Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/algorithms/tests/test_cycles.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import pytest |
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2 import networkx |
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3 import networkx as nx |
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4 |
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5 from networkx.algorithms import find_cycle |
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6 from networkx.algorithms import minimum_cycle_basis |
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7 |
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8 FORWARD = nx.algorithms.edgedfs.FORWARD |
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9 REVERSE = nx.algorithms.edgedfs.REVERSE |
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10 |
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11 |
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12 class TestCycles: |
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13 @classmethod |
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14 def setup_class(cls): |
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15 G = networkx.Graph() |
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16 nx.add_cycle(G, [0, 1, 2, 3]) |
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17 nx.add_cycle(G, [0, 3, 4, 5]) |
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18 nx.add_cycle(G, [0, 1, 6, 7, 8]) |
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19 G.add_edge(8, 9) |
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20 cls.G = G |
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21 |
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22 def is_cyclic_permutation(self, a, b): |
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23 n = len(a) |
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24 if len(b) != n: |
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25 return False |
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26 l = a + a |
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27 return any(l[i : i + n] == b for i in range(n)) |
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28 |
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29 def test_cycle_basis(self): |
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30 G = self.G |
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31 cy = networkx.cycle_basis(G, 0) |
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32 sort_cy = sorted(sorted(c) for c in cy) |
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33 assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5]] |
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34 cy = networkx.cycle_basis(G, 1) |
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35 sort_cy = sorted(sorted(c) for c in cy) |
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36 assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5]] |
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37 cy = networkx.cycle_basis(G, 9) |
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38 sort_cy = sorted(sorted(c) for c in cy) |
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39 assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5]] |
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40 # test disconnected graphs |
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41 nx.add_cycle(G, "ABC") |
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42 cy = networkx.cycle_basis(G, 9) |
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43 sort_cy = sorted(sorted(c) for c in cy[:-1]) + [sorted(cy[-1])] |
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44 assert sort_cy == [[0, 1, 2, 3], [0, 1, 6, 7, 8], [0, 3, 4, 5], ["A", "B", "C"]] |
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45 |
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46 def test_cycle_basis2(self): |
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47 with pytest.raises(nx.NetworkXNotImplemented): |
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48 G = nx.DiGraph() |
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49 cy = networkx.cycle_basis(G, 0) |
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50 |
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51 def test_cycle_basis3(self): |
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52 with pytest.raises(nx.NetworkXNotImplemented): |
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53 G = nx.MultiGraph() |
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54 cy = networkx.cycle_basis(G, 0) |
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55 |
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56 def test_simple_cycles(self): |
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57 edges = [(0, 0), (0, 1), (0, 2), (1, 2), (2, 0), (2, 1), (2, 2)] |
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58 G = nx.DiGraph(edges) |
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59 cc = sorted(nx.simple_cycles(G)) |
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60 ca = [[0], [0, 1, 2], [0, 2], [1, 2], [2]] |
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61 assert len(cc) == len(ca) |
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62 for c in cc: |
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63 assert any(self.is_cyclic_permutation(c, rc) for rc in ca) |
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64 |
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65 def test_simple_cycles_graph(self): |
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66 with pytest.raises(nx.NetworkXNotImplemented): |
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67 G = nx.Graph() |
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68 c = sorted(nx.simple_cycles(G)) |
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69 |
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70 def test_unsortable(self): |
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71 # TODO What does this test do? das 6/2013 |
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72 G = nx.DiGraph() |
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73 nx.add_cycle(G, ["a", 1]) |
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74 c = list(nx.simple_cycles(G)) |
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75 |
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76 def test_simple_cycles_small(self): |
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77 G = nx.DiGraph() |
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78 nx.add_cycle(G, [1, 2, 3]) |
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79 c = sorted(nx.simple_cycles(G)) |
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80 assert len(c) == 1 |
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81 assert self.is_cyclic_permutation(c[0], [1, 2, 3]) |
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82 nx.add_cycle(G, [10, 20, 30]) |
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83 cc = sorted(nx.simple_cycles(G)) |
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84 assert len(cc) == 2 |
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85 ca = [[1, 2, 3], [10, 20, 30]] |
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86 for c in cc: |
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87 assert any(self.is_cyclic_permutation(c, rc) for rc in ca) |
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88 |
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89 def test_simple_cycles_empty(self): |
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90 G = nx.DiGraph() |
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91 assert list(nx.simple_cycles(G)) == [] |
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92 |
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93 def test_complete_directed_graph(self): |
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94 # see table 2 in Johnson's paper |
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95 ncircuits = [1, 5, 20, 84, 409, 2365, 16064] |
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96 for n, c in zip(range(2, 9), ncircuits): |
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97 G = nx.DiGraph(nx.complete_graph(n)) |
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98 assert len(list(nx.simple_cycles(G))) == c |
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99 |
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100 def worst_case_graph(self, k): |
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101 # see figure 1 in Johnson's paper |
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102 # this graph has exactly 3k simple cycles |
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103 G = nx.DiGraph() |
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104 for n in range(2, k + 2): |
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105 G.add_edge(1, n) |
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106 G.add_edge(n, k + 2) |
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107 G.add_edge(2 * k + 1, 1) |
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108 for n in range(k + 2, 2 * k + 2): |
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109 G.add_edge(n, 2 * k + 2) |
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110 G.add_edge(n, n + 1) |
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111 G.add_edge(2 * k + 3, k + 2) |
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112 for n in range(2 * k + 3, 3 * k + 3): |
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113 G.add_edge(2 * k + 2, n) |
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114 G.add_edge(n, 3 * k + 3) |
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115 G.add_edge(3 * k + 3, 2 * k + 2) |
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116 return G |
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117 |
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118 def test_worst_case_graph(self): |
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119 # see figure 1 in Johnson's paper |
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120 for k in range(3, 10): |
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121 G = self.worst_case_graph(k) |
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122 l = len(list(nx.simple_cycles(G))) |
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123 assert l == 3 * k |
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124 |
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125 def test_recursive_simple_and_not(self): |
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126 for k in range(2, 10): |
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127 G = self.worst_case_graph(k) |
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128 cc = sorted(nx.simple_cycles(G)) |
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129 rcc = sorted(nx.recursive_simple_cycles(G)) |
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130 assert len(cc) == len(rcc) |
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131 for c in cc: |
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132 assert any(self.is_cyclic_permutation(c, r) for r in rcc) |
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133 for rc in rcc: |
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134 assert any(self.is_cyclic_permutation(rc, c) for c in cc) |
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135 |
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136 def test_simple_graph_with_reported_bug(self): |
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137 G = nx.DiGraph() |
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138 edges = [ |
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139 (0, 2), |
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140 (0, 3), |
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141 (1, 0), |
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142 (1, 3), |
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143 (2, 1), |
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144 (2, 4), |
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145 (3, 2), |
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146 (3, 4), |
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147 (4, 0), |
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148 (4, 1), |
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149 (4, 5), |
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150 (5, 0), |
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151 (5, 1), |
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152 (5, 2), |
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153 (5, 3), |
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154 ] |
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155 G.add_edges_from(edges) |
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156 cc = sorted(nx.simple_cycles(G)) |
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157 assert len(cc) == 26 |
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158 rcc = sorted(nx.recursive_simple_cycles(G)) |
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159 assert len(cc) == len(rcc) |
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160 for c in cc: |
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161 assert any(self.is_cyclic_permutation(c, rc) for rc in rcc) |
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162 for rc in rcc: |
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163 assert any(self.is_cyclic_permutation(rc, c) for c in cc) |
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164 |
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165 |
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166 # These tests might fail with hash randomization since they depend on |
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167 # edge_dfs. For more information, see the comments in: |
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168 # networkx/algorithms/traversal/tests/test_edgedfs.py |
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169 |
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170 |
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171 class TestFindCycle: |
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172 @classmethod |
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173 def setup_class(cls): |
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174 cls.nodes = [0, 1, 2, 3] |
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175 cls.edges = [(-1, 0), (0, 1), (1, 0), (1, 0), (2, 1), (3, 1)] |
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176 |
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177 def test_graph_nocycle(self): |
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178 G = nx.Graph(self.edges) |
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179 pytest.raises(nx.exception.NetworkXNoCycle, find_cycle, G, self.nodes) |
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180 |
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181 def test_graph_cycle(self): |
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182 G = nx.Graph(self.edges) |
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183 G.add_edge(2, 0) |
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184 x = list(find_cycle(G, self.nodes)) |
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185 x_ = [(0, 1), (1, 2), (2, 0)] |
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186 assert x == x_ |
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187 |
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188 def test_graph_orientation_none(self): |
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189 G = nx.Graph(self.edges) |
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190 G.add_edge(2, 0) |
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191 x = list(find_cycle(G, self.nodes, orientation=None)) |
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192 x_ = [(0, 1), (1, 2), (2, 0)] |
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193 assert x == x_ |
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194 |
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195 def test_graph_orientation_original(self): |
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196 G = nx.Graph(self.edges) |
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197 G.add_edge(2, 0) |
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198 x = list(find_cycle(G, self.nodes, orientation="original")) |
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199 x_ = [(0, 1, FORWARD), (1, 2, FORWARD), (2, 0, FORWARD)] |
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200 assert x == x_ |
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201 |
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202 def test_digraph(self): |
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203 G = nx.DiGraph(self.edges) |
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204 x = list(find_cycle(G, self.nodes)) |
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205 x_ = [(0, 1), (1, 0)] |
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206 assert x == x_ |
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207 |
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208 def test_digraph_orientation_none(self): |
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209 G = nx.DiGraph(self.edges) |
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210 x = list(find_cycle(G, self.nodes, orientation=None)) |
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211 x_ = [(0, 1), (1, 0)] |
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212 assert x == x_ |
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213 |
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214 def test_digraph_orientation_original(self): |
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215 G = nx.DiGraph(self.edges) |
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216 x = list(find_cycle(G, self.nodes, orientation="original")) |
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217 x_ = [(0, 1, FORWARD), (1, 0, FORWARD)] |
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218 assert x == x_ |
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219 |
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220 def test_multigraph(self): |
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221 G = nx.MultiGraph(self.edges) |
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222 x = list(find_cycle(G, self.nodes)) |
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223 x_ = [(0, 1, 0), (1, 0, 1)] # or (1, 0, 2) |
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224 # Hash randomization...could be any edge. |
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225 assert x[0] == x_[0] |
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226 assert x[1][:2] == x_[1][:2] |
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227 |
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228 def test_multidigraph(self): |
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229 G = nx.MultiDiGraph(self.edges) |
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230 x = list(find_cycle(G, self.nodes)) |
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231 x_ = [(0, 1, 0), (1, 0, 0)] # (1, 0, 1) |
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232 assert x[0] == x_[0] |
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233 assert x[1][:2] == x_[1][:2] |
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234 |
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235 def test_digraph_ignore(self): |
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236 G = nx.DiGraph(self.edges) |
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237 x = list(find_cycle(G, self.nodes, orientation="ignore")) |
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238 x_ = [(0, 1, FORWARD), (1, 0, FORWARD)] |
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239 assert x == x_ |
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240 |
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241 def test_digraph_reverse(self): |
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242 G = nx.DiGraph(self.edges) |
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243 x = list(find_cycle(G, self.nodes, orientation="reverse")) |
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244 x_ = [(1, 0, REVERSE), (0, 1, REVERSE)] |
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245 assert x == x_ |
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246 |
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247 def test_multidigraph_ignore(self): |
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248 G = nx.MultiDiGraph(self.edges) |
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249 x = list(find_cycle(G, self.nodes, orientation="ignore")) |
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250 x_ = [(0, 1, 0, FORWARD), (1, 0, 0, FORWARD)] # or (1, 0, 1, 1) |
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251 assert x[0] == x_[0] |
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252 assert x[1][:2] == x_[1][:2] |
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253 assert x[1][3] == x_[1][3] |
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254 |
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255 def test_multidigraph_ignore2(self): |
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256 # Loop traversed an edge while ignoring its orientation. |
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257 G = nx.MultiDiGraph([(0, 1), (1, 2), (1, 2)]) |
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258 x = list(find_cycle(G, [0, 1, 2], orientation="ignore")) |
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259 x_ = [(1, 2, 0, FORWARD), (1, 2, 1, REVERSE)] |
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260 assert x == x_ |
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261 |
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262 def test_multidigraph_original(self): |
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263 # Node 2 doesn't need to be searched again from visited from 4. |
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264 # The goal here is to cover the case when 2 to be researched from 4, |
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265 # when 4 is visited from the first time (so we must make sure that 4 |
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266 # is not visited from 2, and hence, we respect the edge orientation). |
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267 G = nx.MultiDiGraph([(0, 1), (1, 2), (2, 3), (4, 2)]) |
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268 pytest.raises( |
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269 nx.exception.NetworkXNoCycle, |
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270 find_cycle, |
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271 G, |
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272 [0, 1, 2, 3, 4], |
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273 orientation="original", |
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274 ) |
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275 |
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276 def test_dag(self): |
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277 G = nx.DiGraph([(0, 1), (0, 2), (1, 2)]) |
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278 pytest.raises( |
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279 nx.exception.NetworkXNoCycle, find_cycle, G, orientation="original" |
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280 ) |
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281 x = list(find_cycle(G, orientation="ignore")) |
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282 assert x == [(0, 1, FORWARD), (1, 2, FORWARD), (0, 2, REVERSE)] |
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283 |
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284 def test_prev_explored(self): |
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285 # https://github.com/networkx/networkx/issues/2323 |
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286 |
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287 G = nx.DiGraph() |
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288 G.add_edges_from([(1, 0), (2, 0), (1, 2), (2, 1)]) |
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289 pytest.raises(nx.NetworkXNoCycle, find_cycle, G, source=0) |
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290 x = list(nx.find_cycle(G, 1)) |
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291 x_ = [(1, 2), (2, 1)] |
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292 assert x == x_ |
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293 |
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294 x = list(nx.find_cycle(G, 2)) |
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295 x_ = [(2, 1), (1, 2)] |
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296 assert x == x_ |
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297 |
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298 x = list(nx.find_cycle(G)) |
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299 x_ = [(1, 2), (2, 1)] |
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300 assert x == x_ |
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301 |
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302 def test_no_cycle(self): |
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303 # https://github.com/networkx/networkx/issues/2439 |
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304 |
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305 G = nx.DiGraph() |
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306 G.add_edges_from([(1, 2), (2, 0), (3, 1), (3, 2)]) |
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307 pytest.raises(nx.NetworkXNoCycle, find_cycle, G, source=0) |
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308 pytest.raises(nx.NetworkXNoCycle, find_cycle, G) |
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309 |
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310 |
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311 def assert_basis_equal(a, b): |
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312 assert sorted(a) == sorted(b) |
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313 |
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314 |
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315 class TestMinimumCycles: |
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316 @classmethod |
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317 def setup_class(cls): |
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318 T = nx.Graph() |
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319 nx.add_cycle(T, [1, 2, 3, 4], weight=1) |
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320 T.add_edge(2, 4, weight=5) |
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321 cls.diamond_graph = T |
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322 |
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323 def test_unweighted_diamond(self): |
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324 mcb = minimum_cycle_basis(self.diamond_graph) |
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325 assert_basis_equal([sorted(c) for c in mcb], [[1, 2, 4], [2, 3, 4]]) |
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326 |
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327 def test_weighted_diamond(self): |
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328 mcb = minimum_cycle_basis(self.diamond_graph, weight="weight") |
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329 assert_basis_equal([sorted(c) for c in mcb], [[1, 2, 4], [1, 2, 3, 4]]) |
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330 |
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331 def test_dimensionality(self): |
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332 # checks |MCB|=|E|-|V|+|NC| |
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333 ntrial = 10 |
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334 for _ in range(ntrial): |
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335 rg = nx.erdos_renyi_graph(10, 0.3) |
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336 nnodes = rg.number_of_nodes() |
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337 nedges = rg.number_of_edges() |
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338 ncomp = nx.number_connected_components(rg) |
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339 |
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340 dim_mcb = len(minimum_cycle_basis(rg)) |
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341 assert dim_mcb == nedges - nnodes + ncomp |
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342 |
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343 def test_complete_graph(self): |
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344 cg = nx.complete_graph(5) |
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345 mcb = minimum_cycle_basis(cg) |
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346 assert all([len(cycle) == 3 for cycle in mcb]) |
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347 |
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348 def test_tree_graph(self): |
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349 tg = nx.balanced_tree(3, 3) |
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350 assert not minimum_cycle_basis(tg) |