okstra 0.107.2 → 0.109.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (649) hide show
  1. package/package.json +1 -1
  2. package/runtime/BUILD.json +2 -2
  3. package/runtime/prompts/lead/okstra-lead-contract.md +1 -1
  4. package/runtime/prompts/profiles/_common-contract.md +3 -2
  5. package/runtime/python/okstra_ctl/graphify_cmd.py +225 -0
  6. package/runtime/python/okstra_ctl/resolve_task_key.py +15 -9
  7. package/runtime/python/okstra_ctl/session.py +44 -0
  8. package/runtime/python/okstra_project/__init__.py +2 -0
  9. package/runtime/python/okstra_project/state.py +36 -0
  10. package/runtime/python/okstra_token_usage/claude.py +15 -9
  11. package/runtime/python/okstra_token_usage/cli.py +23 -0
  12. package/runtime/python/okstra_token_usage/collect.py +163 -4
  13. package/runtime/python/okstra_vendor/__init__.py +41 -0
  14. package/runtime/python/okstra_vendor/graphify/.vendored-version +1 -0
  15. package/runtime/python/okstra_vendor/graphify/__init__.py +28 -0
  16. package/runtime/python/okstra_vendor/graphify/__main__.py +1371 -0
  17. package/runtime/python/okstra_vendor/graphify/analyze.py +540 -0
  18. package/runtime/python/okstra_vendor/graphify/benchmark.py +129 -0
  19. package/runtime/python/okstra_vendor/graphify/build.py +107 -0
  20. package/runtime/python/okstra_vendor/graphify/cache.py +169 -0
  21. package/runtime/python/okstra_vendor/graphify/cluster.py +137 -0
  22. package/runtime/python/okstra_vendor/graphify/detect.py +510 -0
  23. package/runtime/python/okstra_vendor/graphify/export.py +1014 -0
  24. package/runtime/python/okstra_vendor/graphify/extract.py +3277 -0
  25. package/runtime/python/okstra_vendor/graphify/hooks.py +220 -0
  26. package/runtime/python/okstra_vendor/graphify/ingest.py +297 -0
  27. package/runtime/python/okstra_vendor/graphify/manifest.py +4 -0
  28. package/runtime/python/okstra_vendor/graphify/report.py +175 -0
  29. package/runtime/python/okstra_vendor/graphify/security.py +203 -0
  30. package/runtime/python/okstra_vendor/graphify/serve.py +373 -0
  31. package/runtime/python/okstra_vendor/graphify/skill-aider.md +1184 -0
  32. package/runtime/python/okstra_vendor/graphify/skill-claw.md +1184 -0
  33. package/runtime/python/okstra_vendor/graphify/skill-codex.md +1242 -0
  34. package/runtime/python/okstra_vendor/graphify/skill-copilot.md +1268 -0
  35. package/runtime/python/okstra_vendor/graphify/skill-droid.md +1239 -0
  36. package/runtime/python/okstra_vendor/graphify/skill-kiro.md +1183 -0
  37. package/runtime/python/okstra_vendor/graphify/skill-opencode.md +1238 -0
  38. package/runtime/python/okstra_vendor/graphify/skill-trae.md +1208 -0
  39. package/runtime/python/okstra_vendor/graphify/skill-vscode.md +253 -0
  40. package/runtime/python/okstra_vendor/graphify/skill-windows.md +1245 -0
  41. package/runtime/python/okstra_vendor/graphify/skill.md +1319 -0
  42. package/runtime/python/okstra_vendor/graphify/transcribe.py +182 -0
  43. package/runtime/python/okstra_vendor/graphify/validate.py +72 -0
  44. package/runtime/python/okstra_vendor/graphify/watch.py +188 -0
  45. package/runtime/python/okstra_vendor/graphify/wiki.py +214 -0
  46. package/runtime/python/okstra_vendor/networkx/__init__.py +62 -0
  47. package/runtime/python/okstra_vendor/networkx/algorithms/__init__.py +134 -0
  48. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/__init__.py +26 -0
  49. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clique.py +259 -0
  50. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clustering_coefficient.py +71 -0
  51. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/connectivity.py +412 -0
  52. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/density.py +396 -0
  53. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/distance_measures.py +150 -0
  54. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/dominating_set.py +149 -0
  55. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/kcomponents.py +369 -0
  56. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/matching.py +44 -0
  57. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/maxcut.py +143 -0
  58. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/ramsey.py +53 -0
  59. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/steinertree.py +265 -0
  60. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/__init__.py +0 -0
  61. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_approx_clust_coeff.py +41 -0
  62. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_clique.py +112 -0
  63. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_connectivity.py +199 -0
  64. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_density.py +146 -0
  65. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_distance_measures.py +59 -0
  66. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_dominating_set.py +78 -0
  67. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_kcomponents.py +303 -0
  68. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_matching.py +8 -0
  69. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_maxcut.py +94 -0
  70. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_ramsey.py +31 -0
  71. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_steinertree.py +306 -0
  72. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_traveling_salesman.py +1014 -0
  73. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_treewidth.py +274 -0
  74. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_vertex_cover.py +68 -0
  75. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/traveling_salesman.py +1508 -0
  76. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/treewidth.py +255 -0
  77. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/vertex_cover.py +83 -0
  78. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/__init__.py +5 -0
  79. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/connectivity.py +122 -0
  80. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/correlation.py +302 -0
  81. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/mixing.py +255 -0
  82. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/neighbor_degree.py +160 -0
  83. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/pairs.py +127 -0
  84. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/__init__.py +0 -0
  85. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/base_test.py +81 -0
  86. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_connectivity.py +143 -0
  87. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_correlation.py +122 -0
  88. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_mixing.py +174 -0
  89. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_neighbor_degree.py +107 -0
  90. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_pairs.py +87 -0
  91. package/runtime/python/okstra_vendor/networkx/algorithms/asteroidal.py +164 -0
  92. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/__init__.py +88 -0
  93. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/basic.py +322 -0
  94. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/centrality.py +290 -0
  95. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/cluster.py +289 -0
  96. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/covering.py +57 -0
  97. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/edgelist.py +360 -0
  98. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/extendability.py +105 -0
  99. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/generators.py +603 -0
  100. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/link_analysis.py +316 -0
  101. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matching.py +590 -0
  102. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matrix.py +232 -0
  103. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/projection.py +526 -0
  104. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/redundancy.py +112 -0
  105. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/spectral.py +69 -0
  106. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/__init__.py +0 -0
  107. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_basic.py +125 -0
  108. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_centrality.py +192 -0
  109. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_cluster.py +84 -0
  110. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_covering.py +33 -0
  111. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_edgelist.py +240 -0
  112. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_extendability.py +334 -0
  113. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_generators.py +407 -0
  114. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_link_analysis.py +218 -0
  115. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_matching.py +327 -0
  116. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_matrix.py +138 -0
  117. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_project.py +409 -0
  118. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_redundancy.py +35 -0
  119. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_spectral_bipartivity.py +80 -0
  120. package/runtime/python/okstra_vendor/networkx/algorithms/boundary.py +168 -0
  121. package/runtime/python/okstra_vendor/networkx/algorithms/bridges.py +205 -0
  122. package/runtime/python/okstra_vendor/networkx/algorithms/broadcasting.py +164 -0
  123. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/__init__.py +20 -0
  124. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness.py +591 -0
  125. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness_subset.py +236 -0
  126. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/closeness.py +282 -0
  127. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness.py +364 -0
  128. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness_subset.py +227 -0
  129. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_closeness.py +96 -0
  130. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/degree_alg.py +150 -0
  131. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/dispersion.py +107 -0
  132. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/eigenvector.py +357 -0
  133. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/flow_matrix.py +130 -0
  134. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/group.py +787 -0
  135. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/harmonic.py +88 -0
  136. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/katz.py +331 -0
  137. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/laplacian.py +150 -0
  138. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/load.py +200 -0
  139. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/percolation.py +128 -0
  140. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/reaching.py +209 -0
  141. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/second_order.py +141 -0
  142. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/subgraph_alg.py +361 -0
  143. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/__init__.py +0 -0
  144. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_betweenness_centrality.py +923 -0
  145. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_betweenness_centrality_subset.py +354 -0
  146. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_closeness_centrality.py +274 -0
  147. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_betweenness_centrality.py +259 -0
  148. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_betweenness_centrality_subset.py +147 -0
  149. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_closeness.py +43 -0
  150. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_degree_centrality.py +144 -0
  151. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_dispersion.py +73 -0
  152. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_eigenvector_centrality.py +186 -0
  153. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_group.py +277 -0
  154. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_harmonic_centrality.py +122 -0
  155. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_katz_centrality.py +345 -0
  156. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_laplacian_centrality.py +220 -0
  157. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_load_centrality.py +344 -0
  158. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_percolation_centrality.py +87 -0
  159. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_reaching.py +140 -0
  160. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_second_order_centrality.py +82 -0
  161. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_subgraph.py +110 -0
  162. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_trophic.py +302 -0
  163. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_voterank.py +64 -0
  164. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/trophic.py +181 -0
  165. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/voterank_alg.py +95 -0
  166. package/runtime/python/okstra_vendor/networkx/algorithms/chains.py +172 -0
  167. package/runtime/python/okstra_vendor/networkx/algorithms/chordal.py +443 -0
  168. package/runtime/python/okstra_vendor/networkx/algorithms/clique.py +818 -0
  169. package/runtime/python/okstra_vendor/networkx/algorithms/cluster.py +732 -0
  170. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/__init__.py +4 -0
  171. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/equitable_coloring.py +505 -0
  172. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/greedy_coloring.py +565 -0
  173. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/tests/__init__.py +0 -0
  174. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/tests/test_coloring.py +863 -0
  175. package/runtime/python/okstra_vendor/networkx/algorithms/communicability_alg.py +163 -0
  176. package/runtime/python/okstra_vendor/networkx/algorithms/community/__init__.py +28 -0
  177. package/runtime/python/okstra_vendor/networkx/algorithms/community/asyn_fluid.py +153 -0
  178. package/runtime/python/okstra_vendor/networkx/algorithms/community/bipartitions.py +354 -0
  179. package/runtime/python/okstra_vendor/networkx/algorithms/community/centrality.py +171 -0
  180. package/runtime/python/okstra_vendor/networkx/algorithms/community/community_utils.py +30 -0
  181. package/runtime/python/okstra_vendor/networkx/algorithms/community/divisive.py +216 -0
  182. package/runtime/python/okstra_vendor/networkx/algorithms/community/kclique.py +79 -0
  183. package/runtime/python/okstra_vendor/networkx/algorithms/community/label_propagation.py +338 -0
  184. package/runtime/python/okstra_vendor/networkx/algorithms/community/leiden.py +162 -0
  185. package/runtime/python/okstra_vendor/networkx/algorithms/community/local.py +220 -0
  186. package/runtime/python/okstra_vendor/networkx/algorithms/community/louvain.py +384 -0
  187. package/runtime/python/okstra_vendor/networkx/algorithms/community/lukes.py +227 -0
  188. package/runtime/python/okstra_vendor/networkx/algorithms/community/modularity_max.py +452 -0
  189. package/runtime/python/okstra_vendor/networkx/algorithms/community/quality.py +347 -0
  190. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/__init__.py +0 -0
  191. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_asyn_fluid.py +147 -0
  192. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_bipartitions.py +157 -0
  193. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_centrality.py +85 -0
  194. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_divisive.py +106 -0
  195. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_kclique.py +91 -0
  196. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_label_propagation.py +241 -0
  197. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_leiden.py +138 -0
  198. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_local.py +76 -0
  199. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_louvain.py +264 -0
  200. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_lukes.py +152 -0
  201. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_modularity_max.py +340 -0
  202. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_quality.py +139 -0
  203. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_utils.py +26 -0
  204. package/runtime/python/okstra_vendor/networkx/algorithms/components/__init__.py +6 -0
  205. package/runtime/python/okstra_vendor/networkx/algorithms/components/attracting.py +115 -0
  206. package/runtime/python/okstra_vendor/networkx/algorithms/components/biconnected.py +394 -0
  207. package/runtime/python/okstra_vendor/networkx/algorithms/components/connected.py +282 -0
  208. package/runtime/python/okstra_vendor/networkx/algorithms/components/semiconnected.py +71 -0
  209. package/runtime/python/okstra_vendor/networkx/algorithms/components/strongly_connected.py +359 -0
  210. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/__init__.py +0 -0
  211. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_attracting.py +70 -0
  212. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_biconnected.py +248 -0
  213. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_connected.py +138 -0
  214. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_semiconnected.py +55 -0
  215. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_strongly_connected.py +193 -0
  216. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_weakly_connected.py +96 -0
  217. package/runtime/python/okstra_vendor/networkx/algorithms/components/weakly_connected.py +196 -0
  218. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/__init__.py +11 -0
  219. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/connectivity.py +811 -0
  220. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/cuts.py +616 -0
  221. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/disjoint_paths.py +408 -0
  222. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_augmentation.py +1270 -0
  223. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_kcomponents.py +592 -0
  224. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcomponents.py +220 -0
  225. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcutsets.py +235 -0
  226. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/stoerwagner.py +152 -0
  227. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/__init__.py +0 -0
  228. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_connectivity.py +421 -0
  229. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_cuts.py +309 -0
  230. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_disjoint_paths.py +249 -0
  231. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_edge_augmentation.py +502 -0
  232. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_edge_kcomponents.py +488 -0
  233. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_kcomponents.py +323 -0
  234. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_kcutsets.py +280 -0
  235. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_stoer_wagner.py +102 -0
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@@ -0,0 +1,732 @@
1
+ """Algorithms to characterize the number of triangles in a graph."""
2
+
3
+ from collections import Counter
4
+ from itertools import chain, combinations
5
+
6
+ import networkx as nx
7
+ from networkx.utils import not_implemented_for
8
+
9
+ __all__ = [
10
+ "triangles",
11
+ "all_triangles",
12
+ "average_clustering",
13
+ "clustering",
14
+ "transitivity",
15
+ "square_clustering",
16
+ "generalized_degree",
17
+ ]
18
+
19
+
20
+ @not_implemented_for("directed")
21
+ @nx._dispatchable
22
+ def triangles(G, nodes=None):
23
+ """Compute the number of triangles.
24
+
25
+ Finds the number of triangles that include a node as one vertex.
26
+
27
+ Parameters
28
+ ----------
29
+ G : graph
30
+ A networkx graph
31
+
32
+ nodes : node, iterable of nodes, or None (default=None)
33
+ If a singleton node, return the number of triangles for that node.
34
+ If an iterable, compute the number of triangles for each of those nodes.
35
+ If `None` (the default) compute the number of triangles for all nodes in `G`.
36
+
37
+ Returns
38
+ -------
39
+ out : dict or int
40
+ If `nodes` is a container of nodes, returns number of triangles keyed by node (dict).
41
+ If `nodes` is a specific node, returns number of triangles for the node (int).
42
+
43
+ Examples
44
+ --------
45
+ >>> G = nx.complete_graph(5)
46
+ >>> print(nx.triangles(G, 0))
47
+ 6
48
+ >>> print(nx.triangles(G))
49
+ {0: 6, 1: 6, 2: 6, 3: 6, 4: 6}
50
+ >>> print(list(nx.triangles(G, [0, 1]).values()))
51
+ [6, 6]
52
+
53
+ The total number of unique triangles in `G` can be determined by summing
54
+ the number of triangles for each node and dividing by 3 (because a given
55
+ triangle gets counted three times, once for each of its nodes).
56
+
57
+ >>> sum(nx.triangles(G).values()) // 3
58
+ 10
59
+
60
+ Notes
61
+ -----
62
+ Self loops are ignored.
63
+
64
+ """
65
+ if nodes is not None:
66
+ # If `nodes` represents a single node, return only its number of triangles
67
+ if nodes in G:
68
+ return next(_triangles_and_degree_iter(G, nodes))[2] // 2
69
+
70
+ # if `nodes` is a container of nodes, then return a
71
+ # dictionary mapping node to number of triangles.
72
+ return {v: t // 2 for v, d, t, _ in _triangles_and_degree_iter(G, nodes)}
73
+
74
+ # if nodes is None, then compute triangles for the complete graph
75
+
76
+ # dict used to avoid visiting the same nodes twice
77
+ # this allows calculating/counting each triangle only once
78
+ later_nbrs = {}
79
+
80
+ # iterate over the nodes in a graph
81
+ for node, neighbors in G.adjacency():
82
+ later_nbrs[node] = {n for n in neighbors if n not in later_nbrs and n != node}
83
+
84
+ # instantiate Counter for each node to include isolated nodes
85
+ # add 1 to the count if a nodes neighbor's neighbor is also a neighbor
86
+ triangle_counts = Counter(dict.fromkeys(G, 0))
87
+ for node1, neighbors in later_nbrs.items():
88
+ for node2 in neighbors:
89
+ third_nodes = neighbors & later_nbrs[node2]
90
+ m = len(third_nodes)
91
+ triangle_counts[node1] += m
92
+ triangle_counts[node2] += m
93
+ triangle_counts.update(third_nodes)
94
+
95
+ return dict(triangle_counts)
96
+
97
+
98
+ @not_implemented_for("multigraph")
99
+ def _triangles_and_degree_iter(G, nodes=None):
100
+ """Return an iterator of (node, degree, triangles, generalized degree).
101
+
102
+ This double counts triangles so you may want to divide by 2.
103
+ See degree(), triangles() and generalized_degree() for definitions
104
+ and details.
105
+
106
+ """
107
+ if nodes is None:
108
+ nodes_nbrs = G.adj.items()
109
+ else:
110
+ nodes_nbrs = ((n, G[n]) for n in G.nbunch_iter(nodes))
111
+
112
+ for v, v_nbrs in nodes_nbrs:
113
+ vs = set(v_nbrs) - {v}
114
+ gen_degree = Counter(len(vs & (set(G[w]) - {w})) for w in vs)
115
+ ntriangles = sum(k * val for k, val in gen_degree.items())
116
+ yield (v, len(vs), ntriangles, gen_degree)
117
+
118
+
119
+ @not_implemented_for("multigraph")
120
+ def _weighted_triangles_and_degree_iter(G, nodes=None, weight="weight"):
121
+ """Return an iterator of (node, degree, weighted_triangles).
122
+
123
+ Used for weighted clustering.
124
+ Note: this returns the geometric average weight of edges in the triangle.
125
+ Also, each triangle is counted twice (each direction).
126
+ So you may want to divide by 2.
127
+
128
+ """
129
+ import numpy as np
130
+
131
+ if weight is None or G.number_of_edges() == 0:
132
+ max_weight = 1
133
+ else:
134
+ max_weight = max(d.get(weight, 1) for u, v, d in G.edges(data=True))
135
+ if nodes is None:
136
+ nodes_nbrs = G.adj.items()
137
+ else:
138
+ nodes_nbrs = ((n, G[n]) for n in G.nbunch_iter(nodes))
139
+
140
+ def wt(u, v):
141
+ return G[u][v].get(weight, 1) / max_weight
142
+
143
+ for i, nbrs in nodes_nbrs:
144
+ inbrs = set(nbrs) - {i}
145
+ weighted_triangles = 0
146
+ seen = set()
147
+ for j in inbrs:
148
+ seen.add(j)
149
+ # This avoids counting twice -- we double at the end.
150
+ jnbrs = set(G[j]) - seen
151
+ # Only compute the edge weight once, before the inner inner
152
+ # loop.
153
+ wij = wt(i, j)
154
+ weighted_triangles += np.cbrt(
155
+ [(wij * wt(j, k) * wt(k, i)) for k in inbrs & jnbrs]
156
+ ).sum()
157
+ yield (i, len(inbrs), 2 * float(weighted_triangles))
158
+
159
+
160
+ @not_implemented_for("multigraph")
161
+ def _directed_triangles_and_degree_iter(G, nodes=None):
162
+ """Return an iterator of
163
+ (node, total_degree, reciprocal_degree, directed_triangles).
164
+
165
+ Used for directed clustering.
166
+ Note that unlike `_triangles_and_degree_iter()`, this function counts
167
+ directed triangles so does not count triangles twice.
168
+
169
+ """
170
+ nodes_nbrs = ((n, G._pred[n], G._succ[n]) for n in G.nbunch_iter(nodes))
171
+
172
+ for i, preds, succs in nodes_nbrs:
173
+ ipreds = set(preds) - {i}
174
+ isuccs = set(succs) - {i}
175
+
176
+ directed_triangles = 0
177
+ for j in chain(ipreds, isuccs):
178
+ jpreds = set(G._pred[j]) - {j}
179
+ jsuccs = set(G._succ[j]) - {j}
180
+ directed_triangles += sum(
181
+ 1
182
+ for k in chain(
183
+ (ipreds & jpreds),
184
+ (ipreds & jsuccs),
185
+ (isuccs & jpreds),
186
+ (isuccs & jsuccs),
187
+ )
188
+ )
189
+ dtotal = len(ipreds) + len(isuccs)
190
+ dbidirectional = len(ipreds & isuccs)
191
+ yield (i, dtotal, dbidirectional, directed_triangles)
192
+
193
+
194
+ @not_implemented_for("multigraph")
195
+ def _directed_weighted_triangles_and_degree_iter(G, nodes=None, weight="weight"):
196
+ """Return an iterator of
197
+ (node, total_degree, reciprocal_degree, directed_weighted_triangles).
198
+
199
+ Used for directed weighted clustering.
200
+ Note that unlike `_weighted_triangles_and_degree_iter()`, this function counts
201
+ directed triangles so does not count triangles twice.
202
+
203
+ """
204
+ import numpy as np
205
+
206
+ if weight is None or G.number_of_edges() == 0:
207
+ max_weight = 1
208
+ else:
209
+ max_weight = max(d.get(weight, 1) for u, v, d in G.edges(data=True))
210
+
211
+ nodes_nbrs = ((n, G._pred[n], G._succ[n]) for n in G.nbunch_iter(nodes))
212
+
213
+ def wt(u, v):
214
+ return G[u][v].get(weight, 1) / max_weight
215
+
216
+ for i, preds, succs in nodes_nbrs:
217
+ ipreds = set(preds) - {i}
218
+ isuccs = set(succs) - {i}
219
+
220
+ directed_triangles = 0
221
+ for j in ipreds:
222
+ jpreds = set(G._pred[j]) - {j}
223
+ jsuccs = set(G._succ[j]) - {j}
224
+ directed_triangles += np.cbrt(
225
+ [(wt(j, i) * wt(k, i) * wt(k, j)) for k in ipreds & jpreds]
226
+ ).sum()
227
+ directed_triangles += np.cbrt(
228
+ [(wt(j, i) * wt(k, i) * wt(j, k)) for k in ipreds & jsuccs]
229
+ ).sum()
230
+ directed_triangles += np.cbrt(
231
+ [(wt(j, i) * wt(i, k) * wt(k, j)) for k in isuccs & jpreds]
232
+ ).sum()
233
+ directed_triangles += np.cbrt(
234
+ [(wt(j, i) * wt(i, k) * wt(j, k)) for k in isuccs & jsuccs]
235
+ ).sum()
236
+
237
+ for j in isuccs:
238
+ jpreds = set(G._pred[j]) - {j}
239
+ jsuccs = set(G._succ[j]) - {j}
240
+ directed_triangles += np.cbrt(
241
+ [(wt(i, j) * wt(k, i) * wt(k, j)) for k in ipreds & jpreds]
242
+ ).sum()
243
+ directed_triangles += np.cbrt(
244
+ [(wt(i, j) * wt(k, i) * wt(j, k)) for k in ipreds & jsuccs]
245
+ ).sum()
246
+ directed_triangles += np.cbrt(
247
+ [(wt(i, j) * wt(i, k) * wt(k, j)) for k in isuccs & jpreds]
248
+ ).sum()
249
+ directed_triangles += np.cbrt(
250
+ [(wt(i, j) * wt(i, k) * wt(j, k)) for k in isuccs & jsuccs]
251
+ ).sum()
252
+
253
+ dtotal = len(ipreds) + len(isuccs)
254
+ dbidirectional = len(ipreds & isuccs)
255
+ yield (i, dtotal, dbidirectional, float(directed_triangles))
256
+
257
+
258
+ @not_implemented_for("directed")
259
+ @nx._dispatchable
260
+ def all_triangles(G, nbunch=None):
261
+ """
262
+ Yields all unique triangles in an undirected graph.
263
+
264
+ A triangle is a set of three distinct nodes where each node is connected to
265
+ the other two.
266
+
267
+ Parameters
268
+ ----------
269
+ G : NetworkX graph
270
+ An undirected graph.
271
+
272
+ nbunch : node, iterable of nodes, or None (default=None)
273
+ If a node or iterable of nodes, only triangles involving at least one
274
+ node in `nbunch` are yielded.
275
+ If ``None``, yields all unique triangles in the graph.
276
+
277
+ Yields
278
+ ------
279
+ tuple
280
+ A tuple of three nodes forming a triangle ``(u, v, w)``.
281
+
282
+ Examples
283
+ --------
284
+ >>> G = nx.complete_graph(4)
285
+ >>> sorted([sorted(t) for t in all_triangles(G)])
286
+ [[0, 1, 2], [0, 1, 3], [0, 2, 3], [1, 2, 3]]
287
+
288
+ Notes
289
+ -----
290
+ This algorithm ensures each triangle is yielded once using an internal node ordering.
291
+ In multigraphs, triangles are identified by their unique set of nodes,
292
+ ignoring multiple edges between the same nodes. Self-loops are ignored.
293
+ Runs in ``O(m * d)`` time in the worst case, where ``m`` the number of edges
294
+ and ``d`` the maximum degree.
295
+
296
+ See Also
297
+ --------
298
+ :func:`~networkx.algorithms.triads.all_triads` : related function for directed graphs
299
+ """
300
+ if nbunch is None:
301
+ nbunch = relevant_nodes = G
302
+ else:
303
+ nbunch = dict.fromkeys(G.nbunch_iter(nbunch))
304
+ relevant_nodes = chain(
305
+ nbunch,
306
+ (nbr for node in nbunch for nbr in G.neighbors(node) if nbr not in nbunch),
307
+ )
308
+
309
+ node_to_id = {node: i for i, node in enumerate(relevant_nodes)}
310
+
311
+ for u in nbunch:
312
+ u_id = node_to_id[u]
313
+ u_nbrs = G._adj[u].keys()
314
+ for v in u_nbrs:
315
+ v_id = node_to_id.get(v, -1)
316
+ if v_id <= u_id:
317
+ continue
318
+ v_nbrs = G._adj[v].keys()
319
+ for w in v_nbrs & u_nbrs:
320
+ if node_to_id.get(w, -1) > v_id:
321
+ yield u, v, w
322
+
323
+
324
+ @nx._dispatchable(edge_attrs="weight")
325
+ def average_clustering(G, nodes=None, weight=None, count_zeros=True):
326
+ r"""Compute the average clustering coefficient for the graph G.
327
+
328
+ The clustering coefficient for the graph is the average,
329
+
330
+ .. math::
331
+
332
+ C = \frac{1}{n}\sum_{v \in G} c_v,
333
+
334
+ where :math:`n` is the number of nodes in `G`.
335
+
336
+ Parameters
337
+ ----------
338
+ G : graph
339
+
340
+ nodes : container of nodes, optional (default=all nodes in G)
341
+ Compute average clustering for nodes in this container.
342
+
343
+ weight : string or None, optional (default=None)
344
+ The edge attribute that holds the numerical value used as a weight.
345
+ If None, then each edge has weight 1.
346
+
347
+ count_zeros : bool
348
+ If False include only the nodes with nonzero clustering in the average.
349
+
350
+ Returns
351
+ -------
352
+ avg : float
353
+ Average clustering
354
+
355
+ Examples
356
+ --------
357
+ >>> G = nx.complete_graph(5)
358
+ >>> print(nx.average_clustering(G))
359
+ 1.0
360
+
361
+ Notes
362
+ -----
363
+ This is a space saving routine; it might be faster
364
+ to use the clustering function to get a list and then take the average.
365
+
366
+ Self loops are ignored.
367
+
368
+ References
369
+ ----------
370
+ .. [1] Generalizations of the clustering coefficient to weighted
371
+ complex networks by J. Saramäki, M. Kivelä, J.-P. Onnela,
372
+ K. Kaski, and J. Kertész, Physical Review E, 75 027105 (2007).
373
+ http://jponnela.com/web_documents/a9.pdf
374
+ .. [2] Marcus Kaiser, Mean clustering coefficients: the role of isolated
375
+ nodes and leafs on clustering measures for small-world networks.
376
+ https://arxiv.org/abs/0802.2512
377
+ """
378
+ c = clustering(G, nodes, weight=weight).values()
379
+ if not count_zeros:
380
+ c = [v for v in c if abs(v) > 0]
381
+ return sum(c) / len(c)
382
+
383
+
384
+ @nx._dispatchable(edge_attrs="weight")
385
+ def clustering(G, nodes=None, weight=None):
386
+ r"""Compute the clustering coefficient for nodes.
387
+
388
+ For unweighted graphs, the clustering of a node :math:`u`
389
+ is the fraction of possible triangles through that node that exist,
390
+
391
+ .. math::
392
+
393
+ c_u = \frac{2 T(u)}{deg(u)(deg(u)-1)},
394
+
395
+ where :math:`T(u)` is the number of triangles through node :math:`u` and
396
+ :math:`deg(u)` is the degree of :math:`u`.
397
+
398
+ For weighted graphs, there are several ways to define clustering [1]_.
399
+ the one used here is defined
400
+ as the geometric average of the subgraph edge weights [2]_,
401
+
402
+ .. math::
403
+
404
+ c_u = \frac{1}{deg(u)(deg(u)-1))}
405
+ \sum_{vw} (\hat{w}_{uv} \hat{w}_{uw} \hat{w}_{vw})^{1/3}.
406
+
407
+ The edge weights :math:`\hat{w}_{uv}` are normalized by the maximum weight
408
+ in the network :math:`\hat{w}_{uv} = w_{uv}/\max(w)`.
409
+
410
+ The value of :math:`c_u` is assigned to 0 if :math:`deg(u) < 2`.
411
+
412
+ Additionally, this weighted definition has been generalized to support negative edge weights [3]_.
413
+
414
+ For directed graphs, the clustering is similarly defined as the fraction
415
+ of all possible directed triangles or geometric average of the subgraph
416
+ edge weights for unweighted and weighted directed graph respectively [4]_.
417
+
418
+ .. math::
419
+
420
+ c_u = \frac{T(u)}{2(deg^{tot}(u)(deg^{tot}(u)-1) - 2deg^{\leftrightarrow}(u))},
421
+
422
+ where :math:`T(u)` is the number of directed triangles through node
423
+ :math:`u`, :math:`deg^{tot}(u)` is the sum of in degree and out degree of
424
+ :math:`u` and :math:`deg^{\leftrightarrow}(u)` is the reciprocal degree of
425
+ :math:`u`.
426
+
427
+
428
+ Parameters
429
+ ----------
430
+ G : graph
431
+
432
+ nodes : node, iterable of nodes, or None (default=None)
433
+ If a singleton node, return the number of triangles for that node.
434
+ If an iterable, compute the number of triangles for each of those nodes.
435
+ If `None` (the default) compute the number of triangles for all nodes in `G`.
436
+
437
+ weight : string or None, optional (default=None)
438
+ The edge attribute that holds the numerical value used as a weight.
439
+ If None, then each edge has weight 1.
440
+
441
+ Returns
442
+ -------
443
+ out : float, or dictionary
444
+ Clustering coefficient at specified nodes
445
+
446
+ Examples
447
+ --------
448
+ >>> G = nx.complete_graph(5)
449
+ >>> print(nx.clustering(G, 0))
450
+ 1.0
451
+ >>> print(nx.clustering(G))
452
+ {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0, 4: 1.0}
453
+
454
+ Notes
455
+ -----
456
+ Self loops are ignored.
457
+
458
+ References
459
+ ----------
460
+ .. [1] Generalizations of the clustering coefficient to weighted
461
+ complex networks by J. Saramäki, M. Kivelä, J.-P. Onnela,
462
+ K. Kaski, and J. Kertész, Physical Review E, 75 027105 (2007).
463
+ http://jponnela.com/web_documents/a9.pdf
464
+ .. [2] Intensity and coherence of motifs in weighted complex
465
+ networks by J. P. Onnela, J. Saramäki, J. Kertész, and K. Kaski,
466
+ Physical Review E, 71(6), 065103 (2005).
467
+ .. [3] Generalization of Clustering Coefficients to Signed Correlation Networks
468
+ by G. Costantini and M. Perugini, PloS one, 9(2), e88669 (2014).
469
+ .. [4] Clustering in complex directed networks by G. Fagiolo,
470
+ Physical Review E, 76(2), 026107 (2007).
471
+ """
472
+ if G.is_directed():
473
+ if weight is not None:
474
+ td_iter = _directed_weighted_triangles_and_degree_iter(G, nodes, weight)
475
+ clusterc = {
476
+ v: 0 if t == 0 else t / ((dt * (dt - 1) - 2 * db) * 2)
477
+ for v, dt, db, t in td_iter
478
+ }
479
+ else:
480
+ td_iter = _directed_triangles_and_degree_iter(G, nodes)
481
+ clusterc = {
482
+ v: 0 if t == 0 else t / ((dt * (dt - 1) - 2 * db) * 2)
483
+ for v, dt, db, t in td_iter
484
+ }
485
+ else:
486
+ # The formula 2*T/(d*(d-1)) from docs is t/(d*(d-1)) here b/c t==2*T
487
+ if weight is not None:
488
+ td_iter = _weighted_triangles_and_degree_iter(G, nodes, weight)
489
+ clusterc = {v: 0 if t == 0 else t / (d * (d - 1)) for v, d, t in td_iter}
490
+ else:
491
+ td_iter = _triangles_and_degree_iter(G, nodes)
492
+ clusterc = {v: 0 if t == 0 else t / (d * (d - 1)) for v, d, t, _ in td_iter}
493
+ if nodes in G:
494
+ # Return the value of the sole entry in the dictionary.
495
+ return clusterc[nodes]
496
+ return clusterc
497
+
498
+
499
+ @nx._dispatchable
500
+ def transitivity(G):
501
+ r"""Compute graph transitivity, the fraction of all possible triangles
502
+ present in G.
503
+
504
+ Possible triangles are identified by the number of "triads"
505
+ (two edges with a shared vertex).
506
+
507
+ The transitivity is
508
+
509
+ .. math::
510
+
511
+ T = 3\frac{\#triangles}{\#triads}.
512
+
513
+ Parameters
514
+ ----------
515
+ G : graph
516
+
517
+ Returns
518
+ -------
519
+ out : float
520
+ Transitivity
521
+
522
+ Notes
523
+ -----
524
+ Self loops are ignored.
525
+
526
+ Examples
527
+ --------
528
+ >>> G = nx.complete_graph(5)
529
+ >>> print(nx.transitivity(G))
530
+ 1.0
531
+ """
532
+ triangles_contri = [
533
+ (t, d * (d - 1)) for v, d, t, _ in _triangles_and_degree_iter(G)
534
+ ]
535
+ # If the graph is empty
536
+ if len(triangles_contri) == 0:
537
+ return 0
538
+ triangles, contri = map(sum, zip(*triangles_contri))
539
+ return 0 if triangles == 0 else triangles / contri
540
+
541
+
542
+ @nx._dispatchable
543
+ def square_clustering(G, nodes=None):
544
+ r"""Compute the squares clustering coefficient for nodes.
545
+
546
+ For each node return the fraction of possible squares that exist at
547
+ the node [1]_
548
+
549
+ .. math::
550
+ C_4(v) = \frac{ \sum_{u=1}^{k_v}
551
+ \sum_{w=u+1}^{k_v} q_v(u,w) }{ \sum_{u=1}^{k_v}
552
+ \sum_{w=u+1}^{k_v} [a_v(u,w) + q_v(u,w)]},
553
+
554
+ where :math:`q_v(u,w)` are the number of common neighbors of :math:`u` and
555
+ :math:`w` other than :math:`v` (ie squares), and :math:`a_v(u,w) = (k_u -
556
+ (1+q_v(u,w)+\theta_{uv})) + (k_w - (1+q_v(u,w)+\theta_{uw}))`, where
557
+ :math:`\theta_{uw} = 1` if :math:`u` and :math:`w` are connected and 0
558
+ otherwise. [2]_
559
+
560
+ Parameters
561
+ ----------
562
+ G : graph
563
+
564
+ nodes : container of nodes, optional (default=all nodes in G)
565
+ Compute clustering for nodes in this container.
566
+
567
+ Returns
568
+ -------
569
+ c4 : dictionary
570
+ A dictionary keyed by node with the square clustering coefficient value.
571
+
572
+ Examples
573
+ --------
574
+ >>> G = nx.complete_graph(5)
575
+ >>> print(nx.square_clustering(G, 0))
576
+ 1.0
577
+ >>> print(nx.square_clustering(G))
578
+ {0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0, 4: 1.0}
579
+
580
+ Notes
581
+ -----
582
+ Self loops are ignored.
583
+
584
+ While :math:`C_3(v)` (triangle clustering) gives the probability that
585
+ two neighbors of node v are connected with each other, :math:`C_4(v)` is
586
+ the probability that two neighbors of node v share a common
587
+ neighbor different from v. This algorithm can be applied to both
588
+ bipartite and unipartite networks.
589
+
590
+ References
591
+ ----------
592
+ .. [1] Pedro G. Lind, Marta C. González, and Hans J. Herrmann. 2005
593
+ Cycles and clustering in bipartite networks.
594
+ Physical Review E (72) 056127.
595
+ .. [2] Zhang, Peng et al. Clustering Coefficient and Community Structure of
596
+ Bipartite Networks. Physica A: Statistical Mechanics and its Applications 387.27 (2008): 6869–6875.
597
+ https://arxiv.org/abs/0710.0117v1
598
+ """
599
+ if nodes is None:
600
+ node_iter = G
601
+ else:
602
+ node_iter = G.nbunch_iter(nodes)
603
+ clustering = {}
604
+ _G_adj = G._adj
605
+
606
+ class GAdj(dict):
607
+ """Calculate (and cache) node neighbor sets excluding self-loops."""
608
+
609
+ def __missing__(self, v):
610
+ v_neighbors = self[v] = set(_G_adj[v])
611
+ v_neighbors.discard(v) # Ignore self-loops
612
+ return v_neighbors
613
+
614
+ G_adj = GAdj() # Values are sets of neighbors (no self-loops)
615
+
616
+ for v in node_iter:
617
+ v_neighbors = G_adj[v]
618
+ v_degrees_m1 = len(v_neighbors) - 1 # degrees[v] - 1 (used below)
619
+ if v_degrees_m1 <= 0:
620
+ # Can't form a square without at least two neighbors
621
+ clustering[v] = 0
622
+ continue
623
+
624
+ # Count squares with nodes u-v-w-x from the current node v.
625
+ # Terms of the denominator: potential = uw_degrees - uw_count - triangles - squares
626
+ # uw_degrees: degrees[u] + degrees[w] for each u-w combo
627
+ uw_degrees = 0
628
+ # uw_count: 1 for each u and 1 for each w for all combos (degrees * (degrees - 1))
629
+ uw_count = len(v_neighbors) * v_degrees_m1
630
+ # triangles: 1 for each edge where u-w or w-u are connected (i.e. triangles)
631
+ triangles = 0
632
+ # squares: the number of squares (also the numerator)
633
+ squares = 0
634
+
635
+ # Iterate over all neighbors
636
+ for u in v_neighbors:
637
+ u_neighbors = G_adj[u]
638
+ uw_degrees += len(u_neighbors) * v_degrees_m1
639
+ # P2 from https://arxiv.org/abs/2007.11111
640
+ p2 = len(u_neighbors & v_neighbors)
641
+ # triangles is C_3, sigma_4 from https://arxiv.org/abs/2007.11111
642
+ # This double-counts triangles compared to `triangles` function
643
+ triangles += p2
644
+ # squares is C_4, sigma_12 from https://arxiv.org/abs/2007.11111
645
+ # Include this term, b/c a neighbor u can also be a neighbor of neighbor x
646
+ squares += p2 * (p2 - 1) # Will divide by 2 later
647
+
648
+ # And iterate over all neighbors of neighbors.
649
+ # These nodes x may be the corners opposite v in squares u-v-w-x.
650
+ two_hop_neighbors = set.union(*(G_adj[u] for u in v_neighbors))
651
+ two_hop_neighbors -= v_neighbors # Neighbors already counted above
652
+ two_hop_neighbors.discard(v)
653
+ for x in two_hop_neighbors:
654
+ p2 = len(v_neighbors & G_adj[x])
655
+ squares += p2 * (p2 - 1) # Will divide by 2 later
656
+
657
+ squares //= 2
658
+ potential = uw_degrees - uw_count - triangles - squares
659
+ if potential > 0:
660
+ clustering[v] = squares / potential
661
+ else:
662
+ clustering[v] = 0
663
+ if nodes in G:
664
+ # Return the value of the sole entry in the dictionary.
665
+ return clustering[nodes]
666
+ return clustering
667
+
668
+
669
+ @not_implemented_for("directed")
670
+ @nx._dispatchable
671
+ def generalized_degree(G, nodes=None):
672
+ r"""Compute the generalized degree for nodes.
673
+
674
+ For each node, the generalized degree shows how many edges of given
675
+ triangle multiplicity the node is connected to. The triangle multiplicity
676
+ of an edge is the number of triangles an edge participates in. The
677
+ generalized degree of node :math:`i` can be written as a vector
678
+ :math:`\mathbf{k}_i=(k_i^{(0)}, \dotsc, k_i^{(N-2)})` where
679
+ :math:`k_i^{(j)}` is the number of edges attached to node :math:`i` that
680
+ participate in :math:`j` triangles.
681
+
682
+ Parameters
683
+ ----------
684
+ G : graph
685
+
686
+ nodes : container of nodes, optional (default=all nodes in G)
687
+ Compute the generalized degree for nodes in this container.
688
+
689
+ Returns
690
+ -------
691
+ out : Counter, or dictionary of Counters
692
+ Generalized degree of specified nodes. The Counter is keyed by edge
693
+ triangle multiplicity.
694
+
695
+ Examples
696
+ --------
697
+ >>> G = nx.complete_graph(5)
698
+ >>> print(nx.generalized_degree(G, 0))
699
+ Counter({3: 4})
700
+ >>> print(nx.generalized_degree(G))
701
+ {0: Counter({3: 4}), 1: Counter({3: 4}), 2: Counter({3: 4}), 3: Counter({3: 4}), 4: Counter({3: 4})}
702
+
703
+ To recover the number of triangles attached to a node:
704
+
705
+ >>> k1 = nx.generalized_degree(G, 0)
706
+ >>> sum([k * v for k, v in k1.items()]) / 2 == nx.triangles(G, 0)
707
+ True
708
+
709
+ Notes
710
+ -----
711
+ Self loops are ignored.
712
+
713
+ In a network of N nodes, the highest triangle multiplicity an edge can have
714
+ is N-2.
715
+
716
+ The return value does not include a `zero` entry if no edges of a
717
+ particular triangle multiplicity are present.
718
+
719
+ The number of triangles node :math:`i` is attached to can be recovered from
720
+ the generalized degree :math:`\mathbf{k}_i=(k_i^{(0)}, \dotsc,
721
+ k_i^{(N-2)})` by :math:`(k_i^{(1)}+2k_i^{(2)}+\dotsc +(N-2)k_i^{(N-2)})/2`.
722
+
723
+ References
724
+ ----------
725
+ .. [1] Networks with arbitrary edge multiplicities by V. Zlatić,
726
+ D. Garlaschelli and G. Caldarelli, EPL (Europhysics Letters),
727
+ Volume 97, Number 2 (2012).
728
+ https://iopscience.iop.org/article/10.1209/0295-5075/97/28005
729
+ """
730
+ if nodes in G:
731
+ return next(_triangles_and_degree_iter(G, nodes))[3]
732
+ return {v: gd for v, d, t, gd in _triangles_and_degree_iter(G, nodes)}