annotate env/lib/python3.9/site-packages/networkx/readwrite/tests/test_gexf.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 io
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2 import sys
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3 import time
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4 import pytest
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5
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6 import networkx as nx
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7
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8
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9 class TestGEXF:
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10 @classmethod
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11 def setup_class(cls):
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12 _ = pytest.importorskip("xml.etree.ElementTree")
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13
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14 cls.simple_directed_data = """<?xml version="1.0" encoding="UTF-8"?>
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15 <gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
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16 <graph mode="static" defaultedgetype="directed">
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17 <nodes>
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18 <node id="0" label="Hello" />
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19 <node id="1" label="Word" />
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20 </nodes>
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21 <edges>
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22 <edge id="0" source="0" target="1" />
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23 </edges>
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24 </graph>
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25 </gexf>
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26 """
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27 cls.simple_directed_graph = nx.DiGraph()
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28 cls.simple_directed_graph.add_node("0", label="Hello")
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29 cls.simple_directed_graph.add_node("1", label="World")
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30 cls.simple_directed_graph.add_edge("0", "1", id="0")
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31
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32 cls.simple_directed_fh = io.BytesIO(cls.simple_directed_data.encode("UTF-8"))
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33
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34 cls.attribute_data = """<?xml version="1.0" encoding="UTF-8"?>\
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35 <gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.\
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36 org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/\
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37 1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2">
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38 <meta lastmodifieddate="2009-03-20">
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39 <creator>Gephi.org</creator>
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40 <description>A Web network</description>
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41 </meta>
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42 <graph defaultedgetype="directed">
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43 <attributes class="node">
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44 <attribute id="0" title="url" type="string"/>
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45 <attribute id="1" title="indegree" type="integer"/>
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46 <attribute id="2" title="frog" type="boolean">
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47 <default>true</default>
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48 </attribute>
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49 </attributes>
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50 <nodes>
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51 <node id="0" label="Gephi">
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52 <attvalues>
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53 <attvalue for="0" value="https://gephi.org"/>
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54 <attvalue for="1" value="1"/>
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55 <attvalue for="2" value="false"/>
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56 </attvalues>
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57 </node>
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58 <node id="1" label="Webatlas">
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59 <attvalues>
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60 <attvalue for="0" value="http://webatlas.fr"/>
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61 <attvalue for="1" value="2"/>
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62 <attvalue for="2" value="false"/>
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63 </attvalues>
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64 </node>
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65 <node id="2" label="RTGI">
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66 <attvalues>
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67 <attvalue for="0" value="http://rtgi.fr"/>
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68 <attvalue for="1" value="1"/>
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69 <attvalue for="2" value="true"/>
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70 </attvalues>
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71 </node>
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72 <node id="3" label="BarabasiLab">
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73 <attvalues>
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74 <attvalue for="0" value="http://barabasilab.com"/>
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75 <attvalue for="1" value="1"/>
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76 <attvalue for="2" value="true"/>
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77 </attvalues>
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78 </node>
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79 </nodes>
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80 <edges>
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81 <edge id="0" source="0" target="1" label="foo"/>
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82 <edge id="1" source="0" target="2"/>
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83 <edge id="2" source="1" target="0"/>
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84 <edge id="3" source="2" target="1"/>
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85 <edge id="4" source="0" target="3"/>
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86 </edges>
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87 </graph>
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88 </gexf>
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89 """
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90 cls.attribute_graph = nx.DiGraph()
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91 cls.attribute_graph.graph["node_default"] = {"frog": True}
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92 cls.attribute_graph.add_node(
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93 "0", label="Gephi", url="https://gephi.org", indegree=1, frog=False
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94 )
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95 cls.attribute_graph.add_node(
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96 "1", label="Webatlas", url="http://webatlas.fr", indegree=2, frog=False
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97 )
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98 cls.attribute_graph.add_node(
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99 "2", label="RTGI", url="http://rtgi.fr", indegree=1, frog=True
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100 )
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101 cls.attribute_graph.add_node(
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102 "3",
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103 label="BarabasiLab",
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104 url="http://barabasilab.com",
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105 indegree=1,
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106 frog=True,
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107 )
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108 cls.attribute_graph.add_edge("0", "1", id="0", label="foo")
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109 cls.attribute_graph.add_edge("0", "2", id="1")
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110 cls.attribute_graph.add_edge("1", "0", id="2")
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111 cls.attribute_graph.add_edge("2", "1", id="3")
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112 cls.attribute_graph.add_edge("0", "3", id="4")
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113 cls.attribute_fh = io.BytesIO(cls.attribute_data.encode("UTF-8"))
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114
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115 cls.simple_undirected_data = """<?xml version="1.0" encoding="UTF-8"?>
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116 <gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
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117 <graph mode="static" defaultedgetype="undirected">
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118 <nodes>
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119 <node id="0" label="Hello" />
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120 <node id="1" label="Word" />
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121 </nodes>
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122 <edges>
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123 <edge id="0" source="0" target="1" />
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124 </edges>
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125 </graph>
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126 </gexf>
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127 """
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128 cls.simple_undirected_graph = nx.Graph()
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129 cls.simple_undirected_graph.add_node("0", label="Hello")
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130 cls.simple_undirected_graph.add_node("1", label="World")
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131 cls.simple_undirected_graph.add_edge("0", "1", id="0")
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132
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133 cls.simple_undirected_fh = io.BytesIO(
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134 cls.simple_undirected_data.encode("UTF-8")
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135 )
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136
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137 def test_read_simple_directed_graphml(self):
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138 G = self.simple_directed_graph
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139 H = nx.read_gexf(self.simple_directed_fh)
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140 assert sorted(G.nodes()) == sorted(H.nodes())
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141 assert sorted(G.edges()) == sorted(H.edges())
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142 assert sorted(G.edges(data=True)) == sorted(H.edges(data=True))
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143 self.simple_directed_fh.seek(0)
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144
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145 def test_write_read_simple_directed_graphml(self):
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146 G = self.simple_directed_graph
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147 fh = io.BytesIO()
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148 nx.write_gexf(G, fh)
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149 fh.seek(0)
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150 H = nx.read_gexf(fh)
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151 assert sorted(G.nodes()) == sorted(H.nodes())
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152 assert sorted(G.edges()) == sorted(H.edges())
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153 assert sorted(G.edges(data=True)) == sorted(H.edges(data=True))
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154 self.simple_directed_fh.seek(0)
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155
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156 def test_read_simple_undirected_graphml(self):
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157 G = self.simple_undirected_graph
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158 H = nx.read_gexf(self.simple_undirected_fh)
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159 assert sorted(G.nodes()) == sorted(H.nodes())
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160 assert sorted(sorted(e) for e in G.edges()) == sorted(
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161 sorted(e) for e in H.edges()
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162 )
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163 self.simple_undirected_fh.seek(0)
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164
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165 def test_read_attribute_graphml(self):
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166 G = self.attribute_graph
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167 H = nx.read_gexf(self.attribute_fh)
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168 assert sorted(G.nodes(True)) == sorted(H.nodes(data=True))
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169 ge = sorted(G.edges(data=True))
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170 he = sorted(H.edges(data=True))
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171 for a, b in zip(ge, he):
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172 assert a == b
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173 self.attribute_fh.seek(0)
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174
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175 def test_directed_edge_in_undirected(self):
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176 s = """<?xml version="1.0" encoding="UTF-8"?>
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177 <gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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178 <graph mode="static" defaultedgetype="undirected" name="">
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179 <nodes>
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180 <node id="0" label="Hello" />
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181 <node id="1" label="Word" />
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182 </nodes>
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183 <edges>
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184 <edge id="0" source="0" target="1" type="directed"/>
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185 </edges>
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186 </graph>
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187 </gexf>
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188 """
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189 fh = io.BytesIO(s.encode("UTF-8"))
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190 pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
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191
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192 def test_undirected_edge_in_directed(self):
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193 s = """<?xml version="1.0" encoding="UTF-8"?>
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194 <gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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195 <graph mode="static" defaultedgetype="directed" name="">
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196 <nodes>
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197 <node id="0" label="Hello" />
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198 <node id="1" label="Word" />
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199 </nodes>
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200 <edges>
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201 <edge id="0" source="0" target="1" type="undirected"/>
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202 </edges>
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203 </graph>
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204 </gexf>
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205 """
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206 fh = io.BytesIO(s.encode("UTF-8"))
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207 pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
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208
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209 def test_key_raises(self):
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210 s = """<?xml version="1.0" encoding="UTF-8"?>
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211 <gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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212 <graph mode="static" defaultedgetype="directed" name="">
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213 <nodes>
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214 <node id="0" label="Hello">
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215 <attvalues>
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216 <attvalue for='0' value='1'/>
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217 </attvalues>
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218 </node>
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219 <node id="1" label="Word" />
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220 </nodes>
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221 <edges>
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222 <edge id="0" source="0" target="1" type="undirected"/>
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223 </edges>
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224 </graph>
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225 </gexf>
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226 """
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227 fh = io.BytesIO(s.encode("UTF-8"))
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228 pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
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229
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230 def test_relabel(self):
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231 s = """<?xml version="1.0" encoding="UTF-8"?>
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232 <gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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233 <graph mode="static" defaultedgetype="directed" name="">
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234 <nodes>
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235 <node id="0" label="Hello" />
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236 <node id="1" label="Word" />
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237 </nodes>
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238 <edges>
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239 <edge id="0" source="0" target="1"/>
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240 </edges>
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241 </graph>
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242 </gexf>
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243 """
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244 fh = io.BytesIO(s.encode("UTF-8"))
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245 G = nx.read_gexf(fh, relabel=True)
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246 assert sorted(G.nodes()) == ["Hello", "Word"]
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247
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248 def test_default_attribute(self):
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249 G = nx.Graph()
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250 G.add_node(1, label="1", color="green")
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251 nx.add_path(G, [0, 1, 2, 3])
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252 G.add_edge(1, 2, foo=3)
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253 G.graph["node_default"] = {"color": "yellow"}
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254 G.graph["edge_default"] = {"foo": 7}
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255 fh = io.BytesIO()
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256 nx.write_gexf(G, fh)
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257 fh.seek(0)
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258 H = nx.read_gexf(fh, node_type=int)
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259 assert sorted(G.nodes()) == sorted(H.nodes())
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260 assert sorted(sorted(e) for e in G.edges()) == sorted(
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261 sorted(e) for e in H.edges()
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262 )
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263 # Reading a gexf graph always sets mode attribute to either
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264 # 'static' or 'dynamic'. Remove the mode attribute from the
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265 # read graph for the sake of comparing remaining attributes.
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266 del H.graph["mode"]
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267 assert G.graph == H.graph
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268
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269 def test_serialize_ints_to_strings(self):
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270 G = nx.Graph()
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271 G.add_node(1, id=7, label=77)
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272 fh = io.BytesIO()
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273 nx.write_gexf(G, fh)
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274 fh.seek(0)
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275 H = nx.read_gexf(fh, node_type=int)
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276 assert list(H) == [7]
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277 assert H.nodes[7]["label"] == "77"
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278
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279 # FIXME: We should test xml without caring about their order This is causing a
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280 # problem b/c of a change in Python 3.8
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281 #
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282 # "Prior to Python 3.8, the serialisation order of the XML attributes of
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283 # elements was artificially made predictable by sorting the attributes by their
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284 # name. Based on the now guaranteed ordering of dicts, this arbitrary
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285 # reordering was removed in Python 3.8 to preserve the order in which
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286 # attributes were originally parsed or created by user code."
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287 #
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288 # https://docs.python.org/3.8/library/xml.etree.elementtree.html
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289 # https://bugs.python.org/issue34160
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290
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291 def test_write_with_node_attributes(self):
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292 # Addresses #673.
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293 G = nx.OrderedGraph()
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294 G.add_edges_from([(0, 1), (1, 2), (2, 3)])
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295 for i in range(4):
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296 G.nodes[i]["id"] = i
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297 G.nodes[i]["label"] = i
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298 G.nodes[i]["pid"] = i
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299 G.nodes[i]["start"] = i
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300 G.nodes[i]["end"] = i + 1
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301
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302 if sys.version_info < (3, 8):
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303 expected = f"""<gexf version="1.2" xmlns="http://www.gexf.net/1.2\
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304 draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:\
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305 schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
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306 gexf.xsd">
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307 <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
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308 <creator>NetworkX {nx.__version__}</creator>
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309 </meta>
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310 <graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long">
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311 <nodes>
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312 <node end="1" id="0" label="0" pid="0" start="0" />
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313 <node end="2" id="1" label="1" pid="1" start="1" />
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314 <node end="3" id="2" label="2" pid="2" start="2" />
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315 <node end="4" id="3" label="3" pid="3" start="3" />
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316 </nodes>
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317 <edges>
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318 <edge id="0" source="0" target="1" />
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319 <edge id="1" source="1" target="2" />
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320 <edge id="2" source="2" target="3" />
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321 </edges>
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322 </graph>
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323 </gexf>"""
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324 else:
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325 expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\
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326 ="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation=\
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327 "http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
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328 gexf.xsd" version="1.2">
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329 <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
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330 <creator>NetworkX {nx.__version__}</creator>
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331 </meta>
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332 <graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long">
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333 <nodes>
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334 <node id="0" label="0" pid="0" start="0" end="1" />
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335 <node id="1" label="1" pid="1" start="1" end="2" />
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336 <node id="2" label="2" pid="2" start="2" end="3" />
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337 <node id="3" label="3" pid="3" start="3" end="4" />
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338 </nodes>
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339 <edges>
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340 <edge source="0" target="1" id="0" />
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341 <edge source="1" target="2" id="1" />
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342 <edge source="2" target="3" id="2" />
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343 </edges>
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344 </graph>
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345 </gexf>"""
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346 obtained = "\n".join(nx.generate_gexf(G))
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347 assert expected == obtained
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348
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349 def test_edge_id_construct(self):
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350 G = nx.Graph()
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351 G.add_edges_from([(0, 1, {"id": 0}), (1, 2, {"id": 2}), (2, 3)])
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352
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353 if sys.version_info < (3, 8):
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354 expected = f"""<gexf version="1.2" xmlns="http://www.gexf.net/\
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355 1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:\
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356 schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
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357 gexf.xsd">
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358 <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
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359 <creator>NetworkX {nx.__version__}</creator>
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360 </meta>
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361 <graph defaultedgetype="undirected" mode="static" name="">
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362 <nodes>
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363 <node id="0" label="0" />
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364 <node id="1" label="1" />
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shellac
parents:
diff changeset
365 <node id="2" label="2" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
366 <node id="3" label="3" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
367 </nodes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
368 <edges>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
369 <edge id="0" source="0" target="1" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
370 <edge id="2" source="1" target="2" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
371 <edge id="1" source="2" target="3" />
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shellac
parents:
diff changeset
372 </edges>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
373 </graph>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
374 </gexf>"""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
375 else:
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parents:
diff changeset
376 expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
377 ="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.\
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
378 gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2">
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parents:
diff changeset
379 <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
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shellac
parents:
diff changeset
380 <creator>NetworkX {nx.__version__}</creator>
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shellac
parents:
diff changeset
381 </meta>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
382 <graph defaultedgetype="undirected" mode="static" name="">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
383 <nodes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
384 <node id="0" label="0" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
385 <node id="1" label="1" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
386 <node id="2" label="2" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
387 <node id="3" label="3" />
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shellac
parents:
diff changeset
388 </nodes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
389 <edges>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
390 <edge source="0" target="1" id="0" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
391 <edge source="1" target="2" id="2" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
392 <edge source="2" target="3" id="1" />
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parents:
diff changeset
393 </edges>
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shellac
parents:
diff changeset
394 </graph>
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shellac
parents:
diff changeset
395 </gexf>"""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
396
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
397 obtained = "\n".join(nx.generate_gexf(G))
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shellac
parents:
diff changeset
398 assert expected == obtained
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
399
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shellac
parents:
diff changeset
400 def test_numpy_type(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
401 G = nx.path_graph(4)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
402 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
403 import numpy
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
404 except ImportError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
405 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
406 nx.set_node_attributes(G, {n: n for n in numpy.arange(4)}, "number")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
407 G[0][1]["edge-number"] = numpy.float64(1.1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
408
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
409 if sys.version_info < (3, 8):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
410 expected = f"""<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft"\
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shellac
parents:
diff changeset
411 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
412 ="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
413 <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
414 <creator>NetworkX {nx.__version__}</creator>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
415 </meta>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
416 <graph defaultedgetype="undirected" mode="static" name="">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
417 <attributes class="edge" mode="static">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
418 <attribute id="1" title="edge-number" type="float" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
419 </attributes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
420 <attributes class="node" mode="static">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
421 <attribute id="0" title="number" type="int" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
422 </attributes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
423 <nodes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
424 <node id="0" label="0">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
425 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
426 <attvalue for="0" value="0" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
427 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
428 </node>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
429 <node id="1" label="1">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
430 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
431 <attvalue for="0" value="1" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
432 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
433 </node>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
434 <node id="2" label="2">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
435 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436 <attvalue for="0" value="2" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
437 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
438 </node>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
439 <node id="3" label="3">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
440 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
441 <attvalue for="0" value="3" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
442 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
443 </node>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
444 </nodes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
445 <edges>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
446 <edge id="0" source="0" target="1">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
447 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
448 <attvalue for="1" value="1.1" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
449 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
450 </edge>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
451 <edge id="1" source="1" target="2" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
452 <edge id="2" source="2" target="3" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
453 </edges>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
454 </graph>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
455 </gexf>"""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
456 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
457 expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft"\
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
458 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459 ="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd"\
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
460 version="1.2">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
461 <meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
462 <creator>NetworkX {nx.__version__}</creator>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
463 </meta>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
464 <graph defaultedgetype="undirected" mode="static" name="">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
465 <attributes mode="static" class="edge">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
466 <attribute id="1" title="edge-number" type="float" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
467 </attributes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
468 <attributes mode="static" class="node">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
469 <attribute id="0" title="number" type="int" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
470 </attributes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
471 <nodes>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
472 <node id="0" label="0">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
473 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
474 <attvalue for="0" value="0" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
476 </node>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
477 <node id="1" label="1">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
478 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
479 <attvalue for="0" value="1" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
480 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
481 </node>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 <node id="2" label="2">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
483 <attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
484 <attvalue for="0" value="2" />
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
485 </attvalues>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
486 </node>
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
487 <node id="3" label="3">
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
488 <attvalues>
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diff changeset
489 <attvalue for="0" value="3" />
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diff changeset
490 </attvalues>
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parents:
diff changeset
491 </node>
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parents:
diff changeset
492 </nodes>
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parents:
diff changeset
493 <edges>
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parents:
diff changeset
494 <edge source="0" target="1" id="0">
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parents:
diff changeset
495 <attvalues>
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parents:
diff changeset
496 <attvalue for="1" value="1.1" />
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parents:
diff changeset
497 </attvalues>
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parents:
diff changeset
498 </edge>
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parents:
diff changeset
499 <edge source="1" target="2" id="1" />
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parents:
diff changeset
500 <edge source="2" target="3" id="2" />
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parents:
diff changeset
501 </edges>
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parents:
diff changeset
502 </graph>
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503 </gexf>"""
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parents:
diff changeset
504 obtained = "\n".join(nx.generate_gexf(G))
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parents:
diff changeset
505 assert expected == obtained
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parents:
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506
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diff changeset
507 def test_bool(self):
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diff changeset
508 G = nx.Graph()
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parents:
diff changeset
509 G.add_node(1, testattr=True)
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parents:
diff changeset
510 fh = io.BytesIO()
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parents:
diff changeset
511 nx.write_gexf(G, fh)
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parents:
diff changeset
512 fh.seek(0)
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diff changeset
513 H = nx.read_gexf(fh, node_type=int)
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parents:
diff changeset
514 assert H.nodes[1]["testattr"]
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diff changeset
515
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516 # Test for NaN, INF and -INF
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parents:
diff changeset
517 def test_specials(self):
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diff changeset
518 from math import isnan
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diff changeset
519
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520 inf, nan = float("inf"), float("nan")
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parents:
diff changeset
521 G = nx.Graph()
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parents:
diff changeset
522 G.add_node(1, testattr=inf, strdata="inf", key="a")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
523 G.add_node(2, testattr=nan, strdata="nan", key="b")
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parents:
diff changeset
524 G.add_node(3, testattr=-inf, strdata="-inf", key="c")
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parents:
diff changeset
525
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diff changeset
526 fh = io.BytesIO()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
527 nx.write_gexf(G, fh)
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parents:
diff changeset
528 fh.seek(0)
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parents:
diff changeset
529 filetext = fh.read()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
530 fh.seek(0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
531 H = nx.read_gexf(fh, node_type=int)
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parents:
diff changeset
532
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
533 assert b"INF" in filetext
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
534 assert b"NaN" in filetext
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
535 assert b"-INF" in filetext
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
536
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
537 assert H.nodes[1]["testattr"] == inf
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
538 assert isnan(H.nodes[2]["testattr"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
539 assert H.nodes[3]["testattr"] == -inf
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
540
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
541 assert H.nodes[1]["strdata"] == "inf"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
542 assert H.nodes[2]["strdata"] == "nan"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
543 assert H.nodes[3]["strdata"] == "-inf"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
544
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545 assert H.nodes[1]["networkx_key"] == "a"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
546 assert H.nodes[2]["networkx_key"] == "b"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
547 assert H.nodes[3]["networkx_key"] == "c"
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diff changeset
548
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diff changeset
549 def test_simple_list(self):
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diff changeset
550 G = nx.Graph()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
551 list_value = [(1, 2, 3), (9, 1, 2)]
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diff changeset
552 G.add_node(1, key=list_value)
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diff changeset
553 fh = io.BytesIO()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
554 nx.write_gexf(G, fh)
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diff changeset
555 fh.seek(0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
556 H = nx.read_gexf(fh, node_type=int)
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diff changeset
557 assert H.nodes[1]["networkx_key"] == list_value
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diff changeset
558
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diff changeset
559 def test_dynamic_mode(self):
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diff changeset
560 G = nx.Graph()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
561 G.add_node(1, label="1", color="green")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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diff changeset
562 G.graph["mode"] = "dynamic"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
563 fh = io.BytesIO()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
564 nx.write_gexf(G, fh)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
565 fh.seek(0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
566 H = nx.read_gexf(fh, node_type=int)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
567 assert sorted(G.nodes()) == sorted(H.nodes())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
568 assert sorted(sorted(e) for e in G.edges()) == sorted(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
569 sorted(e) for e in H.edges()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
570 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
571
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
572 def test_multigraph_with_missing_attributes(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
573 G = nx.MultiGraph()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
574 G.add_node(0, label="1", color="green")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
575 G.add_node(1, label="2", color="green")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
576 G.add_edge(0, 1, id="0", wight=3, type="undirected", start=0, end=1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
577 G.add_edge(0, 1, id="1", label="foo", start=0, end=1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
578 G.add_edge(0, 1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
579 fh = io.BytesIO()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
580 nx.write_gexf(G, fh)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
581 fh.seek(0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
582 H = nx.read_gexf(fh, node_type=int)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
583 assert sorted(G.nodes()) == sorted(H.nodes())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 assert sorted(sorted(e) for e in G.edges()) == sorted(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
585 sorted(e) for e in H.edges()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
586 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
587
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
588 def test_missing_viz_attributes(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
589 G = nx.Graph()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
590 G.add_node(0, label="1", color="green")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
591 G.nodes[0]["viz"] = {"size": 54}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
592 G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1, "z": 0}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
593 G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
594 G.nodes[0]["viz"]["shape"] = "http://random.url"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
595 G.nodes[0]["viz"]["thickness"] = 2
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
596 fh = io.BytesIO()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
597 nx.write_gexf(G, fh, version="1.1draft")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
598 fh.seek(0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
599 H = nx.read_gexf(fh, node_type=int)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
600 assert sorted(G.nodes()) == sorted(H.nodes())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
601 assert sorted(sorted(e) for e in G.edges()) == sorted(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
602 sorted(e) for e in H.edges()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
603 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
604
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
605 # Second graph for the other branch
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
606 G = nx.Graph()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
607 G.add_node(0, label="1", color="green")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
608 G.nodes[0]["viz"] = {"size": 54}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
609 G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1, "z": 0}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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610 G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256, "a": 0.5}
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611 G.nodes[0]["viz"]["shape"] = "ftp://random.url"
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612 G.nodes[0]["viz"]["thickness"] = 2
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613 fh = io.BytesIO()
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614 nx.write_gexf(G, fh)
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615 fh.seek(0)
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616 H = nx.read_gexf(fh, node_type=int)
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617 assert sorted(G.nodes()) == sorted(H.nodes())
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618 assert sorted(sorted(e) for e in G.edges()) == sorted(
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619 sorted(e) for e in H.edges()
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620 )
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621
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622 def test_slice_and_spell(self):
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623 # Test spell first, so version = 1.2
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624 G = nx.Graph()
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625 G.add_node(0, label="1", color="green")
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626 G.nodes[0]["spells"] = [(1, 2)]
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627 fh = io.BytesIO()
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628 nx.write_gexf(G, fh)
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629 fh.seek(0)
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630 H = nx.read_gexf(fh, node_type=int)
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631 assert sorted(G.nodes()) == sorted(H.nodes())
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632 assert sorted(sorted(e) for e in G.edges()) == sorted(
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633 sorted(e) for e in H.edges()
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634 )
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635
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636 G = nx.Graph()
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637 G.add_node(0, label="1", color="green")
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638 G.nodes[0]["slices"] = [(1, 2)]
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639 fh = io.BytesIO()
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640 nx.write_gexf(G, fh, version="1.1draft")
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641 fh.seek(0)
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642 H = nx.read_gexf(fh, node_type=int)
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643 assert sorted(G.nodes()) == sorted(H.nodes())
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644 assert sorted(sorted(e) for e in G.edges()) == sorted(
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645 sorted(e) for e in H.edges()
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646 )
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647
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648 def test_add_parent(self):
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649 G = nx.Graph()
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650 G.add_node(0, label="1", color="green", parents=[1, 2])
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651 fh = io.BytesIO()
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652 nx.write_gexf(G, fh)
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653 fh.seek(0)
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654 H = nx.read_gexf(fh, node_type=int)
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655 assert sorted(G.nodes()) == sorted(H.nodes())
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656 assert sorted(sorted(e) for e in G.edges()) == sorted(
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657 sorted(e) for e in H.edges()
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658 )