Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/sitepackages/networkx/algorithms/bipartite/tests/test_project.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author  shellac 

date  Mon, 22 Mar 2021 18:12:50 +0000 
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1 import networkx as nx 
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2 from networkx.algorithms import bipartite 
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3 from networkx.testing import assert_edges_equal, assert_nodes_equal 
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4 
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5 
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6 class TestBipartiteProject: 
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7 def test_path_projected_graph(self): 
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8 G = nx.path_graph(4) 
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9 P = bipartite.projected_graph(G, [1, 3]) 
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10 assert_nodes_equal(list(P), [1, 3]) 
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11 assert_edges_equal(list(P.edges()), [(1, 3)]) 
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12 P = bipartite.projected_graph(G, [0, 2]) 
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13 assert_nodes_equal(list(P), [0, 2]) 
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14 assert_edges_equal(list(P.edges()), [(0, 2)]) 
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15 
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16 def test_path_projected_properties_graph(self): 
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17 G = nx.path_graph(4) 
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18 G.add_node(1, name="one") 
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19 G.add_node(2, name="two") 
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20 P = bipartite.projected_graph(G, [1, 3]) 
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21 assert_nodes_equal(list(P), [1, 3]) 
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22 assert_edges_equal(list(P.edges()), [(1, 3)]) 
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23 assert P.nodes[1]["name"] == G.nodes[1]["name"] 
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24 P = bipartite.projected_graph(G, [0, 2]) 
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25 assert_nodes_equal(list(P), [0, 2]) 
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26 assert_edges_equal(list(P.edges()), [(0, 2)]) 
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27 assert P.nodes[2]["name"] == G.nodes[2]["name"] 
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28 
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29 def test_path_collaboration_projected_graph(self): 
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30 G = nx.path_graph(4) 
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31 P = bipartite.collaboration_weighted_projected_graph(G, [1, 3]) 
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32 assert_nodes_equal(list(P), [1, 3]) 
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33 assert_edges_equal(list(P.edges()), [(1, 3)]) 
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34 P[1][3]["weight"] = 1 
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35 P = bipartite.collaboration_weighted_projected_graph(G, [0, 2]) 
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36 assert_nodes_equal(list(P), [0, 2]) 
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37 assert_edges_equal(list(P.edges()), [(0, 2)]) 
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38 P[0][2]["weight"] = 1 
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39 
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40 def test_directed_path_collaboration_projected_graph(self): 
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41 G = nx.DiGraph() 
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42 nx.add_path(G, range(4)) 
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43 P = bipartite.collaboration_weighted_projected_graph(G, [1, 3]) 
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44 assert_nodes_equal(list(P), [1, 3]) 
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45 assert_edges_equal(list(P.edges()), [(1, 3)]) 
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46 P[1][3]["weight"] = 1 
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47 P = bipartite.collaboration_weighted_projected_graph(G, [0, 2]) 
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48 assert_nodes_equal(list(P), [0, 2]) 
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49 assert_edges_equal(list(P.edges()), [(0, 2)]) 
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50 P[0][2]["weight"] = 1 
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51 
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52 def test_path_weighted_projected_graph(self): 
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53 G = nx.path_graph(4) 
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54 P = bipartite.weighted_projected_graph(G, [1, 3]) 
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55 assert_nodes_equal(list(P), [1, 3]) 
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56 assert_edges_equal(list(P.edges()), [(1, 3)]) 
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57 P[1][3]["weight"] = 1 
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58 P = bipartite.weighted_projected_graph(G, [0, 2]) 
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59 assert_nodes_equal(list(P), [0, 2]) 
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60 assert_edges_equal(list(P.edges()), [(0, 2)]) 
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61 P[0][2]["weight"] = 1 
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62 
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63 def test_path_weighted_projected_directed_graph(self): 
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64 G = nx.DiGraph() 
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65 nx.add_path(G, range(4)) 
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66 P = bipartite.weighted_projected_graph(G, [1, 3]) 
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67 assert_nodes_equal(list(P), [1, 3]) 
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68 assert_edges_equal(list(P.edges()), [(1, 3)]) 
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69 P[1][3]["weight"] = 1 
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70 P = bipartite.weighted_projected_graph(G, [0, 2]) 
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71 assert_nodes_equal(list(P), [0, 2]) 
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72 assert_edges_equal(list(P.edges()), [(0, 2)]) 
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73 P[0][2]["weight"] = 1 
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74 
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75 def test_star_projected_graph(self): 
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76 G = nx.star_graph(3) 
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77 P = bipartite.projected_graph(G, [1, 2, 3]) 
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78 assert_nodes_equal(list(P), [1, 2, 3]) 
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79 assert_edges_equal(list(P.edges()), [(1, 2), (1, 3), (2, 3)]) 
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80 P = bipartite.weighted_projected_graph(G, [1, 2, 3]) 
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81 assert_nodes_equal(list(P), [1, 2, 3]) 
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82 assert_edges_equal(list(P.edges()), [(1, 2), (1, 3), (2, 3)]) 
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83 
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84 P = bipartite.projected_graph(G, [0]) 
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85 assert_nodes_equal(list(P), [0]) 
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86 assert_edges_equal(list(P.edges()), []) 
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87 
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88 def test_project_multigraph(self): 
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89 G = nx.Graph() 
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90 G.add_edge("a", 1) 
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91 G.add_edge("b", 1) 
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92 G.add_edge("a", 2) 
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93 G.add_edge("b", 2) 
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94 P = bipartite.projected_graph(G, "ab") 
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95 assert_edges_equal(list(P.edges()), [("a", "b")]) 
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96 P = bipartite.weighted_projected_graph(G, "ab") 
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97 assert_edges_equal(list(P.edges()), [("a", "b")]) 
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98 P = bipartite.projected_graph(G, "ab", multigraph=True) 
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99 assert_edges_equal(list(P.edges()), [("a", "b"), ("a", "b")]) 
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100 
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101 def test_project_collaboration(self): 
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102 G = nx.Graph() 
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103 G.add_edge("a", 1) 
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104 G.add_edge("b", 1) 
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105 G.add_edge("b", 2) 
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106 G.add_edge("c", 2) 
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107 G.add_edge("c", 3) 
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108 G.add_edge("c", 4) 
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109 G.add_edge("b", 4) 
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110 P = bipartite.collaboration_weighted_projected_graph(G, "abc") 
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111 assert P["a"]["b"]["weight"] == 1 
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112 assert P["b"]["c"]["weight"] == 2 
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113 
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114 def test_directed_projection(self): 
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115 G = nx.DiGraph() 
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116 G.add_edge("A", 1) 
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117 G.add_edge(1, "B") 
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118 G.add_edge("A", 2) 
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119 G.add_edge("B", 2) 
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120 P = bipartite.projected_graph(G, "AB") 
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121 assert_edges_equal(list(P.edges()), [("A", "B")]) 
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122 P = bipartite.weighted_projected_graph(G, "AB") 
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123 assert_edges_equal(list(P.edges()), [("A", "B")]) 
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124 assert P["A"]["B"]["weight"] == 1 
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125 
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126 P = bipartite.projected_graph(G, "AB", multigraph=True) 
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127 assert_edges_equal(list(P.edges()), [("A", "B")]) 
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128 
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129 G = nx.DiGraph() 
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130 G.add_edge("A", 1) 
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131 G.add_edge(1, "B") 
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132 G.add_edge("A", 2) 
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133 G.add_edge(2, "B") 
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134 P = bipartite.projected_graph(G, "AB") 
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135 assert_edges_equal(list(P.edges()), [("A", "B")]) 
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136 P = bipartite.weighted_projected_graph(G, "AB") 
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137 assert_edges_equal(list(P.edges()), [("A", "B")]) 
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138 assert P["A"]["B"]["weight"] == 2 
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139 
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140 P = bipartite.projected_graph(G, "AB", multigraph=True) 
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141 assert_edges_equal(list(P.edges()), [("A", "B"), ("A", "B")]) 
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142 
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143 
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144 class TestBipartiteWeightedProjection: 
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145 @classmethod 
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146 def setup_class(cls): 
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147 # Tore Opsahl's example 
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148 # http://toreopsahl.com/2009/05/01/projectingtwomodenetworksontoweightedonemodenetworks/ 
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149 cls.G = nx.Graph() 
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150 cls.G.add_edge("A", 1) 
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151 cls.G.add_edge("A", 2) 
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152 cls.G.add_edge("B", 1) 
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153 cls.G.add_edge("B", 2) 
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154 cls.G.add_edge("B", 3) 
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155 cls.G.add_edge("B", 4) 
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156 cls.G.add_edge("B", 5) 
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157 cls.G.add_edge("C", 1) 
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158 cls.G.add_edge("D", 3) 
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159 cls.G.add_edge("E", 4) 
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160 cls.G.add_edge("E", 5) 
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161 cls.G.add_edge("E", 6) 
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162 cls.G.add_edge("F", 6) 
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163 # Graph based on figure 6 from Newman (2001) 
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164 cls.N = nx.Graph() 
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165 cls.N.add_edge("A", 1) 
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166 cls.N.add_edge("A", 2) 
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167 cls.N.add_edge("A", 3) 
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168 cls.N.add_edge("B", 1) 
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169 cls.N.add_edge("B", 2) 
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170 cls.N.add_edge("B", 3) 
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171 cls.N.add_edge("C", 1) 
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172 cls.N.add_edge("D", 1) 
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173 cls.N.add_edge("E", 3) 
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174 
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175 def test_project_weighted_shared(self): 
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176 edges = [ 
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177 ("A", "B", 2), 
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178 ("A", "C", 1), 
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179 ("B", "C", 1), 
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180 ("B", "D", 1), 
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181 ("B", "E", 2), 
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182 ("E", "F", 1), 
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183 ] 
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184 Panswer = nx.Graph() 
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185 Panswer.add_weighted_edges_from(edges) 
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186 P = bipartite.weighted_projected_graph(self.G, "ABCDEF") 
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187 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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188 for u, v in list(P.edges()): 
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189 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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190 
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191 edges = [ 
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192 ("A", "B", 3), 
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193 ("A", "E", 1), 
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194 ("A", "C", 1), 
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195 ("A", "D", 1), 
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196 ("B", "E", 1), 
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197 ("B", "C", 1), 
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198 ("B", "D", 1), 
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199 ("C", "D", 1), 
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200 ] 
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201 Panswer = nx.Graph() 
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202 Panswer.add_weighted_edges_from(edges) 
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203 P = bipartite.weighted_projected_graph(self.N, "ABCDE") 
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204 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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205 for u, v in list(P.edges()): 
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206 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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207 
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208 def test_project_weighted_newman(self): 
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209 edges = [ 
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210 ("A", "B", 1.5), 
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211 ("A", "C", 0.5), 
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212 ("B", "C", 0.5), 
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213 ("B", "D", 1), 
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214 ("B", "E", 2), 
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215 ("E", "F", 1), 
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216 ] 
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217 Panswer = nx.Graph() 
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218 Panswer.add_weighted_edges_from(edges) 
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219 P = bipartite.collaboration_weighted_projected_graph(self.G, "ABCDEF") 
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220 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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221 for u, v in list(P.edges()): 
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222 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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223 
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224 edges = [ 
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225 ("A", "B", 11 / 6.0), 
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226 ("A", "E", 1 / 2.0), 
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227 ("A", "C", 1 / 3.0), 
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228 ("A", "D", 1 / 3.0), 
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229 ("B", "E", 1 / 2.0), 
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230 ("B", "C", 1 / 3.0), 
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231 ("B", "D", 1 / 3.0), 
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232 ("C", "D", 1 / 3.0), 
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233 ] 
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234 Panswer = nx.Graph() 
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235 Panswer.add_weighted_edges_from(edges) 
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236 P = bipartite.collaboration_weighted_projected_graph(self.N, "ABCDE") 
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237 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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238 for u, v in list(P.edges()): 
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239 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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240 
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241 def test_project_weighted_ratio(self): 
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242 edges = [ 
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243 ("A", "B", 2 / 6.0), 
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244 ("A", "C", 1 / 6.0), 
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245 ("B", "C", 1 / 6.0), 
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246 ("B", "D", 1 / 6.0), 
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247 ("B", "E", 2 / 6.0), 
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248 ("E", "F", 1 / 6.0), 
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249 ] 
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250 Panswer = nx.Graph() 
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251 Panswer.add_weighted_edges_from(edges) 
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252 P = bipartite.weighted_projected_graph(self.G, "ABCDEF", ratio=True) 
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253 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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254 for u, v in list(P.edges()): 
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255 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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256 
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257 edges = [ 
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258 ("A", "B", 3 / 3.0), 
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259 ("A", "E", 1 / 3.0), 
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260 ("A", "C", 1 / 3.0), 
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261 ("A", "D", 1 / 3.0), 
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262 ("B", "E", 1 / 3.0), 
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263 ("B", "C", 1 / 3.0), 
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264 ("B", "D", 1 / 3.0), 
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265 ("C", "D", 1 / 3.0), 
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266 ] 
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267 Panswer = nx.Graph() 
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268 Panswer.add_weighted_edges_from(edges) 
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269 P = bipartite.weighted_projected_graph(self.N, "ABCDE", ratio=True) 
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270 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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271 for u, v in list(P.edges()): 
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272 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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273 
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274 def test_project_weighted_overlap(self): 
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275 edges = [ 
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276 ("A", "B", 2 / 2.0), 
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277 ("A", "C", 1 / 1.0), 
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278 ("B", "C", 1 / 1.0), 
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279 ("B", "D", 1 / 1.0), 
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280 ("B", "E", 2 / 3.0), 
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281 ("E", "F", 1 / 1.0), 
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282 ] 
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283 Panswer = nx.Graph() 
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284 Panswer.add_weighted_edges_from(edges) 
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285 P = bipartite.overlap_weighted_projected_graph(self.G, "ABCDEF", jaccard=False) 
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286 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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287 for u, v in list(P.edges()): 
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288 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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289 
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290 edges = [ 
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291 ("A", "B", 3 / 3.0), 
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292 ("A", "E", 1 / 1.0), 
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293 ("A", "C", 1 / 1.0), 
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294 ("A", "D", 1 / 1.0), 
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295 ("B", "E", 1 / 1.0), 
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296 ("B", "C", 1 / 1.0), 
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297 ("B", "D", 1 / 1.0), 
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298 ("C", "D", 1 / 1.0), 
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299 ] 
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300 Panswer = nx.Graph() 
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301 Panswer.add_weighted_edges_from(edges) 
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302 P = bipartite.overlap_weighted_projected_graph(self.N, "ABCDE", jaccard=False) 
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303 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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304 for u, v in list(P.edges()): 
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305 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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306 
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307 def test_project_weighted_jaccard(self): 
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308 edges = [ 
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309 ("A", "B", 2 / 5.0), 
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310 ("A", "C", 1 / 2.0), 
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311 ("B", "C", 1 / 5.0), 
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312 ("B", "D", 1 / 5.0), 
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313 ("B", "E", 2 / 6.0), 
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314 ("E", "F", 1 / 3.0), 
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315 ] 
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316 Panswer = nx.Graph() 
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317 Panswer.add_weighted_edges_from(edges) 
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318 P = bipartite.overlap_weighted_projected_graph(self.G, "ABCDEF") 
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319 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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320 for u, v in list(P.edges()): 
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321 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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322 
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323 edges = [ 
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324 ("A", "B", 3 / 3.0), 
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325 ("A", "E", 1 / 3.0), 
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326 ("A", "C", 1 / 3.0), 
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327 ("A", "D", 1 / 3.0), 
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328 ("B", "E", 1 / 3.0), 
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329 ("B", "C", 1 / 3.0), 
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330 ("B", "D", 1 / 3.0), 
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331 ("C", "D", 1 / 1.0), 
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332 ] 
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333 Panswer = nx.Graph() 
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334 Panswer.add_weighted_edges_from(edges) 
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335 P = bipartite.overlap_weighted_projected_graph(self.N, "ABCDE") 
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336 assert_edges_equal(list(P.edges()), Panswer.edges()) 
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337 for u, v in P.edges(): 
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338 assert P[u][v]["weight"] == Panswer[u][v]["weight"] 
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339 
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340 def test_generic_weighted_projected_graph_simple(self): 
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341 def shared(G, u, v): 
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342 return len(set(G[u]) & set(G[v])) 
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343 
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344 B = nx.path_graph(5) 
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345 G = bipartite.generic_weighted_projected_graph( 
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346 B, [0, 2, 4], weight_function=shared 
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347 ) 
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348 assert_nodes_equal(list(G), [0, 2, 4]) 
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349 assert_edges_equal( 
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350 list(list(G.edges(data=True))), 
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351 [(0, 2, {"weight": 1}), (2, 4, {"weight": 1})], 
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352 ) 
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353 
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354 G = bipartite.generic_weighted_projected_graph(B, [0, 2, 4]) 
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355 assert_nodes_equal(list(G), [0, 2, 4]) 
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356 assert_edges_equal( 
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357 list(list(G.edges(data=True))), 
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358 [(0, 2, {"weight": 1}), (2, 4, {"weight": 1})], 
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359 ) 
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360 B = nx.DiGraph() 
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361 nx.add_path(B, range(5)) 
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362 G = bipartite.generic_weighted_projected_graph(B, [0, 2, 4]) 
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363 assert_nodes_equal(list(G), [0, 2, 4]) 
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364 assert_edges_equal( 
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365 list(G.edges(data=True)), [(0, 2, {"weight": 1}), (2, 4, {"weight": 1})] 
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366 ) 
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367 
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368 def test_generic_weighted_projected_graph_custom(self): 
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369 def jaccard(G, u, v): 
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370 unbrs = set(G[u]) 
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371 vnbrs = set(G[v]) 
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372 return float(len(unbrs & vnbrs)) / len(unbrs  vnbrs) 
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373 
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374 def my_weight(G, u, v, weight="weight"): 
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375 w = 0 
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376 for nbr in set(G[u]) & set(G[v]): 
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377 w += G.edges[u, nbr].get(weight, 1) + G.edges[v, nbr].get(weight, 1) 
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378 return w 
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379 
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380 B = nx.bipartite.complete_bipartite_graph(2, 2) 
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381 for i, (u, v) in enumerate(B.edges()): 
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382 B.edges[u, v]["weight"] = i + 1 
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383 G = bipartite.generic_weighted_projected_graph( 
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384 B, [0, 1], weight_function=jaccard 
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385 ) 
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386 assert_edges_equal(list(G.edges(data=True)), [(0, 1, {"weight": 1.0})]) 
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387 G = bipartite.generic_weighted_projected_graph( 
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388 B, [0, 1], weight_function=my_weight 
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389 ) 
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390 assert_edges_equal(list(G.edges(data=True)), [(0, 1, {"weight": 10})]) 
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391 G = bipartite.generic_weighted_projected_graph(B, [0, 1]) 
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392 assert_edges_equal(list(G.edges(data=True)), [(0, 1, {"weight": 2})]) 