Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/networkx/conftest.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 import pytest
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2 import networkx
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3 import sys
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4 import warnings
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5
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6
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7 def pytest_addoption(parser):
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8 parser.addoption(
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9 "--runslow", action="store_true", default=False, help="run slow tests"
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10 )
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11
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12
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13 def pytest_configure(config):
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14 config.addinivalue_line("markers", "slow: mark test as slow to run")
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15
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16
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17 def pytest_collection_modifyitems(config, items):
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18 if config.getoption("--runslow"):
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19 # --runslow given in cli: do not skip slow tests
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20 return
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21 skip_slow = pytest.mark.skip(reason="need --runslow option to run")
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22 for item in items:
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23 if "slow" in item.keywords:
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24 item.add_marker(skip_slow)
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25
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26
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27 # TODO: The warnings below need to be dealt with, but for now we silence them.
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28 @pytest.fixture(autouse=True)
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29 def set_warnings():
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30 warnings.filterwarnings(
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31 "ignore",
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32 category=DeprecationWarning,
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33 message="literal_stringizer is deprecated*",
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34 )
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35 warnings.filterwarnings(
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36 "ignore",
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37 category=DeprecationWarning,
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38 message="literal_destringizer is deprecated*",
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39 )
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40 warnings.filterwarnings(
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41 "ignore", category=DeprecationWarning, message="is_string_like is deprecated*"
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42 )
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43 warnings.filterwarnings(
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44 "ignore", category=DeprecationWarning, message="make_str is deprecated*"
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45 )
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46 warnings.filterwarnings(
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47 "ignore",
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48 category=DeprecationWarning,
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49 message="context manager reversed is deprecated*",
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50 )
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51 warnings.filterwarnings(
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52 "ignore",
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53 category=DeprecationWarning,
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54 message="This will return a generator in 3.0*",
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55 )
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56 warnings.filterwarnings(
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57 "ignore", category=DeprecationWarning, message="betweenness_centrality_source*",
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58 )
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59 warnings.filterwarnings(
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60 "ignore", category=DeprecationWarning, message="edge_betweeness*",
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61 )
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62 warnings.filterwarnings(
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63 "ignore",
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64 category=PendingDeprecationWarning,
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65 message="the matrix subclass is not the recommended way*",
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66 )
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67
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68
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69 @pytest.fixture(autouse=True)
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70 def add_nx(doctest_namespace):
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71 doctest_namespace["nx"] = networkx
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72
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73
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74 # What dependencies are installed?
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75
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76 try:
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77 import numpy
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78
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79 has_numpy = True
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80 except ImportError:
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81 has_numpy = False
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82
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83 try:
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84 import scipy
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85
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86 has_scipy = True
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87 except ImportError:
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88 has_scipy = False
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89
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90 try:
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91 import matplotlib
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92
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93 has_matplotlib = True
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94 except ImportError:
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95 has_matplotlib = False
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96
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97 try:
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98 import pandas
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99
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100 has_pandas = True
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101 except ImportError:
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102 has_pandas = False
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103
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104 try:
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105 import pygraphviz
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106
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107 has_pygraphviz = True
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108 except ImportError:
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109 has_pygraphviz = False
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110
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111 try:
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112 import yaml
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113
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114 has_yaml = True
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115 except ImportError:
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116 has_yaml = False
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117
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118 try:
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119 import pydot
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120
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121 has_pydot = True
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122 except ImportError:
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123 has_pydot = False
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124
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125 try:
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126 import ogr
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127
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128 has_ogr = True
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129 except ImportError:
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130 has_ogr = False
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131
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132
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133 # List of files that pytest should ignore
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134
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135 collect_ignore = []
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136
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137 needs_numpy = [
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138 "algorithms/centrality/current_flow_closeness.py",
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139 "algorithms/node_classification/__init__.py",
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140 "algorithms/non_randomness.py",
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141 "algorithms/shortest_paths/dense.py",
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142 "linalg/bethehessianmatrix.py",
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143 "linalg/laplacianmatrix.py",
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144 "utils/misc.py",
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145 ]
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146 needs_scipy = [
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147 "algorithms/assortativity/correlation.py",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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148 "algorithms/assortativity/mixing.py",
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149 "algorithms/assortativity/pairs.py",
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150 "algorithms/bipartite/matrix.py",
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151 "algorithms/bipartite/spectral.py",
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152 "algorithms/centrality/current_flow_betweenness.py",
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153 "algorithms/centrality/current_flow_betweenness_subset.py",
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154 "algorithms/centrality/eigenvector.py",
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155 "algorithms/centrality/katz.py",
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156 "algorithms/centrality/second_order.py",
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157 "algorithms/centrality/subgraph_alg.py",
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158 "algorithms/communicability_alg.py",
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159 "algorithms/link_analysis/hits_alg.py",
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160 "algorithms/link_analysis/pagerank_alg.py",
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161 "algorithms/node_classification/hmn.py",
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162 "algorithms/node_classification/lgc.py",
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163 "algorithms/similarity.py",
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164 "convert_matrix.py",
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165 "drawing/layout.py",
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166 "generators/spectral_graph_forge.py",
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167 "linalg/algebraicconnectivity.py",
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168 "linalg/attrmatrix.py",
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169 "linalg/graphmatrix.py",
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170 "linalg/modularitymatrix.py",
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171 "linalg/spectrum.py",
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172 "utils/rcm.py",
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173 ]
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174 needs_matplotlib = ["drawing/nx_pylab.py"]
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175 needs_pandas = ["convert_matrix.py"]
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176 needs_yaml = ["readwrite/nx_yaml.py"]
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177 needs_pygraphviz = ["drawing/nx_agraph.py"]
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178 needs_pydot = ["drawing/nx_pydot.py"]
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179 needs_ogr = ["readwrite/nx_shp.py"]
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180
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181 if not has_numpy:
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182 collect_ignore += needs_numpy
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183 if not has_scipy:
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184 collect_ignore += needs_scipy
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185 if not has_matplotlib:
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186 collect_ignore += needs_matplotlib
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187 if not has_pandas:
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188 collect_ignore += needs_pandas
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189 if not has_yaml:
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190 collect_ignore += needs_yaml
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191 if not has_pygraphviz:
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192 collect_ignore += needs_pygraphviz
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193 if not has_pydot:
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194 collect_ignore += needs_pydot
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195 if not has_ogr:
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196 collect_ignore += needs_ogr
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197
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198 # FIXME: This is to avoid errors on AppVeyor
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199 if sys.platform.startswith("win"):
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200 collect_ignore += ["readwrite/graph6.py", "readwrite/sparse6.py"]