blob: 077dead7105e165d1bd5fd07b600d1b47dcdf828 [file] [log] [blame]
#!/usr/bin/env python
from nose.tools import *
import networkx
class BaseGraphTester(object):
""" Tests for data-structure independent graph class features."""
def test_contains(self):
G=self.K3
assert(1 in G )
assert(4 not in G )
assert('b' not in G )
assert([] not in G ) # no exception for nonhashable
assert({1:1} not in G) # no exception for nonhashable
def test_order(self):
G=self.K3
assert_equal(len(G),3)
assert_equal(G.order(),3)
assert_equal(G.number_of_nodes(),3)
def test_nodes_iter(self):
G=self.K3
assert_equal(sorted(G.nodes_iter()),self.k3nodes)
assert_equal(sorted(G.nodes_iter(data=True)),[(0,{}),(1,{}),(2,{})])
def test_nodes(self):
G=self.K3
assert_equal(sorted(G.nodes()),self.k3nodes)
assert_equal(sorted(G.nodes(data=True)),[(0,{}),(1,{}),(2,{})])
def test_has_node(self):
G=self.K3
assert(G.has_node(1))
assert(not G.has_node(4))
assert(not G.has_node([])) # no exception for nonhashable
assert(not G.has_node({1:1})) # no exception for nonhashable
def test_has_edge(self):
G=self.K3
assert_equal(G.has_edge(0,1),True)
assert_equal(G.has_edge(0,-1),False)
def test_neighbors(self):
G=self.K3
assert_equal(sorted(G.neighbors(0)),[1,2])
assert_raises((KeyError,networkx.NetworkXError), G.neighbors,-1)
def test_neighbors_iter(self):
G=self.K3
assert_equal(sorted(G.neighbors_iter(0)),[1,2])
assert_raises((KeyError,networkx.NetworkXError), G.neighbors_iter,-1)
def test_edges(self):
G=self.K3
assert_equal(sorted(G.edges()),[(0,1),(0,2),(1,2)])
assert_equal(sorted(G.edges(0)),[(0,1),(0,2)])
assert_raises((KeyError,networkx.NetworkXError), G.edges,-1)
def test_edges_iter(self):
G=self.K3
assert_equal(sorted(G.edges_iter()),[(0,1),(0,2),(1,2)])
assert_equal(sorted(G.edges_iter(0)),[(0,1),(0,2)])
f=lambda x:list(G.edges_iter(x))
assert_raises((KeyError,networkx.NetworkXError), f, -1)
def test_adjacency_list(self):
G=self.K3
assert_equal(G.adjacency_list(),[[1,2],[0,2],[0,1]])
def test_degree(self):
G=self.K3
assert_equal(list(G.degree().values()),[2,2,2])
assert_equal(G.degree(),{0:2,1:2,2:2})
assert_equal(G.degree(0),2)
assert_equal(G.degree([0]),{0:2})
assert_raises((KeyError,networkx.NetworkXError), G.degree,-1)
def test_weighted_degree(self):
G=self.Graph()
G.add_edge(1,2,weight=2)
G.add_edge(2,3,weight=3)
assert_equal(list(G.degree(weight='weight').values()),[2,5,3])
assert_equal(G.degree(weight='weight'),{1:2,2:5,3:3})
assert_equal(G.degree(1,weight='weight'),2)
assert_equal(G.degree([1],weight='weight'),{1:2})
def test_degree_iter(self):
G=self.K3
assert_equal(list(G.degree_iter()),[(0,2),(1,2),(2,2)])
assert_equal(dict(G.degree_iter()),{0:2,1:2,2:2})
assert_equal(list(G.degree_iter(0)),[(0,2)])
def test_size(self):
G=self.K3
assert_equal(G.size(),3)
assert_equal(G.number_of_edges(),3)
def test_add_star(self):
G=self.K3.copy()
nlist=[12,13,14,15]
G.add_star(nlist)
assert_equal(sorted(G.edges(nlist)),[(12,13),(12,14),(12,15)])
G=self.K3.copy()
G.add_star(nlist,weight=2.0)
assert_equal(sorted(G.edges(nlist,data=True)),\
[(12,13,{'weight':2.}),
(12,14,{'weight':2.}),
(12,15,{'weight':2.})])
def test_add_path(self):
G=self.K3.copy()
nlist=[12,13,14,15]
G.add_path(nlist)
assert_equal(sorted(G.edges(nlist)),[(12,13),(13,14),(14,15)])
G=self.K3.copy()
G.add_path(nlist,weight=2.0)
assert_equal(sorted(G.edges(nlist,data=True)),\
[(12,13,{'weight':2.}),
(13,14,{'weight':2.}),
(14,15,{'weight':2.})])
def test_add_cycle(self):
G=self.K3.copy()
nlist=[12,13,14,15]
oklists=[ [(12,13),(12,15),(13,14),(14,15)], \
[(12,13),(13,14),(14,15),(15,12)] ]
G.add_cycle(nlist)
assert_true(sorted(G.edges(nlist)) in oklists)
G=self.K3.copy()
oklists=[ [(12,13,{'weight':1.}),\
(12,15,{'weight':1.}),\
(13,14,{'weight':1.}),\
(14,15,{'weight':1.})], \
\
[(12,13,{'weight':1.}),\
(13,14,{'weight':1.}),\
(14,15,{'weight':1.}),\
(15,12,{'weight':1.})] \
]
G.add_cycle(nlist,weight=1.0)
assert_true(sorted(G.edges(nlist,data=True)) in oklists)
def test_nbunch_iter(self):
G=self.K3
assert_equal(list(G.nbunch_iter()),self.k3nodes) # all nodes
assert_equal(list(G.nbunch_iter(0)),[0]) # single node
assert_equal(list(G.nbunch_iter([0,1])),[0,1]) # sequence
# sequence with none in graph
assert_equal(list(G.nbunch_iter([-1])),[])
# string sequence with none in graph
assert_equal(list(G.nbunch_iter("foo")),[])
# node not in graph doesn't get caught upon creation of iterator
bunch=G.nbunch_iter(-1)
# but gets caught when iterator used
assert_raises(networkx.NetworkXError,list,bunch)
# unhashable doesn't get caught upon creation of iterator
bunch=G.nbunch_iter([0,1,2,{}])
# but gets caught when iterator hits the unhashable
assert_raises(networkx.NetworkXError,list,bunch)
def test_selfloop_degree(self):
G=self.Graph()
G.add_edge(1,1)
assert_equal(list(G.degree().values()),[2])
assert_equal(G.degree(),{1:2})
assert_equal(G.degree(1),2)
assert_equal(G.degree([1]),{1:2})
assert_equal(G.degree([1],weight='weight'),{1:2})
def test_selfloops(self):
G=self.K3.copy()
G.add_edge(0,0)
assert_equal(G.nodes_with_selfloops(),[0])
assert_equal(G.selfloop_edges(),[(0,0)])
assert_equal(G.number_of_selfloops(),1)
G.remove_edge(0,0)
G.add_edge(0,0)
G.remove_edges_from([(0,0)])
G.add_edge(1,1)
G.remove_node(1)
G.add_edge(0,0)
G.add_edge(1,1)
G.remove_nodes_from([0,1])
class BaseAttrGraphTester(BaseGraphTester):
""" Tests of graph class attribute features."""
def test_weighted_degree(self):
G=self.Graph()
G.add_edge(1,2,weight=2,other=3)
G.add_edge(2,3,weight=3,other=4)
assert_equal(list(G.degree(weight='weight').values()),[2,5,3])
assert_equal(G.degree(weight='weight'),{1:2,2:5,3:3})
assert_equal(G.degree(1,weight='weight'),2)
assert_equal(G.degree([1],weight='weight'),{1:2})
assert_equal(list(G.degree(weight='other').values()),[3,7,4])
assert_equal(G.degree(weight='other'),{1:3,2:7,3:4})
assert_equal(G.degree(1,weight='other'),3)
assert_equal(G.degree([1],weight='other'),{1:3})
def add_attributes(self,G):
G.graph['foo']=[]
G.node[0]['foo']=[]
G.remove_edge(1,2)
ll=[]
G.add_edge(1,2,foo=ll)
G.add_edge(2,1,foo=ll)
# attr_dict must be dict
assert_raises(networkx.NetworkXError,G.add_edge,0,1,attr_dict=[])
def test_name(self):
G=self.Graph(name='')
assert_equal(G.name,"")
G=self.Graph(name='test')
assert_equal(G.__str__(),"test")
assert_equal(G.name,"test")
def test_copy(self):
G=self.K3
self.add_attributes(G)
H=G.copy()
self.is_deepcopy(H,G)
H=G.__class__(G)
self.is_shallow_copy(H,G)
def test_copy_attr(self):
G=self.Graph(foo=[])
G.add_node(0,foo=[])
G.add_edge(1,2,foo=[])
H=G.copy()
self.is_deepcopy(H,G)
H=G.__class__(G) # just copy
self.is_shallow_copy(H,G)
def is_deepcopy(self,H,G):
self.graphs_equal(H,G)
self.different_attrdict(H,G)
self.deep_copy_attrdict(H,G)
def deep_copy_attrdict(self,H,G):
self.deepcopy_graph_attr(H,G)
self.deepcopy_node_attr(H,G)
self.deepcopy_edge_attr(H,G)
def deepcopy_graph_attr(self,H,G):
assert_equal(G.graph['foo'],H.graph['foo'])
G.graph['foo'].append(1)
assert_not_equal(G.graph['foo'],H.graph['foo'])
def deepcopy_node_attr(self,H,G):
assert_equal(G.node[0]['foo'],H.node[0]['foo'])
G.node[0]['foo'].append(1)
assert_not_equal(G.node[0]['foo'],H.node[0]['foo'])
def deepcopy_edge_attr(self,H,G):
assert_equal(G[1][2]['foo'],H[1][2]['foo'])
G[1][2]['foo'].append(1)
assert_not_equal(G[1][2]['foo'],H[1][2]['foo'])
def is_shallow_copy(self,H,G):
self.graphs_equal(H,G)
self.different_attrdict(H,G)
self.shallow_copy_attrdict(H,G)
def shallow_copy_attrdict(self,H,G):
self.shallow_copy_graph_attr(H,G)
self.shallow_copy_node_attr(H,G)
self.shallow_copy_edge_attr(H,G)
def shallow_copy_graph_attr(self,H,G):
assert_equal(G.graph['foo'],H.graph['foo'])
G.graph['foo'].append(1)
assert_equal(G.graph['foo'],H.graph['foo'])
def shallow_copy_node_attr(self,H,G):
assert_equal(G.node[0]['foo'],H.node[0]['foo'])
G.node[0]['foo'].append(1)
assert_equal(G.node[0]['foo'],H.node[0]['foo'])
def shallow_copy_edge_attr(self,H,G):
assert_equal(G[1][2]['foo'],H[1][2]['foo'])
G[1][2]['foo'].append(1)
assert_equal(G[1][2]['foo'],H[1][2]['foo'])
def same_attrdict(self, H, G):
old_foo=H[1][2]['foo']
H.add_edge(1,2,foo='baz')
assert_equal(G.edge,H.edge)
H.add_edge(1,2,foo=old_foo)
assert_equal(G.edge,H.edge)
old_foo=H.node[0]['foo']
H.node[0]['foo']='baz'
assert_equal(G.node,H.node)
H.node[0]['foo']=old_foo
assert_equal(G.node,H.node)
def different_attrdict(self, H, G):
old_foo=H[1][2]['foo']
H.add_edge(1,2,foo='baz')
assert_not_equal(G.edge,H.edge)
H.add_edge(1,2,foo=old_foo)
assert_equal(G.edge,H.edge)
old_foo=H.node[0]['foo']
H.node[0]['foo']='baz'
assert_not_equal(G.node,H.node)
H.node[0]['foo']=old_foo
assert_equal(G.node,H.node)
def graphs_equal(self,H,G):
assert_equal(G.adj,H.adj)
assert_equal(G.edge,H.edge)
assert_equal(G.node,H.node)
assert_equal(G.graph,H.graph)
assert_equal(G.name,H.name)
if not G.is_directed() and not H.is_directed():
assert_true(H.adj[1][2] is H.adj[2][1])
assert_true(G.adj[1][2] is G.adj[2][1])
else: # at least one is directed
if not G.is_directed():
G.pred=G.adj
G.succ=G.adj
if not H.is_directed():
H.pred=H.adj
H.succ=H.adj
assert_equal(G.pred,H.pred)
assert_equal(G.succ,H.succ)
assert_true(H.succ[1][2] is H.pred[2][1])
assert_true(G.succ[1][2] is G.pred[2][1])
def test_graph_attr(self):
G=self.K3
G.graph['foo']='bar'
assert_equal(G.graph['foo'], 'bar')
del G.graph['foo']
assert_equal(G.graph, {})
H=self.Graph(foo='bar')
assert_equal(H.graph['foo'], 'bar')
def test_node_attr(self):
G=self.K3
G.add_node(1,foo='bar')
assert_equal(G.nodes(), [0,1,2])
assert_equal(G.nodes(data=True), [(0,{}),(1,{'foo':'bar'}),(2,{})])
G.node[1]['foo']='baz'
assert_equal(G.nodes(data=True), [(0,{}),(1,{'foo':'baz'}),(2,{})])
def test_node_attr2(self):
G=self.K3
a={'foo':'bar'}
G.add_node(3,attr_dict=a)
assert_equal(G.nodes(), [0,1,2,3])
assert_equal(G.nodes(data=True),
[(0,{}),(1,{}),(2,{}),(3,{'foo':'bar'})])
def test_edge_attr(self):
G=self.Graph()
G.add_edge(1,2,foo='bar')
assert_equal(G.edges(data=True), [(1,2,{'foo':'bar'})])
def test_edge_attr2(self):
G=self.Graph()
G.add_edges_from([(1,2),(3,4)],foo='foo')
assert_equal(sorted(G.edges(data=True)),
[(1,2,{'foo':'foo'}),(3,4,{'foo':'foo'})])
def test_edge_attr3(self):
G=self.Graph()
G.add_edges_from([(1,2,{'weight':32}),(3,4,{'weight':64})],foo='foo')
assert_equal(G.edges(data=True),
[(1,2,{'foo':'foo','weight':32}),\
(3,4,{'foo':'foo','weight':64})])
G.remove_edges_from([(1,2),(3,4)])
G.add_edge(1,2,data=7,spam='bar',bar='foo')
assert_equal(G.edges(data=True),
[(1,2,{'data':7,'spam':'bar','bar':'foo'})])
def test_edge_attr4(self):
G=self.Graph()
G.add_edge(1,2,data=7,spam='bar',bar='foo')
assert_equal(G.edges(data=True),
[(1,2,{'data':7,'spam':'bar','bar':'foo'})])
G[1][2]['data']=10 # OK to set data like this
assert_equal(G.edges(data=True),
[(1,2,{'data':10,'spam':'bar','bar':'foo'})])
G.edge[1][2]['data']=20 # another spelling, "edge"
assert_equal(G.edges(data=True),
[(1,2,{'data':20,'spam':'bar','bar':'foo'})])
G.edge[1][2]['listdata']=[20,200]
G.edge[1][2]['weight']=20
assert_equal(G.edges(data=True),
[(1,2,{'data':20,'spam':'bar',
'bar':'foo','listdata':[20,200],'weight':20})])
def test_attr_dict_not_dict(self):
# attr_dict must be dict
G=self.Graph()
edges=[(1,2)]
assert_raises(networkx.NetworkXError,G.add_edges_from,edges,
attr_dict=[])
def test_to_undirected(self):
G=self.K3
self.add_attributes(G)
H=networkx.Graph(G)
self.is_shallow_copy(H,G)
H=G.to_undirected()
self.is_deepcopy(H,G)
def test_to_directed(self):
G=self.K3
self.add_attributes(G)
H=networkx.DiGraph(G)
self.is_shallow_copy(H,G)
H=G.to_directed()
self.is_deepcopy(H,G)
def test_subgraph(self):
G=self.K3
self.add_attributes(G)
H=G.subgraph([0,1,2,5])
# assert_equal(H.name, 'Subgraph of ('+G.name+')')
H.name=G.name
self.graphs_equal(H,G)
self.same_attrdict(H,G)
self.shallow_copy_attrdict(H,G)
H=G.subgraph(0)
assert_equal(H.adj,{0:{}})
H=G.subgraph([])
assert_equal(H.adj,{})
assert_not_equal(G.adj,{})
def test_selfloops_attr(self):
G=self.K3.copy()
G.add_edge(0,0)
G.add_edge(1,1,weight=2)
assert_equal(G.selfloop_edges(data=True),
[(0,0,{}),(1,1,{'weight':2})])
class TestGraph(BaseAttrGraphTester):
"""Tests specific to dict-of-dict-of-dict graph data structure"""
def setUp(self):
self.Graph=networkx.Graph
# build dict-of-dict-of-dict K3
ed1,ed2,ed3 = ({},{},{})
self.k3adj={0: {1: ed1, 2: ed2},
1: {0: ed1, 2: ed3},
2: {0: ed2, 1: ed3}}
self.k3edges=[(0, 1), (0, 2), (1, 2)]
self.k3nodes=[0, 1, 2]
self.K3=self.Graph()
self.K3.adj=self.K3.edge=self.k3adj
self.K3.node={}
self.K3.node[0]={}
self.K3.node[1]={}
self.K3.node[2]={}
def test_data_input(self):
G=self.Graph(data={1:[2],2:[1]}, name="test")
assert_equal(G.name,"test")
assert_equal(sorted(G.adj.items()),[(1, {2: {}}), (2, {1: {}})])
G=self.Graph({1:[2],2:[1]}, name="test")
assert_equal(G.name,"test")
assert_equal(sorted(G.adj.items()),[(1, {2: {}}), (2, {1: {}})])
def test_adjacency_iter(self):
G=self.K3
assert_equal(dict(G.adjacency_iter()),
{0: {1: {}, 2: {}}, 1: {0: {}, 2: {}}, 2: {0: {}, 1: {}}})
def test_getitem(self):
G=self.K3
assert_equal(G[0],{1: {}, 2: {}})
assert_raises(KeyError, G.__getitem__, 'j')
assert_raises((TypeError,networkx.NetworkXError), G.__getitem__, ['A'])
def test_add_node(self):
G=self.Graph()
G.add_node(0)
assert_equal(G.adj,{0:{}})
# test add attributes
G.add_node(1,c='red')
G.add_node(2,{'c':'blue'})
G.add_node(3,{'c':'blue'},c='red')
assert_raises(networkx.NetworkXError, G.add_node, 4, [])
assert_raises(networkx.NetworkXError, G.add_node, 4, 4)
assert_equal(G.node[1]['c'],'red')
assert_equal(G.node[2]['c'],'blue')
assert_equal(G.node[3]['c'],'red')
# test updating attributes
G.add_node(1,c='blue')
G.add_node(2,{'c':'red'})
G.add_node(3,{'c':'red'},c='blue')
assert_equal(G.node[1]['c'],'blue')
assert_equal(G.node[2]['c'],'red')
assert_equal(G.node[3]['c'],'blue')
def test_add_nodes_from(self):
G=self.Graph()
G.add_nodes_from([0,1,2])
assert_equal(G.adj,{0:{},1:{},2:{}})
# test add attributes
G.add_nodes_from([0,1,2],c='red')
assert_equal(G.node[0]['c'],'red')
assert_equal(G.node[2]['c'],'red')
# test that attribute dicts are not the same
assert(G.node[0] is not G.node[1])
# test updating attributes
G.add_nodes_from([0,1,2],c='blue')
assert_equal(G.node[0]['c'],'blue')
assert_equal(G.node[2]['c'],'blue')
assert(G.node[0] is not G.node[1])
# test tuple input
H=self.Graph()
H.add_nodes_from(G.nodes(data=True))
assert_equal(H.node[0]['c'],'blue')
assert_equal(H.node[2]['c'],'blue')
assert(H.node[0] is not H.node[1])
# specific overrides general
H.add_nodes_from([0,(1,{'c':'green'}),(3,{'c':'cyan'})],c='red')
assert_equal(H.node[0]['c'],'red')
assert_equal(H.node[1]['c'],'green')
assert_equal(H.node[2]['c'],'blue')
assert_equal(H.node[3]['c'],'cyan')
def test_remove_node(self):
G=self.K3
G.remove_node(0)
assert_equal(G.adj,{1:{2:{}},2:{1:{}}})
assert_raises((KeyError,networkx.NetworkXError), G.remove_node,-1)
# generator here to implement list,set,string...
def test_remove_nodes_from(self):
G=self.K3
G.remove_nodes_from([0,1])
assert_equal(G.adj,{2:{}})
G.remove_nodes_from([-1]) # silent fail
def test_add_edge(self):
G=self.Graph()
G.add_edge(0,1)
assert_equal(G.adj,{0: {1: {}}, 1: {0: {}}})
G=self.Graph()
G.add_edge(*(0,1))
assert_equal(G.adj,{0: {1: {}}, 1: {0: {}}})
def test_add_edges_from(self):
G=self.Graph()
G.add_edges_from([(0,1),(0,2,{'weight':3})])
assert_equal(G.adj,{0: {1:{}, 2:{'weight':3}}, 1: {0:{}}, \
2:{0:{'weight':3}}})
G=self.Graph()
G.add_edges_from([(0,1),(0,2,{'weight':3}),(1,2,{'data':4})],data=2)
assert_equal(G.adj,{\
0: {1:{'data':2}, 2:{'weight':3,'data':2}}, \
1: {0:{'data':2}, 2:{'data':4}}, \
2: {0:{'weight':3,'data':2}, 1:{'data':4}} \
})
assert_raises(networkx.NetworkXError,
G.add_edges_from,[(0,)]) # too few in tuple
assert_raises(networkx.NetworkXError,
G.add_edges_from,[(0,1,2,3)]) # too many in tuple
assert_raises(TypeError, G.add_edges_from,[0]) # not a tuple
def test_remove_edge(self):
G=self.K3
G.remove_edge(0,1)
assert_equal(G.adj,{0:{2:{}},1:{2:{}},2:{0:{},1:{}}})
assert_raises((KeyError,networkx.NetworkXError), G.remove_edge,-1,0)
def test_remove_edges_from(self):
G=self.K3
G.remove_edges_from([(0,1)])
assert_equal(G.adj,{0:{2:{}},1:{2:{}},2:{0:{},1:{}}})
G.remove_edges_from([(0,0)]) # silent fail
def test_clear(self):
G=self.K3
G.clear()
assert_equal(G.adj,{})
def test_edges_data(self):
G=self.K3
assert_equal(sorted(G.edges(data=True)),[(0,1,{}),(0,2,{}),(1,2,{})])
assert_equal(sorted(G.edges(0,data=True)),[(0,1,{}),(0,2,{})])
assert_raises((KeyError,networkx.NetworkXError), G.edges,-1)
def test_get_edge_data(self):
G=self.K3
assert_equal(G.get_edge_data(0,1),{})
assert_equal(G[0][1],{})
assert_equal(G.get_edge_data(10,20),None)
assert_equal(G.get_edge_data(-1,0),None)
assert_equal(G.get_edge_data(-1,0,default=1),1)