Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/algorithms/tests/test_threshold.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 """ |
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2 Threshold Graphs |
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3 ================ |
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4 """ |
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5 |
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6 import pytest |
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7 |
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8 import networkx as nx |
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9 import networkx.algorithms.threshold as nxt |
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10 from networkx.algorithms.isomorphism.isomorph import graph_could_be_isomorphic |
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11 from networkx.testing import almost_equal |
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12 |
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13 cnlti = nx.convert_node_labels_to_integers |
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14 |
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15 |
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16 class TestGeneratorThreshold: |
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17 def test_threshold_sequence_graph_test(self): |
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18 G = nx.star_graph(10) |
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19 assert nxt.is_threshold_graph(G) |
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20 assert nxt.is_threshold_sequence(list(d for n, d in G.degree())) |
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21 |
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22 G = nx.complete_graph(10) |
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23 assert nxt.is_threshold_graph(G) |
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24 assert nxt.is_threshold_sequence(list(d for n, d in G.degree())) |
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25 |
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26 deg = [3, 2, 2, 1, 1, 1] |
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27 assert not nxt.is_threshold_sequence(deg) |
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28 |
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29 deg = [3, 2, 2, 1] |
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30 assert nxt.is_threshold_sequence(deg) |
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31 |
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32 G = nx.generators.havel_hakimi_graph(deg) |
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33 assert nxt.is_threshold_graph(G) |
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34 |
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35 def test_creation_sequences(self): |
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36 deg = [3, 2, 2, 1] |
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37 G = nx.generators.havel_hakimi_graph(deg) |
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38 |
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39 with pytest.raises(ValueError): |
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40 nxt.creation_sequence(deg, with_labels=True, compact=True) |
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41 |
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42 cs0 = nxt.creation_sequence(deg) |
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43 H0 = nxt.threshold_graph(cs0) |
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44 assert "".join(cs0) == "ddid" |
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45 |
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46 cs1 = nxt.creation_sequence(deg, with_labels=True) |
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47 H1 = nxt.threshold_graph(cs1) |
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48 assert cs1 == [(1, "d"), (2, "d"), (3, "i"), (0, "d")] |
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49 |
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50 cs2 = nxt.creation_sequence(deg, compact=True) |
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51 H2 = nxt.threshold_graph(cs2) |
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52 assert cs2 == [2, 1, 1] |
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53 assert "".join(nxt.uncompact(cs2)) == "ddid" |
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54 assert graph_could_be_isomorphic(H0, G) |
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55 assert graph_could_be_isomorphic(H0, H1) |
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56 assert graph_could_be_isomorphic(H0, H2) |
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57 |
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58 def test_make_compact(self): |
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59 assert nxt.make_compact(["d", "d", "d", "i", "d", "d"]) == [3, 1, 2] |
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60 assert nxt.make_compact([3, 1, 2]) == [3, 1, 2] |
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61 assert pytest.raises(TypeError, nxt.make_compact, [3.0, 1.0, 2.0]) |
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62 |
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63 def test_uncompact(self): |
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64 assert nxt.uncompact([3, 1, 2]) == ["d", "d", "d", "i", "d", "d"] |
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65 assert nxt.uncompact(["d", "d", "i", "d"]) == ["d", "d", "i", "d"] |
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66 assert nxt.uncompact( |
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67 nxt.uncompact([(1, "d"), (2, "d"), (3, "i"), (0, "d")]) |
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68 ) == nxt.uncompact([(1, "d"), (2, "d"), (3, "i"), (0, "d")]) |
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69 assert pytest.raises(TypeError, nxt.uncompact, [3.0, 1.0, 2.0]) |
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70 |
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71 def test_creation_sequence_to_weights(self): |
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72 assert nxt.creation_sequence_to_weights([3, 1, 2]) == [ |
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73 0.5, |
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74 0.5, |
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75 0.5, |
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76 0.25, |
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77 0.75, |
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78 0.75, |
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79 ] |
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80 assert pytest.raises( |
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81 TypeError, nxt.creation_sequence_to_weights, [3.0, 1.0, 2.0] |
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82 ) |
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83 |
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84 def test_weights_to_creation_sequence(self): |
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85 deg = [3, 2, 2, 1] |
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86 with pytest.raises(ValueError): |
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87 nxt.weights_to_creation_sequence(deg, with_labels=True, compact=True) |
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88 assert nxt.weights_to_creation_sequence(deg, with_labels=True) == [ |
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89 (3, "d"), |
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90 (1, "d"), |
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91 (2, "d"), |
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92 (0, "d"), |
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93 ] |
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94 assert nxt.weights_to_creation_sequence(deg, compact=True) == [4] |
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95 |
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96 def test_find_alternating_4_cycle(self): |
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97 G = nx.Graph() |
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98 G.add_edge(1, 2) |
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99 assert not nxt.find_alternating_4_cycle(G) |
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100 |
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101 def test_shortest_path(self): |
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102 deg = [3, 2, 2, 1] |
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103 G = nx.generators.havel_hakimi_graph(deg) |
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104 cs1 = nxt.creation_sequence(deg, with_labels=True) |
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105 for n, m in [(3, 0), (0, 3), (0, 2), (0, 1), (1, 3), (3, 1), (1, 2), (2, 3)]: |
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106 assert nxt.shortest_path(cs1, n, m) == nx.shortest_path(G, n, m) |
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107 |
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108 spl = nxt.shortest_path_length(cs1, 3) |
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109 spl2 = nxt.shortest_path_length([t for v, t in cs1], 2) |
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110 assert spl == spl2 |
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111 |
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112 spld = {} |
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113 for j, pl in enumerate(spl): |
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114 n = cs1[j][0] |
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115 spld[n] = pl |
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116 assert spld == nx.single_source_shortest_path_length(G, 3) |
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117 |
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118 assert nxt.shortest_path(["d", "d", "d", "i", "d", "d"], 1, 2) == [1, 2] |
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119 assert nxt.shortest_path([3, 1, 2], 1, 2) == [1, 2] |
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120 assert pytest.raises(TypeError, nxt.shortest_path, [3.0, 1.0, 2.0], 1, 2) |
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121 assert pytest.raises(ValueError, nxt.shortest_path, [3, 1, 2], "a", 2) |
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122 assert pytest.raises(ValueError, nxt.shortest_path, [3, 1, 2], 1, "b") |
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123 assert nxt.shortest_path([3, 1, 2], 1, 1) == [1] |
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124 |
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125 def test_shortest_path_length(self): |
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126 assert nxt.shortest_path_length([3, 1, 2], 1) == [1, 0, 1, 2, 1, 1] |
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127 assert nxt.shortest_path_length(["d", "d", "d", "i", "d", "d"], 1) == [ |
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128 1, |
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129 0, |
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130 1, |
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131 2, |
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132 1, |
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133 1, |
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134 ] |
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135 assert nxt.shortest_path_length(("d", "d", "d", "i", "d", "d"), 1) == [ |
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136 1, |
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137 0, |
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138 1, |
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139 2, |
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140 1, |
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141 1, |
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142 ] |
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143 assert pytest.raises(TypeError, nxt.shortest_path, [3.0, 1.0, 2.0], 1) |
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144 |
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145 def random_threshold_sequence(self): |
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146 assert len(nxt.random_threshold_sequence(10, 0.5)) == 10 |
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147 assert nxt.random_threshold_sequence(10, 0.5, seed=42) == [ |
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148 "d", |
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149 "i", |
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150 "d", |
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151 "d", |
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152 "d", |
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153 "i", |
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154 "i", |
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155 "i", |
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156 "d", |
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157 "d", |
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158 ] |
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159 assert pytest.raises(ValueError, nxt.random_threshold_sequence, 10, 1.5) |
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160 |
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161 def test_right_d_threshold_sequence(self): |
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162 assert nxt.right_d_threshold_sequence(3, 2) == ["d", "i", "d"] |
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163 assert pytest.raises(ValueError, nxt.right_d_threshold_sequence, 2, 3) |
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164 |
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165 def test_left_d_threshold_sequence(self): |
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166 assert nxt.left_d_threshold_sequence(3, 2) == ["d", "i", "d"] |
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167 assert pytest.raises(ValueError, nxt.left_d_threshold_sequence, 2, 3) |
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168 |
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169 def test_weights_thresholds(self): |
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170 wseq = [3, 4, 3, 3, 5, 6, 5, 4, 5, 6] |
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171 cs = nxt.weights_to_creation_sequence(wseq, threshold=10) |
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172 wseq = nxt.creation_sequence_to_weights(cs) |
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173 cs2 = nxt.weights_to_creation_sequence(wseq) |
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174 assert cs == cs2 |
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175 |
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176 wseq = nxt.creation_sequence_to_weights(nxt.uncompact([3, 1, 2, 3, 3, 2, 3])) |
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177 assert wseq == [ |
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178 s * 0.125 for s in [4, 4, 4, 3, 5, 5, 2, 2, 2, 6, 6, 6, 1, 1, 7, 7, 7] |
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179 ] |
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180 |
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181 wseq = nxt.creation_sequence_to_weights([3, 1, 2, 3, 3, 2, 3]) |
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182 assert wseq == [ |
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183 s * 0.125 for s in [4, 4, 4, 3, 5, 5, 2, 2, 2, 6, 6, 6, 1, 1, 7, 7, 7] |
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184 ] |
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185 |
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186 wseq = nxt.creation_sequence_to_weights(list(enumerate("ddidiiidididi"))) |
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187 assert wseq == [s * 0.1 for s in [5, 5, 4, 6, 3, 3, 3, 7, 2, 8, 1, 9, 0]] |
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188 |
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189 wseq = nxt.creation_sequence_to_weights("ddidiiidididi") |
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190 assert wseq == [s * 0.1 for s in [5, 5, 4, 6, 3, 3, 3, 7, 2, 8, 1, 9, 0]] |
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191 |
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192 wseq = nxt.creation_sequence_to_weights("ddidiiidididid") |
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193 ws = [s / float(12) for s in [6, 6, 5, 7, 4, 4, 4, 8, 3, 9, 2, 10, 1, 11]] |
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194 assert sum([abs(c - d) for c, d in zip(wseq, ws)]) < 1e-14 |
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195 |
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196 def test_finding_routines(self): |
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197 G = nx.Graph({1: [2], 2: [3], 3: [4], 4: [5], 5: [6]}) |
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198 G.add_edge(2, 4) |
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199 G.add_edge(2, 5) |
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200 G.add_edge(2, 7) |
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201 G.add_edge(3, 6) |
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202 G.add_edge(4, 6) |
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203 |
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204 # Alternating 4 cycle |
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205 assert nxt.find_alternating_4_cycle(G) == [1, 2, 3, 6] |
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206 |
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207 # Threshold graph |
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208 TG = nxt.find_threshold_graph(G) |
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209 assert nxt.is_threshold_graph(TG) |
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210 assert sorted(TG.nodes()) == [1, 2, 3, 4, 5, 7] |
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211 |
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212 cs = nxt.creation_sequence(dict(TG.degree()), with_labels=True) |
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213 assert nxt.find_creation_sequence(G) == cs |
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214 |
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215 def test_fast_versions_properties_threshold_graphs(self): |
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216 cs = "ddiiddid" |
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217 G = nxt.threshold_graph(cs) |
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218 assert nxt.density("ddiiddid") == nx.density(G) |
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219 assert sorted(nxt.degree_sequence(cs)) == sorted(d for n, d in G.degree()) |
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220 |
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221 ts = nxt.triangle_sequence(cs) |
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222 assert ts == list(nx.triangles(G).values()) |
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223 assert sum(ts) // 3 == nxt.triangles(cs) |
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224 |
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225 c1 = nxt.cluster_sequence(cs) |
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226 c2 = list(nx.clustering(G).values()) |
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227 assert almost_equal(sum([abs(c - d) for c, d in zip(c1, c2)]), 0) |
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228 |
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229 b1 = nx.betweenness_centrality(G).values() |
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230 b2 = nxt.betweenness_sequence(cs) |
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231 assert sum([abs(c - d) for c, d in zip(b1, b2)]) < 1e-14 |
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232 |
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233 assert nxt.eigenvalues(cs) == [0, 1, 3, 3, 5, 7, 7, 8] |
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234 |
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235 # Degree Correlation |
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236 assert abs(nxt.degree_correlation(cs) + 0.593038821954) < 1e-12 |
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237 assert nxt.degree_correlation("diiiddi") == -0.8 |
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238 assert nxt.degree_correlation("did") == -1.0 |
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239 assert nxt.degree_correlation("ddd") == 1.0 |
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240 assert nxt.eigenvalues("dddiii") == [0, 0, 0, 0, 3, 3] |
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241 assert nxt.eigenvalues("dddiiid") == [0, 1, 1, 1, 4, 4, 7] |
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242 |
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243 def test_tg_creation_routines(self): |
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244 s = nxt.left_d_threshold_sequence(5, 7) |
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245 s = nxt.right_d_threshold_sequence(5, 7) |
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246 s1 = nxt.swap_d(s, 1.0, 1.0) |
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247 s1 = nxt.swap_d(s, 1.0, 1.0, seed=1) |
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248 |
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249 def test_eigenvectors(self): |
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250 np = pytest.importorskip("numpy") |
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251 eigenval = np.linalg.eigvals |
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252 scipy = pytest.importorskip("scipy") |
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253 |
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254 cs = "ddiiddid" |
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255 G = nxt.threshold_graph(cs) |
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256 (tgeval, tgevec) = nxt.eigenvectors(cs) |
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257 dot = np.dot |
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258 assert [abs(dot(lv, lv) - 1.0) < 1e-9 for lv in tgevec] == [True] * 8 |
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259 lapl = nx.laplacian_matrix(G) |
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260 |
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261 # tgev=[ dot(lv,dot(lapl,lv)) for lv in tgevec ] |
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262 # assert_true(sum([abs(c-d) for c,d in zip(tgev,tgeval)]) < 1e-9) |
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263 # tgev.sort() |
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264 # lev=list(eigenval(lapl)) |
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265 # lev.sort() |
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266 # assert_true(sum([abs(c-d) for c,d in zip(tgev,lev)]) < 1e-9) |
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267 |
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268 def test_create_using(self): |
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269 cs = "ddiiddid" |
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270 G = nxt.threshold_graph(cs) |
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271 assert pytest.raises( |
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272 nx.exception.NetworkXError, |
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273 nxt.threshold_graph, |
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274 cs, |
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275 create_using=nx.DiGraph(), |
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276 ) |
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277 MG = nxt.threshold_graph(cs, create_using=nx.MultiGraph()) |
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278 assert sorted(MG.edges()) == sorted(G.edges()) |