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annotate planemo/lib/python3.7/site-packages/networkx/readwrite/sparse6.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1 # Original author: D. Eppstein, UC Irvine, August 12, 2003.
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2 # The original code at http://www.ics.uci.edu/~eppstein/PADS/ is public domain.
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3 # Copyright (C) 2004-2019 by
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4 # Aric Hagberg <hagberg@lanl.gov>
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5 # Dan Schult <dschult@colgate.edu>
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6 # Pieter Swart <swart@lanl.gov>
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7 # Tomas Gavenciak <gavento@ucw.cz>
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8 # All rights reserved.
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9 # BSD license.
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10 #
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11 # Authors: Tomas Gavenciak <gavento@ucw.cz>
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12 # Aric Hagberg <aric.hagberg@lanl.gov>
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13 """Functions for reading and writing graphs in the *sparse6* format.
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14
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15 The *sparse6* file format is a space-efficient format for large sparse
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16 graphs. For small graphs or large dense graphs, use the *graph6* file
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17 format.
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18
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19 For more information, see the `sparse6`_ homepage.
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20
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21 .. _sparse6: http://users.cecs.anu.edu.au/~bdm/data/formats.html
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22
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23 """
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24 from itertools import chain
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25 import math
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26 import sys
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27
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28 import networkx as nx
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29 from networkx.exception import NetworkXError
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30 from networkx.utils import open_file, not_implemented_for
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31 from networkx.readwrite.graph6 import data_to_n, n_to_data
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32
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33 __all__ = ['from_sparse6_bytes', 'read_sparse6', 'to_sparse6_bytes',
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34 'write_sparse6']
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35
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36
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37 def _generate_sparse6_bytes(G, nodes, header):
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38 """Yield bytes in the sparse6 encoding of a graph.
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39
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40 `G` is an undirected simple graph. `nodes` is the list of nodes for
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41 which the node-induced subgraph will be encoded; if `nodes` is the
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42 list of all nodes in the graph, the entire graph will be
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43 encoded. `header` is a Boolean that specifies whether to generate
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44 the header ``b'>>sparse6<<'`` before the remaining data.
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45
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46 This function generates `bytes` objects in the following order:
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47
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48 1. the header (if requested),
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49 2. the encoding of the number of nodes,
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50 3. each character, one-at-a-time, in the encoding of the requested
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51 node-induced subgraph,
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52 4. a newline character.
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53
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54 This function raises :exc:`ValueError` if the graph is too large for
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55 the graph6 format (that is, greater than ``2 ** 36`` nodes).
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56
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57 """
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58 n = len(G)
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59 if n >= 2 ** 36:
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60 raise ValueError('sparse6 is only defined if number of nodes is less '
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61 'than 2 ** 36')
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62 if header:
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63 yield b'>>sparse6<<'
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64 yield b':'
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65 for d in n_to_data(n):
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66 yield str.encode(chr(d + 63))
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67
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68 k = 1
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69 while 1 << k < n:
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70 k += 1
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71
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72 def enc(x):
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73 """Big endian k-bit encoding of x"""
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74 return [1 if (x & 1 << (k - 1 - i)) else 0 for i in range(k)]
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75
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76 edges = sorted((max(u, v), min(u, v)) for u, v in G.edges())
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77 bits = []
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78 curv = 0
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79 for (v, u) in edges:
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80 if v == curv: # current vertex edge
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81 bits.append(0)
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82 bits.extend(enc(u))
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83 elif v == curv + 1: # next vertex edge
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84 curv += 1
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85 bits.append(1)
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86 bits.extend(enc(u))
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87 else: # skip to vertex v and then add edge to u
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88 curv = v
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89 bits.append(1)
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90 bits.extend(enc(v))
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91 bits.append(0)
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92 bits.extend(enc(u))
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93 if k < 6 and n == (1 << k) and ((-len(bits)) % 6) >= k and curv < (n - 1):
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94 # Padding special case: small k, n=2^k,
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95 # more than k bits of padding needed,
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96 # current vertex is not (n-1) --
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97 # appending 1111... would add a loop on (n-1)
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98 bits.append(0)
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99 bits.extend([1] * ((-len(bits)) % 6))
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100 else:
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101 bits.extend([1] * ((-len(bits)) % 6))
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102
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103 data = [(bits[i + 0] << 5) + (bits[i + 1] << 4) + (bits[i + 2] << 3) + (bits[i + 3] << 2) +
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104 (bits[i + 4] << 1) + (bits[i + 5] << 0) for i in range(0, len(bits), 6)]
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105
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106 for d in data:
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107 yield str.encode(chr(d + 63))
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108 yield b'\n'
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109
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110
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111 def from_sparse6_bytes(string):
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112 """Read an undirected graph in sparse6 format from string.
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113
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114 Parameters
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115 ----------
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116 string : string
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117 Data in sparse6 format
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118
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119 Returns
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120 -------
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121 G : Graph
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122
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123 Raises
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124 ------
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125 NetworkXError
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126 If the string is unable to be parsed in sparse6 format
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127
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128 Examples
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129 --------
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130 >>> G = nx.from_sparse6_bytes(b':A_')
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131 >>> sorted(G.edges())
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132 [(0, 1), (0, 1), (0, 1)]
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133
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134 See Also
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135 --------
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136 read_sparse6, write_sparse6
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137
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138 References
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139 ----------
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140 .. [1] Sparse6 specification
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141 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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142
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143 """
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144 if string.startswith(b'>>sparse6<<'):
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145 string = string[11:]
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146 if not string.startswith(b':'):
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147 raise NetworkXError('Expected leading colon in sparse6')
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148
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149 if sys.version_info < (3, ):
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150 chars = [ord(c) - 63 for c in string[1:]]
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151 else:
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152 chars = [c - 63 for c in string[1:]]
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153 n, data = data_to_n(chars)
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154 k = 1
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155 while 1 << k < n:
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156 k += 1
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157
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158 def parseData():
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159 """Returns stream of pairs b[i], x[i] for sparse6 format."""
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160 chunks = iter(data)
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161 d = None # partial data word
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162 dLen = 0 # how many unparsed bits are left in d
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163
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164 while 1:
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165 if dLen < 1:
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166 try:
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167 d = next(chunks)
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168 except StopIteration:
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169 return
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170 dLen = 6
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171 dLen -= 1
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172 b = (d >> dLen) & 1 # grab top remaining bit
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173
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174 x = d & ((1 << dLen) - 1) # partially built up value of x
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175 xLen = dLen # how many bits included so far in x
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176 while xLen < k: # now grab full chunks until we have enough
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177 try:
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178 d = next(chunks)
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179 except StopIteration:
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180 return
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181 dLen = 6
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182 x = (x << 6) + d
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183 xLen += 6
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184 x = (x >> (xLen - k)) # shift back the extra bits
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185 dLen = xLen - k
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186 yield b, x
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187
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188 v = 0
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189
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190 G = nx.MultiGraph()
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191 G.add_nodes_from(range(n))
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192
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193 multigraph = False
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194 for b, x in parseData():
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195 if b == 1:
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196 v += 1
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197 # padding with ones can cause overlarge number here
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198 if x >= n or v >= n:
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199 break
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200 elif x > v:
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201 v = x
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202 else:
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203 if G.has_edge(x, v):
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204 multigraph = True
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205 G.add_edge(x, v)
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206 if not multigraph:
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207 G = nx.Graph(G)
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208 return G
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209
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210
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211 def to_sparse6_bytes(G, nodes=None, header=True):
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212 """Convert an undirected graph to bytes in sparse6 format.
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213
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214 Parameters
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215 ----------
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216 G : Graph (undirected)
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217
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218 nodes: list or iterable
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219 Nodes are labeled 0...n-1 in the order provided. If None the ordering
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220 given by ``G.nodes()`` is used.
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221
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222 header: bool
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223 If True add '>>sparse6<<' bytes to head of data.
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224
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225 Raises
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226 ------
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227 NetworkXNotImplemented
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228 If the graph is directed.
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229
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230 ValueError
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231 If the graph has at least ``2 ** 36`` nodes; the sparse6 format
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232 is only defined for graphs of order less than ``2 ** 36``.
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233
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234 Examples
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235 --------
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236 >>> nx.to_sparse6_bytes(nx.path_graph(2)) # doctest: +SKIP
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237 b'>>sparse6<<:An\\n'
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238
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239 See Also
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240 --------
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241 to_sparse6_bytes, read_sparse6, write_sparse6_bytes
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242
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243 Notes
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244 -----
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245 The returned bytes end with a newline character.
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246
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247 The format does not support edge or node labels.
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248
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249 References
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250 ----------
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251 .. [1] Graph6 specification
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252 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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253
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254 """
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255 if nodes is not None:
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256 G = G.subgraph(nodes)
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257 G = nx.convert_node_labels_to_integers(G, ordering='sorted')
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258 return b''.join(_generate_sparse6_bytes(G, nodes, header))
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259
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260
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261 @open_file(0, mode='rb')
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262 def read_sparse6(path):
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263 """Read an undirected graph in sparse6 format from path.
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264
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265 Parameters
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266 ----------
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267 path : file or string
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268 File or filename to write.
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269
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270 Returns
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271 -------
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272 G : Graph/Multigraph or list of Graphs/MultiGraphs
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273 If the file contains multiple lines then a list of graphs is returned
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274
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275 Raises
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276 ------
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277 NetworkXError
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278 If the string is unable to be parsed in sparse6 format
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279
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280 Examples
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281 --------
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282 You can read a sparse6 file by giving the path to the file::
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283
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284 >>> import tempfile
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285 >>> with tempfile.NamedTemporaryFile() as f:
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286 ... _ = f.write(b'>>sparse6<<:An\\n')
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287 ... _ = f.seek(0)
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288 ... G = nx.read_sparse6(f.name)
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289 >>> list(G.edges())
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290 [(0, 1)]
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291
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292 You can also read a sparse6 file by giving an open file-like object::
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293
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294 >>> import tempfile
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295 >>> with tempfile.NamedTemporaryFile() as f:
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296 ... _ = f.write(b'>>sparse6<<:An\\n')
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297 ... _ = f.seek(0)
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298 ... G = nx.read_sparse6(f)
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299 >>> list(G.edges())
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300 [(0, 1)]
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301
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302 See Also
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303 --------
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304 read_sparse6, from_sparse6_bytes
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305
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306 References
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307 ----------
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308 .. [1] Sparse6 specification
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309 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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310
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311 """
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312 glist = []
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313 for line in path:
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314 line = line.strip()
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315 if not len(line):
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316 continue
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317 glist.append(from_sparse6_bytes(line))
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318 if len(glist) == 1:
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319 return glist[0]
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320 else:
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321 return glist
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322
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323
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324 @not_implemented_for('directed')
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325 @open_file(1, mode='wb')
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326 def write_sparse6(G, path, nodes=None, header=True):
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327 """Write graph G to given path in sparse6 format.
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328
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329 Parameters
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330 ----------
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331 G : Graph (undirected)
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332
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333 path : file or string
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334 File or filename to write
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335
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336 nodes: list or iterable
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337 Nodes are labeled 0...n-1 in the order provided. If None the ordering
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338 given by G.nodes() is used.
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339
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340 header: bool
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341 If True add '>>sparse6<<' string to head of data
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342
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343 Raises
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344 ------
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345 NetworkXError
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346 If the graph is directed
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347
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348 Examples
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349 --------
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350 You can write a sparse6 file by giving the path to the file::
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351
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352 >>> import tempfile
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353 >>> with tempfile.NamedTemporaryFile() as f:
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354 ... nx.write_sparse6(nx.path_graph(2), f.name)
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355 ... print(f.read()) # doctest: +SKIP
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356 b'>>sparse6<<:An\\n'
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357
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358 You can also write a sparse6 file by giving an open file-like object::
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359
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360 >>> with tempfile.NamedTemporaryFile() as f:
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361 ... nx.write_sparse6(nx.path_graph(2), f)
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362 ... _ = f.seek(0)
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363 ... print(f.read()) # doctest: +SKIP
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364 b'>>sparse6<<:An\\n'
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365
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366 See Also
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367 --------
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368 read_sparse6, from_sparse6_bytes
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369
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370 Notes
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371 -----
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372 The format does not support edge or node labels.
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373
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374 References
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375 ----------
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376 .. [1] Sparse6 specification
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377 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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378
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379 """
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380 if nodes is not None:
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381 G = G.subgraph(nodes)
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382 G = nx.convert_node_labels_to_integers(G, ordering='sorted')
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383 for b in _generate_sparse6_bytes(G, nodes, header):
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384 path.write(b)