Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/utils/decorators.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 from collections import defaultdict |
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2 from os.path import splitext |
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3 from contextlib import contextmanager |
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4 from pathlib import Path |
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5 |
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6 import networkx as nx |
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7 from decorator import decorator |
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8 from networkx.utils import create_random_state, create_py_random_state |
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9 |
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10 __all__ = [ |
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11 "not_implemented_for", |
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12 "open_file", |
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13 "nodes_or_number", |
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14 "preserve_random_state", |
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15 "random_state", |
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16 "np_random_state", |
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17 "py_random_state", |
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18 ] |
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19 |
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20 |
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21 def not_implemented_for(*graph_types): |
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22 """Decorator to mark algorithms as not implemented |
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23 |
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24 Parameters |
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25 ---------- |
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26 graph_types : container of strings |
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27 Entries must be one of 'directed','undirected', 'multigraph', 'graph'. |
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28 |
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29 Returns |
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30 ------- |
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31 _require : function |
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32 The decorated function. |
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33 |
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34 Raises |
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35 ------ |
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36 NetworkXNotImplemented |
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37 If any of the packages cannot be imported |
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38 |
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39 Notes |
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40 ----- |
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41 Multiple types are joined logically with "and". |
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42 For "or" use multiple @not_implemented_for() lines. |
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43 |
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44 Examples |
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45 -------- |
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46 Decorate functions like this:: |
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47 |
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48 @not_implemnted_for('directed') |
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49 def sp_function(G): |
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50 pass |
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51 |
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52 @not_implemnted_for('directed','multigraph') |
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53 def sp_np_function(G): |
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54 pass |
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55 """ |
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56 |
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57 @decorator |
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58 def _not_implemented_for(not_implement_for_func, *args, **kwargs): |
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59 graph = args[0] |
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60 terms = { |
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61 "directed": graph.is_directed(), |
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62 "undirected": not graph.is_directed(), |
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63 "multigraph": graph.is_multigraph(), |
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64 "graph": not graph.is_multigraph(), |
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65 } |
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66 match = True |
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67 try: |
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68 for t in graph_types: |
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69 match = match and terms[t] |
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70 except KeyError as e: |
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71 raise KeyError( |
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72 "use one or more of " "directed, undirected, multigraph, graph" |
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73 ) from e |
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74 if match: |
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75 msg = f"not implemented for {' '.join(graph_types)} type" |
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76 raise nx.NetworkXNotImplemented(msg) |
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77 else: |
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78 return not_implement_for_func(*args, **kwargs) |
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79 |
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80 return _not_implemented_for |
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81 |
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82 |
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83 def _open_gz(path, mode): |
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84 import gzip |
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85 |
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86 return gzip.open(path, mode=mode) |
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87 |
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88 |
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89 def _open_bz2(path, mode): |
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90 import bz2 |
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91 |
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92 return bz2.BZ2File(path, mode=mode) |
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93 |
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94 |
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95 # To handle new extensions, define a function accepting a `path` and `mode`. |
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96 # Then add the extension to _dispatch_dict. |
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97 _dispatch_dict = defaultdict(lambda: open) |
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98 _dispatch_dict[".gz"] = _open_gz |
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99 _dispatch_dict[".bz2"] = _open_bz2 |
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100 _dispatch_dict[".gzip"] = _open_gz |
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101 |
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102 |
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103 def open_file(path_arg, mode="r"): |
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104 """Decorator to ensure clean opening and closing of files. |
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105 |
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106 Parameters |
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107 ---------- |
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108 path_arg : int |
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109 Location of the path argument in args. Even if the argument is a |
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110 named positional argument (with a default value), you must specify its |
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111 index as a positional argument. |
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112 mode : str |
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113 String for opening mode. |
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114 |
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115 Returns |
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116 ------- |
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117 _open_file : function |
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118 Function which cleanly executes the io. |
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119 |
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120 Examples |
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121 -------- |
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122 Decorate functions like this:: |
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123 |
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124 @open_file(0,'r') |
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125 def read_function(pathname): |
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126 pass |
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127 |
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128 @open_file(1,'w') |
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129 def write_function(G,pathname): |
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130 pass |
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131 |
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132 @open_file(1,'w') |
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133 def write_function(G, pathname='graph.dot') |
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134 pass |
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135 |
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136 @open_file('path', 'w+') |
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137 def another_function(arg, **kwargs): |
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138 path = kwargs['path'] |
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139 pass |
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140 """ |
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141 # Note that this decorator solves the problem when a path argument is |
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142 # specified as a string, but it does not handle the situation when the |
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143 # function wants to accept a default of None (and then handle it). |
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144 # Here is an example: |
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145 # |
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146 # @open_file('path') |
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147 # def some_function(arg1, arg2, path=None): |
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148 # if path is None: |
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149 # fobj = tempfile.NamedTemporaryFile(delete=False) |
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150 # close_fobj = True |
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151 # else: |
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152 # # `path` could have been a string or file object or something |
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153 # # similar. In any event, the decorator has given us a file object |
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154 # # and it will close it for us, if it should. |
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155 # fobj = path |
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156 # close_fobj = False |
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157 # |
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158 # try: |
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159 # fobj.write('blah') |
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160 # finally: |
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161 # if close_fobj: |
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162 # fobj.close() |
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163 # |
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164 # Normally, we'd want to use "with" to ensure that fobj gets closed. |
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165 # However, recall that the decorator will make `path` a file object for |
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166 # us, and using "with" would undesirably close that file object. Instead, |
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167 # you use a try block, as shown above. When we exit the function, fobj will |
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168 # be closed, if it should be, by the decorator. |
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169 |
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170 @decorator |
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171 def _open_file(func_to_be_decorated, *args, **kwargs): |
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172 |
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173 # Note that since we have used @decorator, *args, and **kwargs have |
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174 # already been resolved to match the function signature of func. This |
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175 # means default values have been propagated. For example, the function |
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176 # func(x, y, a=1, b=2, **kwargs) if called as func(0,1,b=5,c=10) would |
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177 # have args=(0,1,1,5) and kwargs={'c':10}. |
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178 |
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179 # First we parse the arguments of the decorator. The path_arg could |
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180 # be an positional argument or a keyword argument. Even if it is |
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181 try: |
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182 # path_arg is a required positional argument |
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183 # This works precisely because we are using @decorator |
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184 path = args[path_arg] |
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185 except TypeError: |
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186 # path_arg is a keyword argument. It is "required" in the sense |
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187 # that it must exist, according to the decorator specification, |
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188 # It can exist in `kwargs` by a developer specified default value |
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189 # or it could have been explicitly set by the user. |
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190 try: |
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191 path = kwargs[path_arg] |
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192 except KeyError as e: |
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193 # Could not find the keyword. Thus, no default was specified |
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194 # in the function signature and the user did not provide it. |
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195 msg = f"Missing required keyword argument: {path_arg}" |
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196 raise nx.NetworkXError(msg) from e |
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197 else: |
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198 is_kwarg = True |
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199 except IndexError as e: |
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200 # A "required" argument was missing. This can only happen if |
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201 # the decorator of the function was incorrectly specified. |
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202 # So this probably is not a user error, but a developer error. |
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203 msg = "path_arg of open_file decorator is incorrect" |
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204 raise nx.NetworkXError(msg) from e |
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205 else: |
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206 is_kwarg = False |
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207 |
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208 # Now we have the path_arg. There are two types of input to consider: |
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209 # 1) string representing a path that should be opened |
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210 # 2) an already opened file object |
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211 if isinstance(path, str): |
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212 ext = splitext(path)[1] |
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213 fobj = _dispatch_dict[ext](path, mode=mode) |
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214 close_fobj = True |
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215 elif hasattr(path, "read"): |
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216 # path is already a file-like object |
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217 fobj = path |
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218 close_fobj = False |
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219 elif isinstance(path, Path): |
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220 # path is a pathlib reference to a filename |
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221 fobj = _dispatch_dict[path.suffix](str(path), mode=mode) |
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222 close_fobj = True |
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223 else: |
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224 # could be None, in which case the algorithm will deal with it |
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225 fobj = path |
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226 close_fobj = False |
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227 |
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228 # Insert file object into args or kwargs. |
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229 if is_kwarg: |
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230 new_args = args |
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231 kwargs[path_arg] = fobj |
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232 else: |
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233 # args is a tuple, so we must convert to list before modifying it. |
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234 new_args = list(args) |
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235 new_args[path_arg] = fobj |
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236 |
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237 # Finally, we call the original function, making sure to close the fobj |
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238 try: |
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239 result = func_to_be_decorated(*new_args, **kwargs) |
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240 finally: |
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241 if close_fobj: |
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242 fobj.close() |
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243 |
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244 return result |
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245 |
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246 return _open_file |
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247 |
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248 |
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249 def nodes_or_number(which_args): |
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250 """Decorator to allow number of nodes or container of nodes. |
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251 |
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252 Parameters |
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253 ---------- |
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254 which_args : int or sequence of ints |
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255 Location of the node arguments in args. Even if the argument is a |
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256 named positional argument (with a default value), you must specify its |
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257 index as a positional argument. |
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258 If more than one node argument is allowed, can be a list of locations. |
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259 |
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260 Returns |
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261 ------- |
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262 _nodes_or_numbers : function |
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263 Function which replaces int args with ranges. |
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264 |
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265 Examples |
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266 -------- |
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267 Decorate functions like this:: |
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268 |
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269 @nodes_or_number(0) |
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270 def empty_graph(nodes): |
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271 pass |
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272 |
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273 @nodes_or_number([0,1]) |
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274 def grid_2d_graph(m1, m2, periodic=False): |
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275 pass |
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276 |
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277 @nodes_or_number(1) |
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278 def full_rary_tree(r, n) |
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279 # r is a number. n can be a number of a list of nodes |
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280 pass |
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281 """ |
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282 |
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283 @decorator |
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284 def _nodes_or_number(func_to_be_decorated, *args, **kw): |
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285 # form tuple of arg positions to be converted. |
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286 try: |
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287 iter_wa = iter(which_args) |
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288 except TypeError: |
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289 iter_wa = (which_args,) |
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290 # change each argument in turn |
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291 new_args = list(args) |
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292 for i in iter_wa: |
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293 n = args[i] |
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294 try: |
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295 nodes = list(range(n)) |
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296 except TypeError: |
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297 nodes = tuple(n) |
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298 else: |
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299 if n < 0: |
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300 msg = "Negative number of nodes not valid: {n}" |
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301 raise nx.NetworkXError(msg) |
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302 new_args[i] = (n, nodes) |
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303 return func_to_be_decorated(*new_args, **kw) |
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304 |
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305 return _nodes_or_number |
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306 |
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307 |
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308 def preserve_random_state(func): |
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309 """ Decorator to preserve the numpy.random state during a function. |
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310 |
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311 Parameters |
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312 ---------- |
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313 func : function |
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314 function around which to preserve the random state. |
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315 |
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316 Returns |
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317 ------- |
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318 wrapper : function |
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319 Function which wraps the input function by saving the state before |
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320 calling the function and restoring the function afterward. |
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321 |
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322 Examples |
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323 -------- |
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324 Decorate functions like this:: |
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325 |
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326 @preserve_random_state |
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327 def do_random_stuff(x, y): |
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328 return x + y * numpy.random.random() |
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329 |
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330 Notes |
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331 ----- |
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332 If numpy.random is not importable, the state is not saved or restored. |
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333 """ |
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334 try: |
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335 from numpy.random import get_state, seed, set_state |
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336 |
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337 @contextmanager |
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338 def save_random_state(): |
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339 state = get_state() |
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340 try: |
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341 yield |
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342 finally: |
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343 set_state(state) |
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344 |
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345 def wrapper(*args, **kwargs): |
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346 with save_random_state(): |
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347 seed(1234567890) |
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348 return func(*args, **kwargs) |
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349 |
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350 wrapper.__name__ = func.__name__ |
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351 return wrapper |
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352 except ImportError: |
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353 return func |
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354 |
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355 |
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356 def random_state(random_state_index): |
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357 """Decorator to generate a numpy.random.RandomState instance. |
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358 |
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359 Argument position `random_state_index` is processed by create_random_state. |
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360 The result is a numpy.random.RandomState instance. |
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361 |
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362 Parameters |
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363 ---------- |
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364 random_state_index : int |
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365 Location of the random_state argument in args that is to be used to |
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366 generate the numpy.random.RandomState instance. Even if the argument is |
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367 a named positional argument (with a default value), you must specify |
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368 its index as a positional argument. |
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369 |
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370 Returns |
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371 ------- |
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372 _random_state : function |
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373 Function whose random_state keyword argument is a RandomState instance. |
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374 |
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375 Examples |
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376 -------- |
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377 Decorate functions like this:: |
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378 |
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379 @np_random_state(0) |
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380 def random_float(random_state=None): |
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381 return random_state.rand() |
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382 |
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383 @np_random_state(1) |
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384 def random_array(dims, random_state=1): |
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385 return random_state.rand(*dims) |
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386 |
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387 See Also |
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388 -------- |
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389 py_random_state |
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390 """ |
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391 |
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392 @decorator |
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393 def _random_state(func, *args, **kwargs): |
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394 # Parse the decorator arguments. |
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395 try: |
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396 random_state_arg = args[random_state_index] |
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397 except TypeError as e: |
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398 raise nx.NetworkXError("random_state_index must be an integer") from e |
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399 except IndexError as e: |
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400 raise nx.NetworkXError("random_state_index is incorrect") from e |
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401 |
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402 # Create a numpy.random.RandomState instance |
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403 random_state = create_random_state(random_state_arg) |
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404 |
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405 # args is a tuple, so we must convert to list before modifying it. |
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406 new_args = list(args) |
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407 new_args[random_state_index] = random_state |
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408 return func(*new_args, **kwargs) |
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409 |
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410 return _random_state |
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411 |
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412 |
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413 np_random_state = random_state |
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414 |
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415 |
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416 def py_random_state(random_state_index): |
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417 """Decorator to generate a random.Random instance (or equiv). |
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418 |
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419 Argument position `random_state_index` processed by create_py_random_state. |
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420 The result is either a random.Random instance, or numpy.random.RandomState |
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421 instance with additional attributes to mimic basic methods of Random. |
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422 |
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423 Parameters |
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424 ---------- |
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425 random_state_index : int |
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426 Location of the random_state argument in args that is to be used to |
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427 generate the numpy.random.RandomState instance. Even if the argument is |
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428 a named positional argument (with a default value), you must specify |
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429 its index as a positional argument. |
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430 |
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431 Returns |
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432 ------- |
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433 _random_state : function |
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434 Function whose random_state keyword argument is a RandomState instance. |
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435 |
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436 Examples |
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437 -------- |
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438 Decorate functions like this:: |
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439 |
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440 @py_random_state(0) |
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441 def random_float(random_state=None): |
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442 return random_state.rand() |
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443 |
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444 @py_random_state(1) |
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445 def random_array(dims, random_state=1): |
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446 return random_state.rand(*dims) |
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447 |
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448 See Also |
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449 -------- |
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450 np_random_state |
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451 """ |
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452 |
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453 @decorator |
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454 def _random_state(func, *args, **kwargs): |
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455 # Parse the decorator arguments. |
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456 try: |
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457 random_state_arg = args[random_state_index] |
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458 except TypeError as e: |
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459 raise nx.NetworkXError("random_state_index must be an integer") from e |
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460 except IndexError as e: |
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461 raise nx.NetworkXError("random_state_index is incorrect") from e |
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462 |
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463 # Create a numpy.random.RandomState instance |
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464 random_state = create_py_random_state(random_state_arg) |
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465 |
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466 # args is a tuple, so we must convert to list before modifying it. |
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467 new_args = list(args) |
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468 new_args[random_state_index] = random_state |
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469 return func(*new_args, **kwargs) |
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470 |
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471 return _random_state |