okstra 0.130.4 → 0.131.1

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 (365) hide show
  1. package/README.md +0 -1
  2. package/docs/architecture.md +2 -2
  3. package/docs/cli.md +1 -1
  4. package/docs/for-ai/README.md +0 -2
  5. package/docs/for-ai/skills/okstra-run.md +13 -2
  6. package/docs/for-ai/skills/okstra-setup.md +4 -1
  7. package/docs/project-structure-overview.md +5 -4
  8. package/docs/task-process/implementation-planning.md +13 -0
  9. package/docs/task-process/implementation.md +17 -2
  10. package/package.json +1 -1
  11. package/runtime/BUILD.json +2 -2
  12. package/runtime/agents/workers/report-writer-worker.md +7 -0
  13. package/runtime/bin/lib/okstra/usage.sh +4 -4
  14. package/runtime/prompts/lead/okstra-lead-contract.md +2 -2
  15. package/runtime/prompts/lead/plan-body-verification.md +26 -5
  16. package/runtime/prompts/lead/report-writer.md +6 -2
  17. package/runtime/prompts/profiles/_common-contract.md +2 -1
  18. package/runtime/prompts/profiles/_implementation-deliverable.md +6 -1
  19. package/runtime/prompts/profiles/_implementation-executor.md +2 -2
  20. package/runtime/prompts/profiles/_implementation-verifier.md +33 -10
  21. package/runtime/prompts/profiles/final-verification.md +21 -6
  22. package/runtime/prompts/profiles/implementation-planning.md +16 -4
  23. package/runtime/python/okstra_ctl/codex_dispatch.py +31 -0
  24. package/runtime/python/okstra_ctl/conformance.py +49 -11
  25. package/runtime/python/okstra_ctl/report_finalize.py +52 -1
  26. package/runtime/python/okstra_ctl/run.py +15 -3
  27. package/runtime/python/okstra_ctl/worker_prompt_contract.py +14 -6
  28. package/runtime/python/okstra_ctl/worker_prompt_policy.py +19 -1
  29. package/runtime/python/okstra_vendor/__init__.py +0 -44
  30. package/runtime/schemas/final-report-v1.0.schema.json +99 -5
  31. package/runtime/skills/okstra-run/SKILL.md +11 -4
  32. package/runtime/skills/okstra-setup/SKILL.md +3 -2
  33. package/runtime/skills/okstra-setup/references/project-config.md +16 -7
  34. package/runtime/templates/reports/final-report.template.md +15 -9
  35. package/runtime/templates/reports/i18n/en.json +1 -0
  36. package/runtime/templates/reports/i18n/ko.json +1 -0
  37. package/runtime/validators/lib/fixtures.sh +6 -0
  38. package/runtime/validators/validate-run.py +2019 -96
  39. package/src/cli-registry.mjs +0 -7
  40. package/src/commands/lifecycle/doctor.mjs +0 -9
  41. package/src/lib/skill-catalog.mjs +0 -1
  42. package/docs/for-ai/skills/okstra-graphify.md +0 -64
  43. package/runtime/python/okstra_ctl/graphify_cmd.py +0 -225
  44. package/runtime/python/okstra_vendor/graphify/.vendored-version +0 -1
  45. package/runtime/python/okstra_vendor/graphify/__init__.py +0 -28
  46. package/runtime/python/okstra_vendor/graphify/__main__.py +0 -1371
  47. package/runtime/python/okstra_vendor/graphify/analyze.py +0 -540
  48. package/runtime/python/okstra_vendor/graphify/benchmark.py +0 -129
  49. package/runtime/python/okstra_vendor/graphify/build.py +0 -107
  50. package/runtime/python/okstra_vendor/graphify/cache.py +0 -169
  51. package/runtime/python/okstra_vendor/graphify/cluster.py +0 -137
  52. package/runtime/python/okstra_vendor/graphify/detect.py +0 -510
  53. package/runtime/python/okstra_vendor/graphify/export.py +0 -1014
  54. package/runtime/python/okstra_vendor/graphify/extract.py +0 -3277
  55. package/runtime/python/okstra_vendor/graphify/hooks.py +0 -220
  56. package/runtime/python/okstra_vendor/graphify/ingest.py +0 -297
  57. package/runtime/python/okstra_vendor/graphify/manifest.py +0 -4
  58. package/runtime/python/okstra_vendor/graphify/report.py +0 -175
  59. package/runtime/python/okstra_vendor/graphify/security.py +0 -203
  60. package/runtime/python/okstra_vendor/graphify/serve.py +0 -373
  61. package/runtime/python/okstra_vendor/graphify/skill-aider.md +0 -1184
  62. package/runtime/python/okstra_vendor/graphify/skill-claw.md +0 -1184
  63. package/runtime/python/okstra_vendor/graphify/skill-codex.md +0 -1242
  64. package/runtime/python/okstra_vendor/graphify/skill-copilot.md +0 -1268
  65. package/runtime/python/okstra_vendor/graphify/skill-droid.md +0 -1239
  66. package/runtime/python/okstra_vendor/graphify/skill-kiro.md +0 -1183
  67. package/runtime/python/okstra_vendor/graphify/skill-opencode.md +0 -1238
  68. package/runtime/python/okstra_vendor/graphify/skill-trae.md +0 -1208
  69. package/runtime/python/okstra_vendor/graphify/skill-vscode.md +0 -253
  70. package/runtime/python/okstra_vendor/graphify/skill-windows.md +0 -1245
  71. package/runtime/python/okstra_vendor/graphify/skill.md +0 -1319
  72. package/runtime/python/okstra_vendor/graphify/transcribe.py +0 -182
  73. package/runtime/python/okstra_vendor/graphify/validate.py +0 -72
  74. package/runtime/python/okstra_vendor/graphify/watch.py +0 -188
  75. package/runtime/python/okstra_vendor/graphify/wiki.py +0 -214
  76. package/runtime/python/okstra_vendor/networkx/__init__.py +0 -62
  77. package/runtime/python/okstra_vendor/networkx/algorithms/__init__.py +0 -134
  78. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/__init__.py +0 -26
  79. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clique.py +0 -259
  80. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clustering_coefficient.py +0 -71
  81. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/connectivity.py +0 -412
  82. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/density.py +0 -396
  83. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/distance_measures.py +0 -150
  84. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/dominating_set.py +0 -149
  85. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/kcomponents.py +0 -369
  86. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/matching.py +0 -44
  87. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/maxcut.py +0 -143
  88. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/ramsey.py +0 -53
  89. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/steinertree.py +0 -265
  90. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/traveling_salesman.py +0 -1508
  91. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/treewidth.py +0 -255
  92. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/vertex_cover.py +0 -83
  93. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/__init__.py +0 -5
  94. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/connectivity.py +0 -122
  95. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/correlation.py +0 -302
  96. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/mixing.py +0 -255
  97. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/neighbor_degree.py +0 -160
  98. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/pairs.py +0 -127
  99. package/runtime/python/okstra_vendor/networkx/algorithms/asteroidal.py +0 -164
  100. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/__init__.py +0 -88
  101. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/basic.py +0 -322
  102. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/centrality.py +0 -290
  103. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/cluster.py +0 -289
  104. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/covering.py +0 -57
  105. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/edgelist.py +0 -360
  106. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/extendability.py +0 -105
  107. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/generators.py +0 -603
  108. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/link_analysis.py +0 -316
  109. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matching.py +0 -590
  110. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matrix.py +0 -232
  111. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/projection.py +0 -526
  112. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/redundancy.py +0 -112
  113. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/spectral.py +0 -69
  114. package/runtime/python/okstra_vendor/networkx/algorithms/boundary.py +0 -168
  115. package/runtime/python/okstra_vendor/networkx/algorithms/bridges.py +0 -205
  116. package/runtime/python/okstra_vendor/networkx/algorithms/broadcasting.py +0 -164
  117. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/__init__.py +0 -20
  118. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness.py +0 -591
  119. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness_subset.py +0 -236
  120. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/closeness.py +0 -282
  121. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness.py +0 -364
  122. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness_subset.py +0 -227
  123. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_closeness.py +0 -96
  124. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/degree_alg.py +0 -150
  125. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/dispersion.py +0 -107
  126. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/eigenvector.py +0 -357
  127. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/flow_matrix.py +0 -130
  128. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/group.py +0 -787
  129. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/harmonic.py +0 -88
  130. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/katz.py +0 -331
  131. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/laplacian.py +0 -150
  132. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/load.py +0 -200
  133. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/percolation.py +0 -128
  134. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/reaching.py +0 -209
  135. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/second_order.py +0 -141
  136. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/subgraph_alg.py +0 -361
  137. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/trophic.py +0 -181
  138. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/voterank_alg.py +0 -95
  139. package/runtime/python/okstra_vendor/networkx/algorithms/chains.py +0 -172
  140. package/runtime/python/okstra_vendor/networkx/algorithms/chordal.py +0 -443
  141. package/runtime/python/okstra_vendor/networkx/algorithms/clique.py +0 -818
  142. package/runtime/python/okstra_vendor/networkx/algorithms/cluster.py +0 -732
  143. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/__init__.py +0 -4
  144. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/equitable_coloring.py +0 -505
  145. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/greedy_coloring.py +0 -565
  146. package/runtime/python/okstra_vendor/networkx/algorithms/communicability_alg.py +0 -163
  147. package/runtime/python/okstra_vendor/networkx/algorithms/community/__init__.py +0 -28
  148. package/runtime/python/okstra_vendor/networkx/algorithms/community/asyn_fluid.py +0 -153
  149. package/runtime/python/okstra_vendor/networkx/algorithms/community/bipartitions.py +0 -354
  150. package/runtime/python/okstra_vendor/networkx/algorithms/community/centrality.py +0 -171
  151. package/runtime/python/okstra_vendor/networkx/algorithms/community/community_utils.py +0 -30
  152. package/runtime/python/okstra_vendor/networkx/algorithms/community/divisive.py +0 -216
  153. package/runtime/python/okstra_vendor/networkx/algorithms/community/kclique.py +0 -79
  154. package/runtime/python/okstra_vendor/networkx/algorithms/community/label_propagation.py +0 -338
  155. package/runtime/python/okstra_vendor/networkx/algorithms/community/leiden.py +0 -162
  156. package/runtime/python/okstra_vendor/networkx/algorithms/community/local.py +0 -220
  157. package/runtime/python/okstra_vendor/networkx/algorithms/community/louvain.py +0 -384
  158. package/runtime/python/okstra_vendor/networkx/algorithms/community/lukes.py +0 -227
  159. package/runtime/python/okstra_vendor/networkx/algorithms/community/modularity_max.py +0 -452
  160. package/runtime/python/okstra_vendor/networkx/algorithms/community/quality.py +0 -347
  161. package/runtime/python/okstra_vendor/networkx/algorithms/components/__init__.py +0 -6
  162. package/runtime/python/okstra_vendor/networkx/algorithms/components/attracting.py +0 -115
  163. package/runtime/python/okstra_vendor/networkx/algorithms/components/biconnected.py +0 -394
  164. package/runtime/python/okstra_vendor/networkx/algorithms/components/connected.py +0 -282
  165. package/runtime/python/okstra_vendor/networkx/algorithms/components/semiconnected.py +0 -71
  166. package/runtime/python/okstra_vendor/networkx/algorithms/components/strongly_connected.py +0 -359
  167. package/runtime/python/okstra_vendor/networkx/algorithms/components/weakly_connected.py +0 -196
  168. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/__init__.py +0 -11
  169. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/connectivity.py +0 -811
  170. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/cuts.py +0 -616
  171. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/disjoint_paths.py +0 -408
  172. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_augmentation.py +0 -1270
  173. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_kcomponents.py +0 -592
  174. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcomponents.py +0 -220
  175. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcutsets.py +0 -235
  176. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/stoerwagner.py +0 -152
  177. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/utils.py +0 -88
  178. package/runtime/python/okstra_vendor/networkx/algorithms/core.py +0 -588
  179. package/runtime/python/okstra_vendor/networkx/algorithms/covering.py +0 -142
  180. package/runtime/python/okstra_vendor/networkx/algorithms/cuts.py +0 -416
  181. package/runtime/python/okstra_vendor/networkx/algorithms/cycles.py +0 -1234
  182. package/runtime/python/okstra_vendor/networkx/algorithms/d_separation.py +0 -677
  183. package/runtime/python/okstra_vendor/networkx/algorithms/dag.py +0 -1392
  184. package/runtime/python/okstra_vendor/networkx/algorithms/distance_measures.py +0 -1095
  185. package/runtime/python/okstra_vendor/networkx/algorithms/distance_regular.py +0 -272
  186. package/runtime/python/okstra_vendor/networkx/algorithms/dominance.py +0 -142
  187. package/runtime/python/okstra_vendor/networkx/algorithms/dominating.py +0 -268
  188. package/runtime/python/okstra_vendor/networkx/algorithms/efficiency_measures.py +0 -167
  189. package/runtime/python/okstra_vendor/networkx/algorithms/euler.py +0 -470
  190. package/runtime/python/okstra_vendor/networkx/algorithms/flow/__init__.py +0 -11
  191. package/runtime/python/okstra_vendor/networkx/algorithms/flow/boykovkolmogorov.py +0 -370
  192. package/runtime/python/okstra_vendor/networkx/algorithms/flow/capacityscaling.py +0 -407
  193. package/runtime/python/okstra_vendor/networkx/algorithms/flow/dinitz_alg.py +0 -238
  194. package/runtime/python/okstra_vendor/networkx/algorithms/flow/edmondskarp.py +0 -241
  195. package/runtime/python/okstra_vendor/networkx/algorithms/flow/gomory_hu.py +0 -178
  196. package/runtime/python/okstra_vendor/networkx/algorithms/flow/maxflow.py +0 -611
  197. package/runtime/python/okstra_vendor/networkx/algorithms/flow/mincost.py +0 -356
  198. package/runtime/python/okstra_vendor/networkx/algorithms/flow/networksimplex.py +0 -662
  199. package/runtime/python/okstra_vendor/networkx/algorithms/flow/preflowpush.py +0 -425
  200. package/runtime/python/okstra_vendor/networkx/algorithms/flow/shortestaugmentingpath.py +0 -300
  201. package/runtime/python/okstra_vendor/networkx/algorithms/flow/utils.py +0 -194
  202. package/runtime/python/okstra_vendor/networkx/algorithms/graph_hashing.py +0 -435
  203. package/runtime/python/okstra_vendor/networkx/algorithms/graphical.py +0 -483
  204. package/runtime/python/okstra_vendor/networkx/algorithms/hierarchy.py +0 -57
  205. package/runtime/python/okstra_vendor/networkx/algorithms/hybrid.py +0 -196
  206. package/runtime/python/okstra_vendor/networkx/algorithms/isolate.py +0 -107
  207. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/__init__.py +0 -7
  208. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/ismags.py +0 -1306
  209. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/isomorph.py +0 -336
  210. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/isomorphvf2.py +0 -1262
  211. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/matchhelpers.py +0 -352
  212. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/temporalisomorphvf2.py +0 -308
  213. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/tree_isomorphism.py +0 -264
  214. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/vf2pp.py +0 -1102
  215. package/runtime/python/okstra_vendor/networkx/algorithms/isomorphism/vf2userfunc.py +0 -192
  216. package/runtime/python/okstra_vendor/networkx/algorithms/link_analysis/__init__.py +0 -2
  217. package/runtime/python/okstra_vendor/networkx/algorithms/link_analysis/hits_alg.py +0 -337
  218. package/runtime/python/okstra_vendor/networkx/algorithms/link_analysis/pagerank_alg.py +0 -498
  219. package/runtime/python/okstra_vendor/networkx/algorithms/link_prediction.py +0 -687
  220. package/runtime/python/okstra_vendor/networkx/algorithms/lowest_common_ancestors.py +0 -280
  221. package/runtime/python/okstra_vendor/networkx/algorithms/matching.py +0 -1148
  222. package/runtime/python/okstra_vendor/networkx/algorithms/minors/__init__.py +0 -27
  223. package/runtime/python/okstra_vendor/networkx/algorithms/minors/contraction.py +0 -738
  224. package/runtime/python/okstra_vendor/networkx/algorithms/mis.py +0 -78
  225. package/runtime/python/okstra_vendor/networkx/algorithms/moral.py +0 -59
  226. package/runtime/python/okstra_vendor/networkx/algorithms/node_classification.py +0 -219
  227. package/runtime/python/okstra_vendor/networkx/algorithms/non_randomness.py +0 -155
  228. package/runtime/python/okstra_vendor/networkx/algorithms/operators/__init__.py +0 -4
  229. package/runtime/python/okstra_vendor/networkx/algorithms/operators/all.py +0 -324
  230. package/runtime/python/okstra_vendor/networkx/algorithms/operators/binary.py +0 -468
  231. package/runtime/python/okstra_vendor/networkx/algorithms/operators/product.py +0 -633
  232. package/runtime/python/okstra_vendor/networkx/algorithms/operators/unary.py +0 -77
  233. package/runtime/python/okstra_vendor/networkx/algorithms/perfect_graph.py +0 -73
  234. package/runtime/python/okstra_vendor/networkx/algorithms/planar_drawing.py +0 -464
  235. package/runtime/python/okstra_vendor/networkx/algorithms/planarity.py +0 -1463
  236. package/runtime/python/okstra_vendor/networkx/algorithms/polynomials.py +0 -306
  237. package/runtime/python/okstra_vendor/networkx/algorithms/reciprocity.py +0 -98
  238. package/runtime/python/okstra_vendor/networkx/algorithms/regular.py +0 -167
  239. package/runtime/python/okstra_vendor/networkx/algorithms/richclub.py +0 -138
  240. package/runtime/python/okstra_vendor/networkx/algorithms/shortest_paths/__init__.py +0 -5
  241. package/runtime/python/okstra_vendor/networkx/algorithms/shortest_paths/astar.py +0 -239
  242. package/runtime/python/okstra_vendor/networkx/algorithms/shortest_paths/dense.py +0 -264
  243. package/runtime/python/okstra_vendor/networkx/algorithms/shortest_paths/generic.py +0 -716
  244. package/runtime/python/okstra_vendor/networkx/algorithms/shortest_paths/unweighted.py +0 -625
  245. package/runtime/python/okstra_vendor/networkx/algorithms/shortest_paths/weighted.py +0 -2542
  246. package/runtime/python/okstra_vendor/networkx/algorithms/similarity.py +0 -2107
  247. package/runtime/python/okstra_vendor/networkx/algorithms/simple_paths.py +0 -966
  248. package/runtime/python/okstra_vendor/networkx/algorithms/smallworld.py +0 -404
  249. package/runtime/python/okstra_vendor/networkx/algorithms/smetric.py +0 -30
  250. package/runtime/python/okstra_vendor/networkx/algorithms/sparsifiers.py +0 -296
  251. package/runtime/python/okstra_vendor/networkx/algorithms/structuralholes.py +0 -374
  252. package/runtime/python/okstra_vendor/networkx/algorithms/summarization.py +0 -564
  253. package/runtime/python/okstra_vendor/networkx/algorithms/swap.py +0 -406
  254. package/runtime/python/okstra_vendor/networkx/algorithms/threshold.py +0 -981
  255. package/runtime/python/okstra_vendor/networkx/algorithms/time_dependent.py +0 -142
  256. package/runtime/python/okstra_vendor/networkx/algorithms/tournament.py +0 -406
  257. package/runtime/python/okstra_vendor/networkx/algorithms/traversal/__init__.py +0 -5
  258. package/runtime/python/okstra_vendor/networkx/algorithms/traversal/beamsearch.py +0 -90
  259. package/runtime/python/okstra_vendor/networkx/algorithms/traversal/breadth_first_search.py +0 -576
  260. package/runtime/python/okstra_vendor/networkx/algorithms/traversal/depth_first_search.py +0 -529
  261. package/runtime/python/okstra_vendor/networkx/algorithms/traversal/edgebfs.py +0 -185
  262. package/runtime/python/okstra_vendor/networkx/algorithms/traversal/edgedfs.py +0 -182
  263. package/runtime/python/okstra_vendor/networkx/algorithms/tree/__init__.py +0 -7
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@@ -1,818 +0,0 @@
1
- """Functions for finding and manipulating cliques.
2
-
3
- Finding the largest clique in a graph is NP-complete problem, so most of
4
- these algorithms have an exponential running time; for more information,
5
- see the Wikipedia article on the clique problem [1]_.
6
-
7
- .. [1] clique problem:: https://en.wikipedia.org/wiki/Clique_problem
8
-
9
- """
10
-
11
- from collections import Counter, defaultdict, deque
12
- from itertools import chain, combinations, islice
13
-
14
- import networkx as nx
15
- from networkx.utils import not_implemented_for
16
-
17
- __all__ = [
18
- "find_cliques",
19
- "find_cliques_recursive",
20
- "make_max_clique_graph",
21
- "make_clique_bipartite",
22
- "node_clique_number",
23
- "number_of_cliques",
24
- "enumerate_all_cliques",
25
- "max_weight_clique",
26
- ]
27
-
28
-
29
- @not_implemented_for("directed")
30
- @nx._dispatchable
31
- def enumerate_all_cliques(G):
32
- """Returns all cliques in an undirected graph.
33
-
34
- This function returns an iterator over cliques, each of which is a
35
- list of nodes. The iteration is ordered by cardinality of the
36
- cliques: first all cliques of size one, then all cliques of size
37
- two, etc.
38
-
39
- Parameters
40
- ----------
41
- G : NetworkX graph
42
- An undirected graph.
43
-
44
- Returns
45
- -------
46
- iterator
47
- An iterator over cliques, each of which is a list of nodes in
48
- `G`. The cliques are ordered according to size.
49
-
50
- Notes
51
- -----
52
- To obtain a list of all cliques, use
53
- `list(enumerate_all_cliques(G))`. However, be aware that in the
54
- worst-case, the length of this list can be exponential in the number
55
- of nodes in the graph (for example, when the graph is the complete
56
- graph). This function avoids storing all cliques in memory by only
57
- keeping current candidate node lists in memory during its search.
58
-
59
- The implementation is adapted from the algorithm by Zhang, et
60
- al. (2005) [1]_ to output all cliques discovered.
61
-
62
- This algorithm ignores self-loops and parallel edges, since cliques
63
- are not conventionally defined with such edges.
64
-
65
- References
66
- ----------
67
- .. [1] Yun Zhang, Abu-Khzam, F.N., Baldwin, N.E., Chesler, E.J.,
68
- Langston, M.A., Samatova, N.F.,
69
- "Genome-Scale Computational Approaches to Memory-Intensive
70
- Applications in Systems Biology".
71
- *Supercomputing*, 2005. Proceedings of the ACM/IEEE SC 2005
72
- Conference, pp. 12, 12--18 Nov. 2005.
73
- <https://doi.org/10.1109/SC.2005.29>.
74
-
75
- """
76
- index = {}
77
- nbrs = {}
78
- for u in G:
79
- index[u] = len(index)
80
- # Neighbors of u that appear after u in the iteration order of G.
81
- nbrs[u] = {v for v in G[u] if v not in index}
82
-
83
- queue = deque(([u], sorted(nbrs[u], key=index.__getitem__)) for u in G)
84
- # Loop invariants:
85
- # 1. len(base) is nondecreasing.
86
- # 2. (base + cnbrs) is sorted with respect to the iteration order of G.
87
- # 3. cnbrs is a set of common neighbors of nodes in base.
88
- while queue:
89
- base, cnbrs = map(list, queue.popleft())
90
- yield base
91
- for i, u in enumerate(cnbrs):
92
- # Use generators to reduce memory consumption.
93
- queue.append(
94
- (
95
- chain(base, [u]),
96
- filter(nbrs[u].__contains__, islice(cnbrs, i + 1, None)),
97
- )
98
- )
99
-
100
-
101
- @not_implemented_for("directed")
102
- @nx._dispatchable
103
- def find_cliques(G, nodes=None):
104
- """Returns all maximal cliques in an undirected graph.
105
-
106
- For each node *n*, a *maximal clique for n* is a largest complete
107
- subgraph containing *n*. The largest maximal clique is sometimes
108
- called the *maximum clique*.
109
-
110
- This function returns an iterator over cliques, each of which is a
111
- list of nodes. It is an iterative implementation, so should not
112
- suffer from recursion depth issues.
113
-
114
- This function accepts a list of `nodes` and only the maximal cliques
115
- containing all of these `nodes` are returned. It can considerably speed up
116
- the running time if some specific cliques are desired.
117
-
118
- Parameters
119
- ----------
120
- G : NetworkX graph
121
- An undirected graph.
122
-
123
- nodes : list, optional (default=None)
124
- If provided, only yield *maximal cliques* containing all nodes in `nodes`.
125
- If `nodes` isn't a clique itself, a ValueError is raised.
126
-
127
- Returns
128
- -------
129
- iterator
130
- An iterator over maximal cliques, each of which is a list of
131
- nodes in `G`. If `nodes` is provided, only the maximal cliques
132
- containing all the nodes in `nodes` are returned. The order of
133
- cliques is arbitrary.
134
-
135
- Raises
136
- ------
137
- ValueError
138
- If `nodes` is not a clique.
139
-
140
- Examples
141
- --------
142
- >>> from pprint import pprint # For nice dict formatting
143
- >>> G = nx.karate_club_graph()
144
- >>> sum(1 for c in nx.find_cliques(G)) # The number of maximal cliques in G
145
- 36
146
- >>> max(nx.find_cliques(G), key=len) # The largest maximal clique in G
147
- [0, 1, 2, 3, 13]
148
-
149
- The size of the largest maximal clique is known as the *clique number* of
150
- the graph, which can be found directly with:
151
-
152
- >>> max(len(c) for c in nx.find_cliques(G))
153
- 5
154
-
155
- One can also compute the number of maximal cliques in `G` that contain a given
156
- node. The following produces a dictionary keyed by node whose
157
- values are the number of maximal cliques in `G` that contain the node:
158
-
159
- >>> from collections import Counter
160
- >>> from itertools import chain
161
- >>> counts = Counter(chain.from_iterable(nx.find_cliques(G)))
162
- >>> pprint(dict(counts))
163
- {0: 13,
164
- 1: 6,
165
- 2: 7,
166
- 3: 3,
167
- 4: 2,
168
- 5: 3,
169
- 6: 3,
170
- 7: 1,
171
- 8: 3,
172
- 9: 2,
173
- 10: 2,
174
- 11: 1,
175
- 12: 1,
176
- 13: 2,
177
- 14: 1,
178
- 15: 1,
179
- 16: 1,
180
- 17: 1,
181
- 18: 1,
182
- 19: 2,
183
- 20: 1,
184
- 21: 1,
185
- 22: 1,
186
- 23: 3,
187
- 24: 2,
188
- 25: 2,
189
- 26: 1,
190
- 27: 3,
191
- 28: 2,
192
- 29: 2,
193
- 30: 2,
194
- 31: 4,
195
- 32: 9,
196
- 33: 14}
197
-
198
- Or, similarly, the maximal cliques in `G` that contain a given node.
199
- For example, the 4 maximal cliques that contain node 31:
200
-
201
- >>> [c for c in nx.find_cliques(G) if 31 in c]
202
- [[0, 31], [33, 32, 31], [33, 28, 31], [24, 25, 31]]
203
-
204
- See Also
205
- --------
206
- find_cliques_recursive
207
- A recursive version of the same algorithm.
208
-
209
- Notes
210
- -----
211
- To obtain a list of all maximal cliques, use
212
- `list(find_cliques(G))`. However, be aware that in the worst-case,
213
- the length of this list can be exponential in the number of nodes in
214
- the graph. This function avoids storing all cliques in memory by
215
- only keeping current candidate node lists in memory during its search.
216
-
217
- This implementation is based on the algorithm published by Bron and
218
- Kerbosch (1973) [1]_, as adapted by Tomita, Tanaka and Takahashi
219
- (2006) [2]_ and discussed in Cazals and Karande (2008) [3]_. It
220
- essentially unrolls the recursion used in the references to avoid
221
- issues of recursion stack depth (for a recursive implementation, see
222
- :func:`find_cliques_recursive`).
223
-
224
- This algorithm ignores self-loops and parallel edges, since cliques
225
- are not conventionally defined with such edges.
226
-
227
- References
228
- ----------
229
- .. [1] Bron, C. and Kerbosch, J.
230
- "Algorithm 457: finding all cliques of an undirected graph".
231
- *Communications of the ACM* 16, 9 (Sep. 1973), 575--577.
232
- <http://portal.acm.org/citation.cfm?doid=362342.362367>
233
-
234
- .. [2] Etsuji Tomita, Akira Tanaka, Haruhisa Takahashi,
235
- "The worst-case time complexity for generating all maximal
236
- cliques and computational experiments",
237
- *Theoretical Computer Science*, Volume 363, Issue 1,
238
- Computing and Combinatorics,
239
- 10th Annual International Conference on
240
- Computing and Combinatorics (COCOON 2004), 25 October 2006, Pages 28--42
241
- <https://doi.org/10.1016/j.tcs.2006.06.015>
242
-
243
- .. [3] F. Cazals, C. Karande,
244
- "A note on the problem of reporting maximal cliques",
245
- *Theoretical Computer Science*,
246
- Volume 407, Issues 1--3, 6 November 2008, Pages 564--568,
247
- <https://doi.org/10.1016/j.tcs.2008.05.010>
248
-
249
- """
250
- if len(G) == 0:
251
- return
252
-
253
- adj = {u: {v for v in G[u] if v != u} for u in G}
254
-
255
- # Initialize Q with the given nodes and subg, cand with their nbrs
256
- Q = nodes[:] if nodes is not None else []
257
- cand = set(G)
258
- for node in Q:
259
- if node not in cand:
260
- raise ValueError(f"The given `nodes` {nodes} do not form a clique")
261
- cand &= adj[node]
262
-
263
- if not cand:
264
- yield Q[:]
265
- return
266
-
267
- subg = cand.copy()
268
- stack = []
269
- Q.append(None)
270
-
271
- u = max(subg, key=lambda u: len(cand & adj[u]))
272
- ext_u = cand - adj[u]
273
-
274
- try:
275
- while True:
276
- if ext_u:
277
- q = ext_u.pop()
278
- cand.remove(q)
279
- Q[-1] = q
280
- adj_q = adj[q]
281
- subg_q = subg & adj_q
282
- if not subg_q:
283
- yield Q[:]
284
- else:
285
- cand_q = cand & adj_q
286
- if cand_q:
287
- stack.append((subg, cand, ext_u))
288
- Q.append(None)
289
- subg = subg_q
290
- cand = cand_q
291
- u = max(subg, key=lambda u: len(cand & adj[u]))
292
- ext_u = cand - adj[u]
293
- else:
294
- Q.pop()
295
- subg, cand, ext_u = stack.pop()
296
- except IndexError:
297
- pass
298
-
299
-
300
- @not_implemented_for("directed")
301
- @nx._dispatchable
302
- def find_cliques_recursive(G, nodes=None):
303
- """Returns all maximal cliques in a graph.
304
-
305
- For each node *v*, a *maximal clique for v* is a largest complete
306
- subgraph containing *v*. The largest maximal clique is sometimes
307
- called the *maximum clique*.
308
-
309
- This function returns an iterator over cliques, each of which is a
310
- list of nodes. It is a recursive implementation, so may suffer from
311
- recursion depth issues, but is included for pedagogical reasons.
312
- For a non-recursive implementation, see :func:`find_cliques`.
313
-
314
- This function accepts a list of `nodes` and only the maximal cliques
315
- containing all of these `nodes` are returned. It can considerably speed up
316
- the running time if some specific cliques are desired.
317
-
318
- Parameters
319
- ----------
320
- G : NetworkX graph
321
- An undirected graph.
322
-
323
- nodes : list, optional (default=None)
324
- If provided, only yield *maximal cliques* containing all nodes in `nodes`.
325
- If `nodes` isn't a clique itself, a ValueError is raised.
326
-
327
- Returns
328
- -------
329
- iterator
330
- An iterator over maximal cliques, each of which is a list of
331
- nodes in `G`. If `nodes` is provided, only the maximal cliques
332
- containing all the nodes in `nodes` are yielded. The order of
333
- cliques is arbitrary.
334
-
335
- Raises
336
- ------
337
- NetworkXNotImplemented
338
- If `G` is directed.
339
-
340
- ValueError
341
- If `nodes` is not a clique.
342
-
343
- See Also
344
- --------
345
- find_cliques
346
- An iterative version of the same algorithm. See docstring for examples.
347
-
348
- Notes
349
- -----
350
- To obtain a list of all maximal cliques, use
351
- `list(find_cliques_recursive(G))`. However, be aware that in the
352
- worst-case, the length of this list can be exponential in the number
353
- of nodes in the graph. This function avoids storing all cliques in memory
354
- by only keeping current candidate node lists in memory during its search.
355
-
356
- This implementation is based on the algorithm published by Bron and
357
- Kerbosch (1973) [1]_, as adapted by Tomita, Tanaka and Takahashi
358
- (2006) [2]_ and discussed in Cazals and Karande (2008) [3]_. For a
359
- non-recursive implementation, see :func:`find_cliques`.
360
-
361
- This algorithm ignores self-loops and parallel edges, since cliques
362
- are not conventionally defined with such edges.
363
-
364
- References
365
- ----------
366
- .. [1] Bron, C. and Kerbosch, J.
367
- "Algorithm 457: finding all cliques of an undirected graph".
368
- *Communications of the ACM* 16, 9 (Sep. 1973), 575--577.
369
- <http://portal.acm.org/citation.cfm?doid=362342.362367>
370
-
371
- .. [2] Etsuji Tomita, Akira Tanaka, Haruhisa Takahashi,
372
- "The worst-case time complexity for generating all maximal
373
- cliques and computational experiments",
374
- *Theoretical Computer Science*, Volume 363, Issue 1,
375
- Computing and Combinatorics,
376
- 10th Annual International Conference on
377
- Computing and Combinatorics (COCOON 2004), 25 October 2006, Pages 28--42
378
- <https://doi.org/10.1016/j.tcs.2006.06.015>
379
-
380
- .. [3] F. Cazals, C. Karande,
381
- "A note on the problem of reporting maximal cliques",
382
- *Theoretical Computer Science*,
383
- Volume 407, Issues 1--3, 6 November 2008, Pages 564--568,
384
- <https://doi.org/10.1016/j.tcs.2008.05.010>
385
-
386
- """
387
- if len(G) == 0:
388
- return iter([])
389
-
390
- adj = {u: {v for v in G[u] if v != u} for u in G}
391
-
392
- # Initialize Q with the given nodes and subg, cand with their nbrs
393
- Q = nodes[:] if nodes is not None else []
394
- cand_init = set(G)
395
- for node in Q:
396
- if node not in cand_init:
397
- raise ValueError(f"The given `nodes` {nodes} do not form a clique")
398
- cand_init &= adj[node]
399
-
400
- if not cand_init:
401
- return iter([Q])
402
-
403
- subg_init = cand_init.copy()
404
-
405
- def expand(subg, cand):
406
- u = max(subg, key=lambda u: len(cand & adj[u]))
407
- for q in cand - adj[u]:
408
- cand.remove(q)
409
- Q.append(q)
410
- adj_q = adj[q]
411
- subg_q = subg & adj_q
412
- if not subg_q:
413
- yield Q[:]
414
- else:
415
- cand_q = cand & adj_q
416
- if cand_q:
417
- yield from expand(subg_q, cand_q)
418
- Q.pop()
419
-
420
- return expand(subg_init, cand_init)
421
-
422
-
423
- @nx._dispatchable(returns_graph=True)
424
- def make_max_clique_graph(G, create_using=None):
425
- """Returns the maximal clique graph of the given graph.
426
-
427
- The nodes of the maximal clique graph of `G` are the cliques of
428
- `G` and an edge joins two cliques if the cliques are not disjoint.
429
-
430
- Parameters
431
- ----------
432
- G : NetworkX graph
433
-
434
- create_using : NetworkX graph constructor, optional (default=nx.Graph)
435
- Graph type to create. If graph instance, then cleared before populated.
436
-
437
- Returns
438
- -------
439
- NetworkX graph
440
- A graph whose nodes are the cliques of `G` and whose edges
441
- join two cliques if they are not disjoint.
442
-
443
- Notes
444
- -----
445
- This function behaves like the following code::
446
-
447
- import networkx as nx
448
-
449
- G = nx.make_clique_bipartite(G)
450
- cliques = [v for v in G.nodes() if G.nodes[v]["bipartite"] == 0]
451
- G = nx.bipartite.projected_graph(G, cliques)
452
- G = nx.relabel_nodes(G, {-v: v - 1 for v in G})
453
-
454
- It should be faster, though, since it skips all the intermediate
455
- steps.
456
-
457
- """
458
- if create_using is None:
459
- B = G.__class__()
460
- else:
461
- B = nx.empty_graph(0, create_using)
462
- cliques = list(enumerate(set(c) for c in find_cliques(G)))
463
- # Add a numbered node for each clique.
464
- B.add_nodes_from(i for i, c in cliques)
465
- # Join cliques by an edge if they share a node.
466
- clique_pairs = combinations(cliques, 2)
467
- B.add_edges_from((i, j) for (i, c1), (j, c2) in clique_pairs if c1 & c2)
468
- return B
469
-
470
-
471
- @nx._dispatchable(returns_graph=True)
472
- def make_clique_bipartite(G, fpos=None, create_using=None, name=None):
473
- """Returns the bipartite clique graph corresponding to `G`.
474
-
475
- In the returned bipartite graph, the "bottom" nodes are the nodes of
476
- `G` and the "top" nodes represent the maximal cliques of `G`.
477
- There is an edge from node *v* to clique *C* in the returned graph
478
- if and only if *v* is an element of *C*.
479
-
480
- Parameters
481
- ----------
482
- G : NetworkX graph
483
- An undirected graph.
484
-
485
- fpos : bool
486
- If True or not None, the returned graph will have an
487
- additional attribute, `pos`, a dictionary mapping node to
488
- position in the Euclidean plane.
489
-
490
- create_using : NetworkX graph constructor, optional (default=nx.Graph)
491
- Graph type to create. If graph instance, then cleared before populated.
492
-
493
- Returns
494
- -------
495
- NetworkX graph
496
- A bipartite graph whose "bottom" set is the nodes of the graph
497
- `G`, whose "top" set is the cliques of `G`, and whose edges
498
- join nodes of `G` to the cliques that contain them.
499
-
500
- The nodes of the graph `G` have the node attribute
501
- 'bipartite' set to 1 and the nodes representing cliques
502
- have the node attribute 'bipartite' set to 0, as is the
503
- convention for bipartite graphs in NetworkX.
504
-
505
- """
506
- B = nx.empty_graph(0, create_using)
507
- B.clear()
508
- # The "bottom" nodes in the bipartite graph are the nodes of the
509
- # original graph, G.
510
- B.add_nodes_from(G, bipartite=1)
511
- for i, cl in enumerate(find_cliques(G)):
512
- # The "top" nodes in the bipartite graph are the cliques. These
513
- # nodes get negative numbers as labels.
514
- name = -i - 1
515
- B.add_node(name, bipartite=0)
516
- B.add_edges_from((v, name) for v in cl)
517
- return B
518
-
519
-
520
- @nx._dispatchable
521
- def node_clique_number(G, nodes=None, cliques=None, separate_nodes=False):
522
- """Returns the size of the largest maximal clique containing each given node.
523
-
524
- Returns a single or list depending on input nodes.
525
- An optional list of cliques can be input if already computed.
526
-
527
- Parameters
528
- ----------
529
- G : NetworkX graph
530
- An undirected graph.
531
-
532
- cliques : list, optional (default=None)
533
- A list of cliques, each of which is itself a list of nodes.
534
- If not specified, the list of all cliques will be computed
535
- using :func:`find_cliques`.
536
-
537
- Returns
538
- -------
539
- int or dict
540
- If `nodes` is a single node, returns the size of the
541
- largest maximal clique in `G` containing that node.
542
- Otherwise return a dict keyed by node to the size
543
- of the largest maximal clique containing that node.
544
-
545
- See Also
546
- --------
547
- find_cliques
548
- find_cliques yields the maximal cliques of G.
549
- It accepts a `nodes` argument which restricts consideration to
550
- maximal cliques containing all the given `nodes`.
551
- The search for the cliques is optimized for `nodes`.
552
- number_of_cliques
553
- """
554
- if cliques is None:
555
- if nodes is not None:
556
- # Use ego_graph to decrease size of graph
557
- # check for single node
558
- if nodes in G:
559
- return max(len(c) for c in find_cliques(nx.ego_graph(G, nodes)))
560
- # handle multiple nodes
561
- return {
562
- n: max(len(c) for c in find_cliques(nx.ego_graph(G, n))) for n in nodes
563
- }
564
-
565
- # nodes is None--find all cliques
566
- cliques = list(find_cliques(G))
567
-
568
- # single node requested
569
- if nodes in G:
570
- return max(len(c) for c in cliques if nodes in c)
571
-
572
- # multiple nodes requested
573
- # preprocess all nodes (faster than one at a time for even 2 nodes)
574
- size_for_n = defaultdict(int)
575
- for c in cliques:
576
- size_of_c = len(c)
577
- for n in c:
578
- if size_for_n[n] < size_of_c:
579
- size_for_n[n] = size_of_c
580
- if nodes is None:
581
- return size_for_n
582
- return {n: size_for_n[n] for n in nodes}
583
-
584
-
585
- def number_of_cliques(G, nodes=None, cliques=None):
586
- """Return the number of maximal cliques each node is part of.
587
-
588
- Output is a single value or dict depending on `nodes`.
589
- Optional list of cliques can be input if already computed.
590
-
591
- Parameters
592
- ----------
593
- G : NetworkX graph
594
- An undirected graph.
595
-
596
- nodes : list or None, optional (default=None)
597
- A list of nodes to return the number of maximal cliques for.
598
- If `None`, return the number of maximal cliques for all nodes.
599
-
600
- cliques : list or None, optional (default=None)
601
- A precomputed list of maximal cliques to use for the calculation.
602
-
603
- Returns
604
- -------
605
- int or dict
606
- If `nodes` is a single node, return the number of maximal cliques it is
607
- part of. If `nodes` is a list, return a dictionary keyed by node to the
608
- number of maximal cliques it is part of.
609
-
610
- Raises
611
- ------
612
- NetworkXNotImplemented
613
- If `G` is directed.
614
-
615
- See Also
616
- --------
617
- find_cliques
618
- node_clique_number
619
-
620
- Examples
621
- --------
622
- Compute the number of maximal cliques a node is part of:
623
-
624
- >>> G = nx.complete_graph(3)
625
- >>> nx.add_cycle(G, [0, 3, 4])
626
- >>> nx.number_of_cliques(G, nodes=0)
627
- 2
628
- >>> nx.number_of_cliques(G, nodes=1)
629
- 1
630
-
631
- Or, for a list of nodes:
632
-
633
- >>> nx.number_of_cliques(G, nodes=[0, 1])
634
- {0: 2, 1: 1}
635
-
636
- If no explicit `nodes` are provided, all nodes are considered:
637
-
638
- >>> nx.number_of_cliques(G)
639
- {0: 2, 1: 1, 2: 1, 3: 1, 4: 1}
640
-
641
- The list of maximal cliques can also be precomputed:
642
-
643
- >>> cl = list(nx.find_cliques(G))
644
- >>> nx.number_of_cliques(G, cliques=cl)
645
- {0: 2, 1: 1, 2: 1, 3: 1, 4: 1}
646
- """
647
- if cliques is None:
648
- cliques = find_cliques(G)
649
-
650
- if nodes is None:
651
- nodes = list(G.nodes()) # none, get entire graph
652
-
653
- if not isinstance(nodes, list): # check for a list
654
- v = nodes
655
- # assume it is a single value
656
- numcliq = sum(1 for c in cliques if v in c)
657
- else:
658
- numcliq = Counter(chain.from_iterable(cliques))
659
- numcliq = {v: numcliq[v] for v in nodes} # return a dict
660
- return numcliq
661
-
662
-
663
- class MaxWeightClique:
664
- """A class for the maximum weight clique algorithm.
665
-
666
- This class is a helper for the `max_weight_clique` function. The class
667
- should not normally be used directly.
668
-
669
- Parameters
670
- ----------
671
- G : NetworkX graph
672
- The undirected graph for which a maximum weight clique is sought
673
- weight : string or None, optional (default='weight')
674
- The node attribute that holds the integer value used as a weight.
675
- If None, then each node has weight 1.
676
-
677
- Attributes
678
- ----------
679
- G : NetworkX graph
680
- The undirected graph for which a maximum weight clique is sought
681
- node_weights: dict
682
- The weight of each node
683
- incumbent_nodes : list
684
- The nodes of the incumbent clique (the best clique found so far)
685
- incumbent_weight: int
686
- The weight of the incumbent clique
687
- """
688
-
689
- def __init__(self, G, weight):
690
- self.G = G
691
- self.incumbent_nodes = []
692
- self.incumbent_weight = 0
693
-
694
- if weight is None:
695
- self.node_weights = {v: 1 for v in G.nodes()}
696
- else:
697
- for v in G.nodes():
698
- if weight not in G.nodes[v]:
699
- errmsg = f"Node {v!r} does not have the requested weight field."
700
- raise KeyError(errmsg)
701
- if not isinstance(G.nodes[v][weight], int):
702
- errmsg = f"The {weight!r} field of node {v!r} is not an integer."
703
- raise ValueError(errmsg)
704
- self.node_weights = {v: G.nodes[v][weight] for v in G.nodes()}
705
-
706
- def update_incumbent_if_improved(self, C, C_weight):
707
- """Update the incumbent if the node set C has greater weight.
708
-
709
- C is assumed to be a clique.
710
- """
711
- if C_weight > self.incumbent_weight:
712
- self.incumbent_nodes = C[:]
713
- self.incumbent_weight = C_weight
714
-
715
- def greedily_find_independent_set(self, P):
716
- """Greedily find an independent set of nodes from a set of
717
- nodes P."""
718
- independent_set = []
719
- P = P[:]
720
- while P:
721
- v = P[0]
722
- independent_set.append(v)
723
- P = [w for w in P if v != w and not self.G.has_edge(v, w)]
724
- return independent_set
725
-
726
- def find_branching_nodes(self, P, target):
727
- """Find a set of nodes to branch on."""
728
- residual_wt = {v: self.node_weights[v] for v in P}
729
- total_wt = 0
730
- P = P[:]
731
- while P:
732
- independent_set = self.greedily_find_independent_set(P)
733
- min_wt_in_class = min(residual_wt[v] for v in independent_set)
734
- total_wt += min_wt_in_class
735
- if total_wt > target:
736
- break
737
- for v in independent_set:
738
- residual_wt[v] -= min_wt_in_class
739
- P = [v for v in P if residual_wt[v] != 0]
740
- return P
741
-
742
- def expand(self, C, C_weight, P):
743
- """Look for the best clique that contains all the nodes in C and zero or
744
- more of the nodes in P, backtracking if it can be shown that no such
745
- clique has greater weight than the incumbent.
746
- """
747
- self.update_incumbent_if_improved(C, C_weight)
748
- branching_nodes = self.find_branching_nodes(P, self.incumbent_weight - C_weight)
749
- while branching_nodes:
750
- v = branching_nodes.pop()
751
- P.remove(v)
752
- new_C = C + [v]
753
- new_C_weight = C_weight + self.node_weights[v]
754
- new_P = [w for w in P if self.G.has_edge(v, w)]
755
- self.expand(new_C, new_C_weight, new_P)
756
-
757
- def find_max_weight_clique(self):
758
- """Find a maximum weight clique."""
759
- # Sort nodes in reverse order of degree for speed
760
- nodes = sorted(self.G.nodes(), key=lambda v: self.G.degree(v), reverse=True)
761
- nodes = [v for v in nodes if self.node_weights[v] > 0]
762
- self.expand([], 0, nodes)
763
-
764
-
765
- @not_implemented_for("directed")
766
- @nx._dispatchable(node_attrs="weight")
767
- def max_weight_clique(G, weight="weight"):
768
- """Find a maximum weight clique in G.
769
-
770
- A *clique* in a graph is a set of nodes such that every two distinct nodes
771
- are adjacent. The *weight* of a clique is the sum of the weights of its
772
- nodes. A *maximum weight clique* of graph G is a clique C in G such that
773
- no clique in G has weight greater than the weight of C.
774
-
775
- Parameters
776
- ----------
777
- G : NetworkX graph
778
- Undirected graph
779
- weight : string or None, optional (default='weight')
780
- The node attribute that holds the integer value used as a weight.
781
- If None, then each node has weight 1.
782
-
783
- Returns
784
- -------
785
- clique : list
786
- the nodes of a maximum weight clique
787
- weight : int
788
- the weight of a maximum weight clique
789
-
790
- Notes
791
- -----
792
- The implementation is recursive, and therefore it may run into recursion
793
- depth issues if G contains a clique whose number of nodes is close to the
794
- recursion depth limit.
795
-
796
- At each search node, the algorithm greedily constructs a weighted
797
- independent set cover of part of the graph in order to find a small set of
798
- nodes on which to branch. The algorithm is very similar to the algorithm
799
- of Tavares et al. [1]_, other than the fact that the NetworkX version does
800
- not use bitsets. This style of algorithm for maximum weight clique (and
801
- maximum weight independent set, which is the same problem but on the
802
- complement graph) has a decades-long history. See Algorithm B of Warren
803
- and Hicks [2]_ and the references in that paper.
804
-
805
- References
806
- ----------
807
- .. [1] Tavares, W.A., Neto, M.B.C., Rodrigues, C.D., Michelon, P.: Um
808
- algoritmo de branch and bound para o problema da clique máxima
809
- ponderada. Proceedings of XLVII SBPO 1 (2015).
810
-
811
- .. [2] Warren, Jeffrey S, Hicks, Illya V.: Combinatorial Branch-and-Bound
812
- for the Maximum Weight Independent Set Problem. Technical Report,
813
- Texas A&M University (2016).
814
- """
815
-
816
- mwc = MaxWeightClique(G, weight)
817
- mwc.find_max_weight_clique()
818
- return mwc.incumbent_nodes, mwc.incumbent_weight