|
||
|
|
|
||
|
|
# Dict of [dicts, lists]
|
||
|
|
G = {"a": 0}
|
||
|
|
pytest.raises(TypeError, to_networkx_graph, G)
|
||
|
|
|
||
|
|
# list or generator of edges
|
||
|
|
class G:
|
||
|
|
next = None
|
||
|
|
|
||
|
|
pytest.raises(nx.NetworkXError, to_networkx_graph, G)
|
||
|
|
|
||
|
|
# no match
|
||
|
|
pytest.raises(nx.NetworkXError, to_networkx_graph, "a")
|
||
|
|
|
||
|
|
def test_digraphs(self):
|
||
|
|
for dest, source in [
|
||
|
|
(to_dict_of_dicts, from_dict_of_dicts),
|
||
|
|
(to_dict_of_lists, from_dict_of_lists),
|
||
|
|
]:
|
||
|
|
G = cycle_graph(10)
|
||
|
|
|
||
|
|
# Dict of [dicts, lists]
|
||
|
|
dod = dest(G)
|
||
|
|
GG = source(dod)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GG.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GG.edges()))
|
||
|
|
GW = to_networkx_graph(dod)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GW.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GW.edges()))
|
||
|
|
GI = nx.Graph(dod)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GI.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GI.edges()))
|
||
|
|
|
||
|
|
G = cycle_graph(10, create_using=nx.DiGraph)
|
||
|
|
dod = dest(G)
|
||
|
|
GG = source(dod, create_using=nx.DiGraph)
|
||
|
|
assert sorted(G.nodes()) == sorted(GG.nodes())
|
||
|
|
assert sorted(G.edges()) == sorted(GG.edges())
|
||
|
|
GW = to_networkx_graph(dod, create_using=nx.DiGraph)
|
||
|
|
assert sorted(G.nodes()) == sorted(GW.nodes())
|
||
|
|
assert sorted(G.edges()) == sorted(GW.edges())
|
||
|
|
GI = nx.DiGraph(dod)
|
||
|
|
assert sorted(G.nodes()) == sorted(GI.nodes())
|
||
|
|
assert sorted(G.edges()) == sorted(GI.edges())
|
||
|
|
|
||
|
|
def test_graph(self):
|
||
|
|
g = nx.cycle_graph(10)
|
||
|
|
G = nx.Graph()
|
||
|
|
G.add_nodes_from(g)
|
||
|
|
G.add_weighted_edges_from((u, v, u) for u, v in g.edges())
|
||
|
|
|
||
|
|
# Dict of dicts
|
||
|
|
dod = to_dict_of_dicts(G)
|
||
|
|
GG = from_dict_of_dicts(dod, create_using=nx.Graph)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GG.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GG.edges()))
|
||
|
|
GW = to_networkx_graph(dod, create_using=nx.Graph)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GW.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GW.edges()))
|
||
|
|
GI = nx.Graph(dod)
|
||
|
|
assert sorted(G.nodes()) == sorted(GI.nodes())
|
||
|
|
assert sorted(G.edges()) == sorted(GI.edges())
|
||
|
|
|
||
|
|
# Dict of lists
|
||
|
|
dol = to_dict_of_lists(G)
|
||
|
|
GG = from_dict_of_lists(dol, create_using=nx.Graph)
|
||
|
|
# dict of lists throws away edge data so set it to none
|
||
|
|
enone = [(u, v, {}) for (u, v, d) in G.edges(data=True)]
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GG.nodes()))
|
||
|
|
assert_edges_equal(enone, sorted(GG.edges(data=True)))
|
||
|
|
GW = to_networkx_graph(dol, create_using=nx.Graph)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GW.nodes()))
|
||
|
|
assert_edges_equal(enone, sorted(GW.edges(data=True)))
|
||
|
|
GI = nx.Graph(dol)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GI.nodes()))
|
||
|
|
assert_edges_equal(enone, sorted(GI.edges(data=True)))
|
||
|
|
|
||
|
|
def test_with_multiedges_self_loops(self):
|
||
|
|
G = cycle_graph(10)
|
||
|
|
XG = nx.Graph()
|
||
|
|
XG.add_nodes_from(G)
|
||
|
|
XG.add_weighted_edges_from((u, v, u) for u, v in G.edges())
|
||
|
|
XGM = nx.MultiGraph()
|
||
|
|
XGM.add_nodes_from(G)
|
||
|
|
XGM.add_weighted_edges_from((u, v, u) for u, v in G.edges())
|
||
|
|
XGM.add_edge(0, 1, weight=2) # multiedge
|
||
|
|
XGS = nx.Graph()
|
||
|
|
XGS.add_nodes_from(G)
|
||
|
|
XGS.add_weighted_edges_from((u, v, u) for u, v in G.edges())
|
||
|
|
XGS.add_edge(0, 0, weight=100) # self loop
|
||
|
|
|
||
|
|
# Dict of dicts
|
||
|
|
# with self loops, OK
|
||
|
|
dod = to_dict_of_dicts(XGS)
|
||
|
|
GG = from_dict_of_dicts(dod, create_using=nx.Graph)
|
||
|
|
assert_nodes_equal(XGS.nodes(), GG.nodes())
|
||
|
|
assert_edges_equal(XGS.edges(), GG.edges())
|
||
|
|
GW = to_networkx_graph(dod, create_using=nx.Graph)
|
||
|
|
assert_nodes_equal(XGS.nodes(), GW.nodes())
|
||
|
|
assert_edges_equal(XGS.edges(), GW.edges())
|
||
|
|
GI = nx.Graph(dod)
|
||
|
|
assert_nodes_equal(XGS.nodes(), GI.nodes())
|
||
|
|
assert_edges_equal(XGS.edges(), GI.edges())
|
||
|
|
|
||
|
|
# Dict of lists
|
||
|
|
# with self loops, OK
|
||
|
|
dol = to_dict_of_lists(XGS)
|
||
|
|
GG = from_dict_of_lists(dol, create_using=nx.Graph)
|
||
|
|
# dict of lists throws away edge data so set it to none
|
||
|
|
enone = [(u, v, {}) for (u, v, d) in XGS.edges(data=True)]
|
||
|
|
assert_nodes_equal(sorted(XGS.nodes()), sorted(GG.nodes()))
|
||
|
|
assert_edges_equal(enone, sorted(GG.edges(data=True)))
|
||
|
|
GW = to_networkx_graph(dol, create_using=nx.Graph)
|
||
|
|
assert_nodes_equal(sorted(XGS.nodes()), sorted(GW.nodes()))
|
||
|
|
assert_edges_equal(enone, sorted(GW.edges(data=True)))
|
||
|
|
GI = nx.Graph(dol)
|
||
|
|
assert_nodes_equal(sorted(XGS.nodes()), sorted(GI.nodes()))
|
||
|
|
assert_edges_equal(enone, sorted(GI.edges(data=True)))
|
||
|
|
|
||
|
|
# Dict of dicts
|
||
|
|
# with multiedges, OK
|
||
|
|
dod = to_dict_of_dicts(XGM)
|
||
|
|
GG = from_dict_of_dicts(dod, create_using=nx.MultiGraph, multigraph_input=True)
|
||
|
|
assert_nodes_equal(sorted(XGM.nodes()), sorted(GG.nodes()))
|
||
|
|
assert_edges_equal(sorted(XGM.edges()), sorted(GG.edges()))
|
||
|
|
GW = to_networkx_graph(dod, create_using=nx.MultiGraph, multigraph_input=True)
|
||
|
|
assert_nodes_equal(sorted(XGM.nodes()), sorted(GW.nodes()))
|
||
|
|
assert_edges_equal(sorted(XGM.edges()), sorted(GW.edges()))
|
||
|
|
GI = nx.MultiGraph(dod) # convert can't tell whether to duplicate edges!
|
||
|
|
assert_nodes_equal(sorted(XGM.nodes()), sorted(GI.nodes()))
|
||
|
|
# assert_not_equal(sorted(XGM.edges()), sorted(GI.edges()))
|
||
|
|
assert not sorted(XGM.edges()) == sorted(GI.edges())
|
||
|
|
GE = from_dict_of_dicts(dod, create_using=nx.MultiGraph, multigraph_input=False)
|
||
|
|
assert_nodes_equal(sorted(XGM.nodes()), sorted(GE.nodes()))
|
||
|
|
assert sorted(XGM.edges()) != sorted(GE.edges())
|
||
|
|
GI = nx.MultiGraph(XGM)
|
||
|
|
assert_nodes_equal(sorted(XGM.nodes()), sorted(GI.nodes()))
|
||
|
|
assert_edges_equal(sorted(XGM.edges()), sorted(GI.edges()))
|
||
|
|
GM = nx.MultiGraph(G)
|
||
|
|
assert_nodes_equal(sorted(GM.nodes()), sorted(G.nodes()))
|
||
|
|
assert_edges_equal(sorted(GM.edges()), sorted(G.edges()))
|
||
|
|
|
||
|
|
# Dict of lists
|
||
|
|
# with multiedges, OK, but better write as DiGraph else you'll
|
||
|
|
# get double edges
|
||
|
|
dol = to_dict_of_lists(G)
|
||
|
|
GG = from_dict_of_lists(dol, create_using=nx.MultiGraph)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GG.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GG.edges()))
|
||
|
|
GW = to_networkx_graph(dol, create_using=nx.MultiGraph)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GW.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GW.edges()))
|
||
|
|
GI = nx.MultiGraph(dol)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(GI.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(GI.edges()))
|
||
|
|
|
||
|
|
def test_edgelists(self):
|
||
|
|
P = nx.path_graph(4)
|
||
|
|
e = [(0, 1), (1, 2), (2, 3)]
|
||
|
|
G = nx.Graph(e)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(P.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(P.edges()))
|
||
|
|
assert_edges_equal(sorted(G.edges(data=True)), sorted(P.edges(data=True)))
|
||
|
|
|
||
|
|
e = [(0, 1, {}), (1, 2, {}), (2, 3, {})]
|
||
|
|
G = nx.Graph(e)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(P.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(P.edges()))
|
||
|
|
assert_edges_equal(sorted(G.edges(data=True)), sorted(P.edges(data=True)))
|
||
|
|
|
||
|
|
e = ((n, n + 1) for n in range(3))
|
||
|
|
G = nx.Graph(e)
|
||
|
|
assert_nodes_equal(sorted(G.nodes()), sorted(P.nodes()))
|
||
|
|
assert_edges_equal(sorted(G.edges()), sorted(P.edges()))
|
||
|
|
assert_edges_equal(sorted(G.edges(data=True)), sorted(P.edges(data=True)))
|
||
|
|
|
||
|
|
def test_directed_to_undirected(self):
|
||
|
|
edges1 = [(0, 1), (1, 2), (2, 0)]
|
||
|
|
edges2 = [(0, 1), (1, 2), (0, 2)]
|
||
|
|
assert self.edgelists_equal(nx.Graph(nx.DiGraph(edges1)).edges(), edges1)
|
||
|
|
assert self.edgelists_equal(nx.Graph(nx.DiGraph(edges2)).edges(), edges1)
|
||
|
|
assert self.edgelists_equal(nx.MultiGraph(nx.DiGraph(edges1)).edges(), edges1)
|
||
|
|
assert self.edgelists_equal(nx.MultiGraph(nx.DiGraph(edges2)).edges(), edges1)
|
||
|
|
|
||
|
|
assert self.edgelists_equal(
|
||
|
|
nx.MultiGraph(nx.MultiDiGraph(edges1)).edges(), edges1
|
||
|
|
)
|
||
|
|
assert self.edgelists_equal(
|
||
|
|
nx.MultiGraph(nx.MultiDiGraph(edges2)).edges(), edges1
|
||
|
|
)
|
||
|
|
|
||
|
|
assert self.edgelists_equal(nx.Graph(nx.MultiDiGraph(edges1)).edges(), edges1)
|
||
|
|
assert self.edgelists_equal(nx.Graph(nx.MultiDiGraph(edges2)).edges(), edges1)
|
||
|
|
|
||
|
|
def test_attribute_dict_integrity(self):
|
||
|
|
# we must not replace dict-like graph data structures with dicts
|
||
|
|
G = nx.OrderedGraph()
|
||
|
|
G.add_nodes_from("abc")
|
||
|
|
H = to_networkx_graph(G, create_using=nx.OrderedGraph)
|
||
|
|
assert list(H.nodes) == list(G.nodes)
|
||
|
|
H = nx.OrderedDiGraph(G)
|
||
|
|
assert list(H.nodes) == list(G.nodes)
|
||
|
|
|
||
|
|
def test_to_edgelist(self):
|
||
|
|
G = nx.Graph([(1, 1)])
|
||
|
|
elist = nx.to_edgelist(G, nodelist=list(G))
|
||
|
|
assert_edges_equal(G.edges(data=True), elist)
|
||
|
|
|
||
|
|
def test_custom_node_attr_dict_safekeeping(self):
|
||
|
|
class custom_dict(dict):
|
||
|
|
pass
|
||
|
|
|
||
|
|
class Custom(nx.Graph):
|
||
|
|
node_attr_dict_factory = custom_dict
|
||
|
|
|
||
|
|
g = nx.Graph()
|
||
|
|
g.add_node(1, weight=1)
|
||
|
|
|
||
|
|
h = Custom(g)
|
||
|
|
assert isinstance(g._node[1], dict)
|
||
|
|
assert isinstance(h._node[1], custom_dict)
|
||
|
|
|
||
|
|
# this raise exception
|
||
|
|
# h._node.update((n, dd.copy()) for n, dd in g.nodes.items())
|
||
|
|
# assert isinstance(h._node[1], custom_dict)
|