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Commit b93fa303 authored by Tiago Peixoto's avatar Tiago Peixoto
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Update doctests

parent 581ba9fe
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in 171 minutes and 44 seconds
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src/graph_tool/__init__.py
View file @ b93fa303
......@@ -1828,9 +1828,9 @@ class Graph(object):
--------
>>> g = gt.random_graph(6, lambda: 1, directed=False)
>>> g.get_edges()
array([[0, 4, 0],
[2, 1, 2],
[5, 3, 1]], dtype=uint64)
array([[2, 1, 2],
[3, 4, 0],
[5, 0, 1]], dtype=uint64)
"""
edges = libcore.get_edge_list(self.__graph)
E = edges.shape[0] // 3
......
src/graph_tool/clustering/__init__.py
View file @ b93fa303
......@@ -121,7 +121,7 @@ def local_clustering(g, prop=None, undirected=True):
>>> g = gt.random_graph(1000, lambda: (5,5))
>>> clust = gt.local_clustering(g)
>>> print(gt.vertex_average(g, clust))
(0.006177777777777778, 0.00036966184079941211)
(0.008177777777777779, 0.00042080229075093...)
References
----------
......@@ -182,7 +182,7 @@ def global_clustering(g):
>>> g = gt.random_graph(1000, lambda: (5,5))
>>> print(gt.global_clustering(g))
(0.006177777777777778, 0.0003700318726720...)
(0.008177777777777779, 0.0004212235142651...)
References
----------
......@@ -263,11 +263,11 @@ def extended_clustering(g, props=None, max_depth=3, undirected=False):
>>> for i in range(0, 5):
... print(gt.vertex_average(g, clusts[i]))
...
(0.00421, 0.00041685103920811...)
(0.027226666666666666, 0.00100735228307788...)
(0.11549166666666667, 0.00208139908541773...)
(0.4128066666666666, 0.00294792212319872...)
(0.4205716666666667, 0.00315646574114149...)
(0.0050483333333333335, 0.0004393940240073...)
(0.024593787878787878, 0.0009963004021144...)
(0.11238924242424242, 0.001909615401971...)
(0.40252272727272725, 0.003113987400030...)
(0.43629378787878786, 0.003144159256565...)
References
----------
......@@ -349,10 +349,9 @@ def motifs(g, k, p=1.0, motif_list=None, return_maps=False):
>>> g = gt.random_graph(1000, lambda: (5,5))
>>> motifs, counts = gt.motifs(gt.GraphView(g, directed=False), 4)
>>> print(len(motifs))
13
18
>>> print(counts)
[115408, 388542, 1031, 1182, 2662, 2138, 833, 28, 16, 5, 5, 3, 4]
[115557, 390005, 627, 700, 1681, 2815, 820, 12, 27, 44, 15, 7, 12, 4, 6, 1, 2, 1]
References
----------
......@@ -523,7 +522,7 @@ def motif_significance(g, k, n_shuffles=100, p=1.0, motif_list=None,
>>> print(len(motifs))
11
>>> print(zscores)
[0.04162670293683441, 0.046769781223679897, 0.55888261369689918, 0.82906624302416043, -0.41384527710386287, -0.42070845824900477, -1.3262411347517733, 1.82, -0.13, -0.37, -0.22]
[0.22728646681107012, 0.21409572051644973, 0.0070220407889021114, 0.58721419671233477, -0.37770179603294357, -0.34847335047837341, 0.88618118013255021, -0.08, -0.2, -0.38, -0.2]
"""
s_ms, counts = motifs(g, k, p, motif_list)
......
src/graph_tool/stats/__init__.py
View file @ b93fa303
......@@ -231,7 +231,7 @@ def vertex_average(g, deg):
>>> from numpy.random import poisson
>>> g = gt.random_graph(1000, lambda: (poisson(5), poisson(5)))
>>> print(gt.vertex_average(g, "in"))
(4.975, 0.068675869124460318)
(4.96, 0.067988234276233406)
"""
if isinstance(deg, PropertyMap) and "string" in deg.value_type():
......@@ -293,7 +293,7 @@ def edge_average(g, eprop):
>>> eprop = g.new_edge_property("double")
>>> eprop.get_array()[:] = random(g.num_edges())
>>> print(gt.edge_average(g, eprop))
(0.4989741369720412, 0.004101065927783254)
(0.49888156584192045, 0.0040967399234187541)
"""
if "string" in eprop.value_type():
......@@ -426,10 +426,10 @@ def distance_histogram(g, weight=None, bins=[0, 1], samples=None,
>>> g = gt.random_graph(100, lambda: (3, 3))
>>> hist = gt.distance_histogram(g)
>>> print(hist)
[array([ 0., 300., 865., 2214., 3857., 2480., 184.]), array([0, 1, 2, 3, 4, 5, 6, 7], dtype=uint...)]
[array([ 0., 300., 880., 2269., 3974., 2358., 119.]), array([0, 1, 2, 3, 4, 5, 6, 7], dtype=uint64)]
>>> hist = gt.distance_histogram(g, samples=10)
>>> print(hist)
[array([ 0., 30., 88., 226., 391., 240., 15.]), array([0, 1, 2, 3, 4, 5, 6, 7], dtype=uint...)]
[array([ 0., 30., 87., 223., 394., 239., 17.]), array([0, 1, 2, 3, 4, 5, 6, 7], dtype=uint64)]
"""
if samples is not None:
......
src/graph_tool/topology/__init__.py
View file @ b93fa303
......@@ -169,7 +169,7 @@ def similarity(g1, g2, eweight1=None, eweight2=None, label1=None, label2=None,
>>> gt.similarity(u, g)
1.0
>>> gt.random_rewire(u)
24
22
>>> gt.similarity(u, g)
0.04666666666666667
......@@ -860,9 +860,10 @@ def dominator_tree(g, root, dom_map=None):
>>> root = [v for v in g.vertices() if v.in_degree() == 0]
>>> dom = gt.dominator_tree(g, root[0])
>>> print(dom.a)
[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
[ 0 0 0 0 0 0 0 74 0 0 0 97 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 64 67 0 0 67 0 0 74 0 0 0 0 23 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0]
References
----------
......@@ -909,8 +910,8 @@ def topological_sort(g):
>>> g.set_edge_filter(tree)
>>> sort = gt.topological_sort(g)
>>> print(sort)
[29 28 27 26 23 24 22 21 20 18 17 16 15 14 11 10 9 6 5 4 19 12 13 3 2
25 1 0 7 8]
[28 26 29 27 23 22 18 17 16 20 21 15 12 11 10 25 14 9 8 7 5 3 2 24 4
6 1 0 19 13]
References
----------
......@@ -1018,18 +1019,17 @@ def label_components(g, vprop=None, directed=None, attractors=False):
>>> g = gt.random_graph(100, lambda: (poisson(2), poisson(2)))
>>> comp, hist, is_attractor = gt.label_components(g, attractors=True)
>>> print(comp.a)
[13 13 13 13 14 12 13 15 16 13 17 19 13 13 13 20 13 13 13 10 13 13 22 13 13
4 13 13 2 23 13 13 24 13 13 26 27 13 13 13 13 0 13 13 3 13 13 13 28 1
6 13 13 13 13 5 13 13 13 13 13 13 13 9 13 11 13 29 13 13 13 13 18 13 30
31 13 13 32 13 33 34 35 13 13 21 13 25 8 36 13 13 13 13 13 37 13 13 7 13]
[ 9 9 9 9 10 1 9 11 12 9 9 9 9 9 9 13 9 9 9 0 9 9 16 9 9
3 9 9 4 17 9 9 18 9 9 19 20 9 9 9 14 5 9 9 6 9 9 9 21 9
9 9 9 9 9 9 9 9 9 9 9 9 9 2 9 8 9 22 15 9 9 9 9 9 23
25 9 9 26 27 28 29 30 9 9 9 9 9 9 31 9 9 9 9 9 32 9 9 7 24]
>>> print(hist)
[ 1 1 1 1 1 1 1 1 1 1 1 1 1 63 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1]
[ 1 1 1 1 1 1 1 1 1 68 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1]
>>> print(is_attractor)
[ True False True True True False False True False True True True
True False True False False False False False False False False False
False False False False False False False False False True False True
False False]
[ True True True True True True True True True False True False
False False False False False False False False False False False False
False False False False True False True False False]
"""
if vprop is None:
......@@ -1090,9 +1090,9 @@ def label_largest_component(g, directed=None):
>>> g = gt.random_graph(100, lambda: poisson(1), directed=False)
>>> l = gt.label_largest_component(g)
>>> print(l.a)
[0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0
1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0
0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 1 0 0 1 0]
[0 0 0 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 1 0 0 0 0 0 0 0
0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0]
>>> u = gt.GraphView(g, vfilt=l) # extract the largest component as a graph
>>> print(u.num_vertices())
18
......@@ -1141,18 +1141,18 @@ def label_out_component(g, root, label=None):
>>> g = gt.random_graph(100, lambda: poisson(2.2), directed=False)
>>> l = gt.label_out_component(g, g.vertex(2))
>>> print(l.a)
[1 1 1 1 1 1 1 0 1 1 1 0 1 1 0 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 0 0 0 1 1 1 1
1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 0 0
1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 0]
[1 1 1 1 1 1 0 1 1 1 0 0 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1
1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 0 1 0 1 1 1 0 1
1 1 0 0 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 0 1 1 1 0]
The in-component can be obtained by reversing the graph.
>>> l = gt.label_out_component(gt.GraphView(g, reversed=True, directed=True),
... g.vertex(1))
>>> print(l.a)
[0 1 1 1 1 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 1 1 0 0 0 1 1 0 0 0 0 1 0 1
1 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 1 0 1 1 1 1 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0
1 0 0 0 0 1 1 1 0 0 1 1 0 0 0 1 1 0 1 1 0 0 1 0 1 0]
[0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
"""
if label is None:
......@@ -1228,18 +1228,18 @@ def label_biconnected_components(g, eprop=None, vprop=None):
>>> g = gt.random_graph(100, lambda: poisson(2), directed=False)
>>> comp, art, hist = gt.label_biconnected_components(g)
>>> print(comp.a)
[20 38 37 37 37 11 44 37 37 6 37 18 37 37 34 37 3 37 37 37 37 37 37 27 37
32 37 21 14 23 37 37 37 29 37 37 37 37 2 1 37 37 37 37 41 40 37 37 10 37
37 37 42 37 37 37 37 37 37 37 37 31 35 37 7 37 37 37 37 19 28 37 37 36 39
5 37 37 8 22 43 37 37 37 37 30 37 15 25 17 9 12 0 33 45 26 4 16 13 24
37]
[26 26 26 26 26 26 26 26 19 25 26 26 23 26 26 26 26 6 26 24 18 26 26 13 26
26 26 26 26 26 26 26 26 26 26 16 29 26 26 26 26 26 26 15 26 26 26 26 26 0
26 26 12 2 26 26 26 26 26 26 26 26 9 3 26 28 26 26 8 26 4 26 26 26 14
26 26 26 26 30 11 26 26 26 20 26 26 27 26 33 26 22 17 7 5 32 21 26 1 10
31]
>>> print(art.a)
[1 0 1 1 0 1 0 0 0 1 0 0 1 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0
1 1 0 0 1 0 0 0 1 1 0 0 0 1 0 1 0 1 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1 1
1 0 0 0 0 0 0 1 1 0 0 0 1 0 1 1 0 0 0 1 0 0 0 1 0 0]
[1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 0
1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0
1 0 0 1 0 0 0 1 1 0 0 1 0 0 1 1 0 0 0 1 0 0 1 0 0 0]
>>> print(hist)
[ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 56 1 1 1 1 1 1 1 1]
1 68 1 1 1 1 1 1 1]
"""
......@@ -1613,49 +1613,49 @@ def shortest_distance(g, source=None, target=None, weights=None,
>>> g = gt.random_graph(100, lambda: (poisson(3), poisson(3)))
>>> dist = gt.shortest_distance(g, source=g.vertex(0))
>>> print(dist.a)
[ 0 1 5 4 2147483647 4
9 5 8 5 7 6
3 5 6 8 3 3
5 6 2147483647 1 4 5
5 2 5 7 4 5
5 5 4 4 5 2
5 2147483647 5 2 2147483647 6
5 6 6 2 5 4
3 6 5 4 4 5
3 3 5 5 1 5
4 6 3 4 3 3
7 5 5 4 2147483647 2147483647
2 5 3 5 5 6
3 5 6 6 5 4
5 3 6 3 4 2147483647
4 6 4 4 4 4
6 5 4 4]
[ 0 4 5 6 2147483647 5
4 3 2147483647 4 4 6
6 5 5 4 4 2
5 1 2147483647 6 5 5
5 7 5 4 6 5
5 4 1 4 4 3
5 2147483647 5 1 2147483647 2
2 7 4 5 5 5
6 5 5 3 2 7
5 4 3 5 4 6
3 5 5 3 4 4
6 4 4 5 2147483647 2147483647
2 5 7 3 2147483647 2147483647
5 6 4 7 4 4
3 4 6 4 3 2147483647
5 6 3 4 6 5
5 3 4 5]
>>>
>>> dist = gt.shortest_distance(g)
>>> print(dist[g.vertex(0)].a)
[ 0 1 5 4 2147483647 4
9 5 8 5 7 6
3 5 6 8 3 3
5 6 2147483647 1 4 5
5 2 5 7 4 5
5 5 4 4 5 2
5 2147483647 5 2 2147483647 6
5 6 6 2 5 4
3 6 5 4 4 5
3 3 5 5 1 5
4 6 3 4 3 3
7 5 5 4 2147483647 2147483647
2 5 3 5 5 6
3 5 6 6 5 4
5 3 6 3 4 2147483647
4 6 4 4 4 4
6 5 4 4]
[ 0 4 5 6 2147483647 5
4 3 2147483647 4 4 6
6 5 5 4 4 2
5 1 2147483647 6 5 5
5 7 5 4 6 5
5 4 1 4 4 3
5 2147483647 5 1 2147483647 2
2 7 4 5 5 5
6 5 5 3 2 7
5 4 3 5 4 6
3 5 5 3 4 4
6 4 4 5 2147483647 2147483647
2 5 7 3 2147483647 2147483647
5 6 4 7 4 4
3 4 6 4 3 2147483647
5 6 3 4 6 5
5 3 4 5]
>>> dist = gt.shortest_distance(g, source=g.vertex(0), target=g.vertex(2))
>>> print(dist)
5
>>> dist = gt.shortest_distance(g, source=g.vertex(0), target=[g.vertex(2), g.vertex(6)])
>>> print(dist)
[5 9]
[5 4]
References
----------
......@@ -1802,9 +1802,9 @@ def shortest_path(g, source, target, weights=None, negative_weights=False,
>>> g = gt.random_graph(300, lambda: (poisson(4), poisson(4)))
>>> vlist, elist = gt.shortest_path(g, g.vertex(10), g.vertex(11))
>>> print([str(v) for v in vlist])
['10', '11']
['10', '131', '118', '207', '195', '11']
>>> print([str(e) for e in elist])
['(10, 11)']
['(10, 131)', '(131, 118)', '(118, 207)', '(207, 195)', '(195, 11)']
References
----------
......@@ -2060,8 +2060,8 @@ def all_circuits(g, unique=False):
>>> g = gt.random_graph(10, lambda: (1, 1))
>>> for c in gt.all_circuits(g):
... print(c)
[0 8 4 5 3]
[1 6 7 9 2]
[0 4 7 1 8 2]
[3 9 6 5]
References
----------
......@@ -2134,7 +2134,7 @@ def pseudo_diameter(g, source=None, weights=None):
>>> print(dist)
10.0
>>> print(int(ends[0]), int(ends[1]))
0 165
0 11
References
----------
......
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