okstra 0.108.0 → 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 (642) hide show
  1. package/package.json +1 -1
  2. package/runtime/BUILD.json +2 -2
  3. package/runtime/prompts/profiles/_common-contract.md +1 -1
  4. package/runtime/python/okstra_ctl/graphify_cmd.py +225 -0
  5. package/runtime/python/okstra_ctl/resolve_task_key.py +15 -9
  6. package/runtime/python/okstra_project/__init__.py +2 -0
  7. package/runtime/python/okstra_project/state.py +36 -0
  8. package/runtime/python/okstra_vendor/__init__.py +41 -0
  9. package/runtime/python/okstra_vendor/graphify/.vendored-version +1 -0
  10. package/runtime/python/okstra_vendor/graphify/__init__.py +28 -0
  11. package/runtime/python/okstra_vendor/graphify/__main__.py +1371 -0
  12. package/runtime/python/okstra_vendor/graphify/analyze.py +540 -0
  13. package/runtime/python/okstra_vendor/graphify/benchmark.py +129 -0
  14. package/runtime/python/okstra_vendor/graphify/build.py +107 -0
  15. package/runtime/python/okstra_vendor/graphify/cache.py +169 -0
  16. package/runtime/python/okstra_vendor/graphify/cluster.py +137 -0
  17. package/runtime/python/okstra_vendor/graphify/detect.py +510 -0
  18. package/runtime/python/okstra_vendor/graphify/export.py +1014 -0
  19. package/runtime/python/okstra_vendor/graphify/extract.py +3277 -0
  20. package/runtime/python/okstra_vendor/graphify/hooks.py +220 -0
  21. package/runtime/python/okstra_vendor/graphify/ingest.py +297 -0
  22. package/runtime/python/okstra_vendor/graphify/manifest.py +4 -0
  23. package/runtime/python/okstra_vendor/graphify/report.py +175 -0
  24. package/runtime/python/okstra_vendor/graphify/security.py +203 -0
  25. package/runtime/python/okstra_vendor/graphify/serve.py +373 -0
  26. package/runtime/python/okstra_vendor/graphify/skill-aider.md +1184 -0
  27. package/runtime/python/okstra_vendor/graphify/skill-claw.md +1184 -0
  28. package/runtime/python/okstra_vendor/graphify/skill-codex.md +1242 -0
  29. package/runtime/python/okstra_vendor/graphify/skill-copilot.md +1268 -0
  30. package/runtime/python/okstra_vendor/graphify/skill-droid.md +1239 -0
  31. package/runtime/python/okstra_vendor/graphify/skill-kiro.md +1183 -0
  32. package/runtime/python/okstra_vendor/graphify/skill-opencode.md +1238 -0
  33. package/runtime/python/okstra_vendor/graphify/skill-trae.md +1208 -0
  34. package/runtime/python/okstra_vendor/graphify/skill-vscode.md +253 -0
  35. package/runtime/python/okstra_vendor/graphify/skill-windows.md +1245 -0
  36. package/runtime/python/okstra_vendor/graphify/skill.md +1319 -0
  37. package/runtime/python/okstra_vendor/graphify/transcribe.py +182 -0
  38. package/runtime/python/okstra_vendor/graphify/validate.py +72 -0
  39. package/runtime/python/okstra_vendor/graphify/watch.py +188 -0
  40. package/runtime/python/okstra_vendor/graphify/wiki.py +214 -0
  41. package/runtime/python/okstra_vendor/networkx/__init__.py +62 -0
  42. package/runtime/python/okstra_vendor/networkx/algorithms/__init__.py +134 -0
  43. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/__init__.py +26 -0
  44. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clique.py +259 -0
  45. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clustering_coefficient.py +71 -0
  46. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/connectivity.py +412 -0
  47. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/density.py +396 -0
  48. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/distance_measures.py +150 -0
  49. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/dominating_set.py +149 -0
  50. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/kcomponents.py +369 -0
  51. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/matching.py +44 -0
  52. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/maxcut.py +143 -0
  53. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/ramsey.py +53 -0
  54. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/steinertree.py +265 -0
  55. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/__init__.py +0 -0
  56. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_approx_clust_coeff.py +41 -0
  57. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_clique.py +112 -0
  58. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_connectivity.py +199 -0
  59. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_density.py +146 -0
  60. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_distance_measures.py +59 -0
  61. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_dominating_set.py +78 -0
  62. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_kcomponents.py +303 -0
  63. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_matching.py +8 -0
  64. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_maxcut.py +94 -0
  65. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_ramsey.py +31 -0
  66. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_steinertree.py +306 -0
  67. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_traveling_salesman.py +1014 -0
  68. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_treewidth.py +274 -0
  69. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_vertex_cover.py +68 -0
  70. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/traveling_salesman.py +1508 -0
  71. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/treewidth.py +255 -0
  72. package/runtime/python/okstra_vendor/networkx/algorithms/approximation/vertex_cover.py +83 -0
  73. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/__init__.py +5 -0
  74. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/connectivity.py +122 -0
  75. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/correlation.py +302 -0
  76. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/mixing.py +255 -0
  77. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/neighbor_degree.py +160 -0
  78. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/pairs.py +127 -0
  79. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/__init__.py +0 -0
  80. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/base_test.py +81 -0
  81. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_connectivity.py +143 -0
  82. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_correlation.py +122 -0
  83. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_mixing.py +174 -0
  84. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_neighbor_degree.py +107 -0
  85. package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_pairs.py +87 -0
  86. package/runtime/python/okstra_vendor/networkx/algorithms/asteroidal.py +164 -0
  87. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/__init__.py +88 -0
  88. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/basic.py +322 -0
  89. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/centrality.py +290 -0
  90. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/cluster.py +289 -0
  91. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/covering.py +57 -0
  92. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/edgelist.py +360 -0
  93. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/extendability.py +105 -0
  94. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/generators.py +603 -0
  95. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/link_analysis.py +316 -0
  96. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matching.py +590 -0
  97. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matrix.py +232 -0
  98. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/projection.py +526 -0
  99. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/redundancy.py +112 -0
  100. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/spectral.py +69 -0
  101. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/__init__.py +0 -0
  102. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_basic.py +125 -0
  103. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_centrality.py +192 -0
  104. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_cluster.py +84 -0
  105. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_covering.py +33 -0
  106. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_edgelist.py +240 -0
  107. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_extendability.py +334 -0
  108. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_generators.py +407 -0
  109. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_link_analysis.py +218 -0
  110. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_matching.py +327 -0
  111. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_matrix.py +138 -0
  112. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_project.py +409 -0
  113. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_redundancy.py +35 -0
  114. package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_spectral_bipartivity.py +80 -0
  115. package/runtime/python/okstra_vendor/networkx/algorithms/boundary.py +168 -0
  116. package/runtime/python/okstra_vendor/networkx/algorithms/bridges.py +205 -0
  117. package/runtime/python/okstra_vendor/networkx/algorithms/broadcasting.py +164 -0
  118. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/__init__.py +20 -0
  119. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness.py +591 -0
  120. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness_subset.py +236 -0
  121. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/closeness.py +282 -0
  122. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness.py +364 -0
  123. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness_subset.py +227 -0
  124. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_closeness.py +96 -0
  125. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/degree_alg.py +150 -0
  126. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/dispersion.py +107 -0
  127. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/eigenvector.py +357 -0
  128. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/flow_matrix.py +130 -0
  129. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/group.py +787 -0
  130. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/harmonic.py +88 -0
  131. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/katz.py +331 -0
  132. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/laplacian.py +150 -0
  133. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/load.py +200 -0
  134. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/percolation.py +128 -0
  135. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/reaching.py +209 -0
  136. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/second_order.py +141 -0
  137. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/subgraph_alg.py +361 -0
  138. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/__init__.py +0 -0
  139. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_betweenness_centrality.py +923 -0
  140. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_betweenness_centrality_subset.py +354 -0
  141. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_closeness_centrality.py +274 -0
  142. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_betweenness_centrality.py +259 -0
  143. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_betweenness_centrality_subset.py +147 -0
  144. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_closeness.py +43 -0
  145. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_degree_centrality.py +144 -0
  146. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_dispersion.py +73 -0
  147. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_eigenvector_centrality.py +186 -0
  148. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_group.py +277 -0
  149. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_harmonic_centrality.py +122 -0
  150. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_katz_centrality.py +345 -0
  151. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_laplacian_centrality.py +220 -0
  152. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_load_centrality.py +344 -0
  153. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_percolation_centrality.py +87 -0
  154. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_reaching.py +140 -0
  155. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_second_order_centrality.py +82 -0
  156. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_subgraph.py +110 -0
  157. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_trophic.py +302 -0
  158. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_voterank.py +64 -0
  159. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/trophic.py +181 -0
  160. package/runtime/python/okstra_vendor/networkx/algorithms/centrality/voterank_alg.py +95 -0
  161. package/runtime/python/okstra_vendor/networkx/algorithms/chains.py +172 -0
  162. package/runtime/python/okstra_vendor/networkx/algorithms/chordal.py +443 -0
  163. package/runtime/python/okstra_vendor/networkx/algorithms/clique.py +818 -0
  164. package/runtime/python/okstra_vendor/networkx/algorithms/cluster.py +732 -0
  165. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/__init__.py +4 -0
  166. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/equitable_coloring.py +505 -0
  167. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/greedy_coloring.py +565 -0
  168. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/tests/__init__.py +0 -0
  169. package/runtime/python/okstra_vendor/networkx/algorithms/coloring/tests/test_coloring.py +863 -0
  170. package/runtime/python/okstra_vendor/networkx/algorithms/communicability_alg.py +163 -0
  171. package/runtime/python/okstra_vendor/networkx/algorithms/community/__init__.py +28 -0
  172. package/runtime/python/okstra_vendor/networkx/algorithms/community/asyn_fluid.py +153 -0
  173. package/runtime/python/okstra_vendor/networkx/algorithms/community/bipartitions.py +354 -0
  174. package/runtime/python/okstra_vendor/networkx/algorithms/community/centrality.py +171 -0
  175. package/runtime/python/okstra_vendor/networkx/algorithms/community/community_utils.py +30 -0
  176. package/runtime/python/okstra_vendor/networkx/algorithms/community/divisive.py +216 -0
  177. package/runtime/python/okstra_vendor/networkx/algorithms/community/kclique.py +79 -0
  178. package/runtime/python/okstra_vendor/networkx/algorithms/community/label_propagation.py +338 -0
  179. package/runtime/python/okstra_vendor/networkx/algorithms/community/leiden.py +162 -0
  180. package/runtime/python/okstra_vendor/networkx/algorithms/community/local.py +220 -0
  181. package/runtime/python/okstra_vendor/networkx/algorithms/community/louvain.py +384 -0
  182. package/runtime/python/okstra_vendor/networkx/algorithms/community/lukes.py +227 -0
  183. package/runtime/python/okstra_vendor/networkx/algorithms/community/modularity_max.py +452 -0
  184. package/runtime/python/okstra_vendor/networkx/algorithms/community/quality.py +347 -0
  185. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/__init__.py +0 -0
  186. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_asyn_fluid.py +147 -0
  187. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_bipartitions.py +157 -0
  188. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_centrality.py +85 -0
  189. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_divisive.py +106 -0
  190. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_kclique.py +91 -0
  191. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_label_propagation.py +241 -0
  192. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_leiden.py +138 -0
  193. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_local.py +76 -0
  194. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_louvain.py +264 -0
  195. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_lukes.py +152 -0
  196. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_modularity_max.py +340 -0
  197. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_quality.py +139 -0
  198. package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_utils.py +26 -0
  199. package/runtime/python/okstra_vendor/networkx/algorithms/components/__init__.py +6 -0
  200. package/runtime/python/okstra_vendor/networkx/algorithms/components/attracting.py +115 -0
  201. package/runtime/python/okstra_vendor/networkx/algorithms/components/biconnected.py +394 -0
  202. package/runtime/python/okstra_vendor/networkx/algorithms/components/connected.py +282 -0
  203. package/runtime/python/okstra_vendor/networkx/algorithms/components/semiconnected.py +71 -0
  204. package/runtime/python/okstra_vendor/networkx/algorithms/components/strongly_connected.py +359 -0
  205. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/__init__.py +0 -0
  206. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_attracting.py +70 -0
  207. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_biconnected.py +248 -0
  208. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_connected.py +138 -0
  209. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_semiconnected.py +55 -0
  210. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_strongly_connected.py +193 -0
  211. package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_weakly_connected.py +96 -0
  212. package/runtime/python/okstra_vendor/networkx/algorithms/components/weakly_connected.py +196 -0
  213. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/__init__.py +11 -0
  214. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/connectivity.py +811 -0
  215. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/cuts.py +616 -0
  216. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/disjoint_paths.py +408 -0
  217. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_augmentation.py +1270 -0
  218. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_kcomponents.py +592 -0
  219. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcomponents.py +220 -0
  220. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcutsets.py +235 -0
  221. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/stoerwagner.py +152 -0
  222. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/__init__.py +0 -0
  223. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_connectivity.py +421 -0
  224. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_cuts.py +309 -0
  225. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_disjoint_paths.py +249 -0
  226. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_edge_augmentation.py +502 -0
  227. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_edge_kcomponents.py +488 -0
  228. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_kcomponents.py +323 -0
  229. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_kcutsets.py +280 -0
  230. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_stoer_wagner.py +102 -0
  231. package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/utils.py +88 -0
  232. package/runtime/python/okstra_vendor/networkx/algorithms/core.py +588 -0
  233. package/runtime/python/okstra_vendor/networkx/algorithms/covering.py +142 -0
  234. package/runtime/python/okstra_vendor/networkx/algorithms/cuts.py +416 -0
  235. package/runtime/python/okstra_vendor/networkx/algorithms/cycles.py +1234 -0
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@@ -0,0 +1,1070 @@
1
+ """Functions for generating trees.
2
+
3
+ The functions sampling trees at random in this module come
4
+ in two variants: labeled and unlabeled. The labeled variants
5
+ sample from every possible tree with the given number of nodes
6
+ uniformly at random. The unlabeled variants sample from every
7
+ possible *isomorphism class* of trees with the given number
8
+ of nodes uniformly at random.
9
+
10
+ To understand the difference, consider the following example.
11
+ There are two isomorphism classes of trees with four nodes.
12
+ One is that of the path graph, the other is that of the
13
+ star graph. The unlabeled variant will return a line graph or
14
+ a star graph with probability 1/2.
15
+
16
+ The labeled variant will return the line graph
17
+ with probability 3/4 and the star graph with probability 1/4,
18
+ because there are more labeled variants of the line graph
19
+ than of the star graph. More precisely, the line graph has
20
+ an automorphism group of order 2, whereas the star graph has
21
+ an automorphism group of order 6, so the line graph has three
22
+ times as many labeled variants as the star graph, and thus
23
+ three more chances to be drawn.
24
+
25
+ Additionally, some functions in this module can sample rooted
26
+ trees and forests uniformly at random. A rooted tree is a tree
27
+ with a designated root node. A rooted forest is a disjoint union
28
+ of rooted trees.
29
+ """
30
+
31
+ from collections import Counter, defaultdict
32
+ from math import comb, factorial
33
+
34
+ import networkx as nx
35
+ from networkx.utils import py_random_state
36
+
37
+ __all__ = [
38
+ "prefix_tree",
39
+ "prefix_tree_recursive",
40
+ "random_labeled_tree",
41
+ "random_labeled_rooted_tree",
42
+ "random_labeled_rooted_forest",
43
+ "random_unlabeled_tree",
44
+ "random_unlabeled_rooted_tree",
45
+ "random_unlabeled_rooted_forest",
46
+ ]
47
+
48
+
49
+ @nx._dispatchable(graphs=None, returns_graph=True)
50
+ def prefix_tree(paths):
51
+ """Creates a directed prefix tree from a list of paths.
52
+
53
+ Usually the paths are described as strings or lists of integers.
54
+
55
+ A "prefix tree" represents the prefix structure of the strings.
56
+ Each node represents a prefix of some string. The root represents
57
+ the empty prefix with children for the single letter prefixes which
58
+ in turn have children for each double letter prefix starting with
59
+ the single letter corresponding to the parent node, and so on.
60
+
61
+ More generally the prefixes do not need to be strings. A prefix refers
62
+ to the start of a sequence. The root has children for each one element
63
+ prefix and they have children for each two element prefix that starts
64
+ with the one element sequence of the parent, and so on.
65
+
66
+ Note that this implementation uses integer nodes with an attribute.
67
+ Each node has an attribute "source" whose value is the original element
68
+ of the path to which this node corresponds. For example, suppose `paths`
69
+ consists of one path: "can". Then the nodes `[1, 2, 3]` which represent
70
+ this path have "source" values "c", "a" and "n".
71
+
72
+ All the descendants of a node have a common prefix in the sequence/path
73
+ associated with that node. From the returned tree, the prefix for each
74
+ node can be constructed by traversing the tree up to the root and
75
+ accumulating the "source" values along the way.
76
+
77
+ The root node is always `0` and has "source" attribute `None`.
78
+ The root is the only node with in-degree zero.
79
+ The nil node is always `-1` and has "source" attribute `"NIL"`.
80
+ The nil node is the only node with out-degree zero.
81
+
82
+
83
+ Parameters
84
+ ----------
85
+ paths: iterable of paths
86
+ An iterable of paths which are themselves sequences.
87
+ Matching prefixes among these sequences are identified with
88
+ nodes of the prefix tree. One leaf of the tree is associated
89
+ with each path. (Identical paths are associated with the same
90
+ leaf of the tree.)
91
+
92
+
93
+ Returns
94
+ -------
95
+ tree: DiGraph
96
+ A directed graph representing an arborescence consisting of the
97
+ prefix tree generated by `paths`. Nodes are directed "downward",
98
+ from parent to child. A special "synthetic" root node is added
99
+ to be the parent of the first node in each path. A special
100
+ "synthetic" leaf node, the "nil" node `-1`, is added to be the child
101
+ of all nodes representing the last element in a path. (The
102
+ addition of this nil node technically makes this not an
103
+ arborescence but a directed acyclic graph; removing the nil node
104
+ makes it an arborescence.)
105
+
106
+
107
+ Notes
108
+ -----
109
+ The prefix tree is also known as a *trie*.
110
+
111
+
112
+ Examples
113
+ --------
114
+ Create a prefix tree from a list of strings with common prefixes::
115
+
116
+ >>> paths = ["ab", "abs", "ad"]
117
+ >>> T = nx.prefix_tree(paths)
118
+ >>> list(T.edges)
119
+ [(0, 1), (1, 2), (1, 4), (2, -1), (2, 3), (3, -1), (4, -1)]
120
+
121
+ The leaf nodes can be obtained as predecessors of the nil node::
122
+
123
+ >>> root, NIL = 0, -1
124
+ >>> list(T.predecessors(NIL))
125
+ [2, 3, 4]
126
+
127
+ To recover the original paths that generated the prefix tree,
128
+ traverse up the tree from the node `-1` to the node `0`::
129
+
130
+ >>> recovered = []
131
+ >>> for v in T.predecessors(NIL):
132
+ ... prefix = ""
133
+ ... while v != root:
134
+ ... prefix = str(T.nodes[v]["source"]) + prefix
135
+ ... v = next(T.predecessors(v)) # only one predecessor
136
+ ... recovered.append(prefix)
137
+ >>> sorted(recovered)
138
+ ['ab', 'abs', 'ad']
139
+ """
140
+
141
+ def get_children(parent, paths):
142
+ children = defaultdict(list)
143
+ # Populate dictionary with key(s) as the child/children of the root and
144
+ # value(s) as the remaining paths of the corresponding child/children
145
+ for path in paths:
146
+ # If path is empty, we add an edge to the NIL node.
147
+ if not path:
148
+ tree.add_edge(parent, NIL)
149
+ continue
150
+ child, *rest = path
151
+ # `child` may exist as the head of more than one path in `paths`.
152
+ children[child].append(rest)
153
+ return children
154
+
155
+ # Initialize the prefix tree with a root node and a nil node.
156
+ tree = nx.DiGraph()
157
+ root = 0
158
+ tree.add_node(root, source=None)
159
+ NIL = -1
160
+ tree.add_node(NIL, source="NIL")
161
+ children = get_children(root, paths)
162
+ stack = [(root, iter(children.items()))]
163
+ while stack:
164
+ parent, remaining_children = stack[-1]
165
+ try:
166
+ child, remaining_paths = next(remaining_children)
167
+ # Pop item off stack if there are no remaining children
168
+ except StopIteration:
169
+ stack.pop()
170
+ continue
171
+ # We relabel each child with an unused name.
172
+ new_name = len(tree) - 1
173
+ # The "source" node attribute stores the original node name.
174
+ tree.add_node(new_name, source=child)
175
+ tree.add_edge(parent, new_name)
176
+ children = get_children(new_name, remaining_paths)
177
+ stack.append((new_name, iter(children.items())))
178
+
179
+ return tree
180
+
181
+
182
+ @nx._dispatchable(graphs=None, returns_graph=True)
183
+ def prefix_tree_recursive(paths):
184
+ """Recursively creates a directed prefix tree from a list of paths.
185
+
186
+ The original recursive version of prefix_tree for comparison. It is
187
+ the same algorithm but the recursion is unrolled onto a stack.
188
+
189
+ Usually the paths are described as strings or lists of integers.
190
+
191
+ A "prefix tree" represents the prefix structure of the strings.
192
+ Each node represents a prefix of some string. The root represents
193
+ the empty prefix with children for the single letter prefixes which
194
+ in turn have children for each double letter prefix starting with
195
+ the single letter corresponding to the parent node, and so on.
196
+
197
+ More generally the prefixes do not need to be strings. A prefix refers
198
+ to the start of a sequence. The root has children for each one element
199
+ prefix and they have children for each two element prefix that starts
200
+ with the one element sequence of the parent, and so on.
201
+
202
+ Note that this implementation uses integer nodes with an attribute.
203
+ Each node has an attribute "source" whose value is the original element
204
+ of the path to which this node corresponds. For example, suppose `paths`
205
+ consists of one path: "can". Then the nodes `[1, 2, 3]` which represent
206
+ this path have "source" values "c", "a" and "n".
207
+
208
+ All the descendants of a node have a common prefix in the sequence/path
209
+ associated with that node. From the returned tree, ehe prefix for each
210
+ node can be constructed by traversing the tree up to the root and
211
+ accumulating the "source" values along the way.
212
+
213
+ The root node is always `0` and has "source" attribute `None`.
214
+ The root is the only node with in-degree zero.
215
+ The nil node is always `-1` and has "source" attribute `"NIL"`.
216
+ The nil node is the only node with out-degree zero.
217
+
218
+
219
+ Parameters
220
+ ----------
221
+ paths: iterable of paths
222
+ An iterable of paths which are themselves sequences.
223
+ Matching prefixes among these sequences are identified with
224
+ nodes of the prefix tree. One leaf of the tree is associated
225
+ with each path. (Identical paths are associated with the same
226
+ leaf of the tree.)
227
+
228
+
229
+ Returns
230
+ -------
231
+ tree: DiGraph
232
+ A directed graph representing an arborescence consisting of the
233
+ prefix tree generated by `paths`. Nodes are directed "downward",
234
+ from parent to child. A special "synthetic" root node is added
235
+ to be the parent of the first node in each path. A special
236
+ "synthetic" leaf node, the "nil" node `-1`, is added to be the child
237
+ of all nodes representing the last element in a path. (The
238
+ addition of this nil node technically makes this not an
239
+ arborescence but a directed acyclic graph; removing the nil node
240
+ makes it an arborescence.)
241
+
242
+
243
+ Notes
244
+ -----
245
+ The prefix tree is also known as a *trie*.
246
+
247
+
248
+ Examples
249
+ --------
250
+ Create a prefix tree from a list of strings with common prefixes::
251
+
252
+ >>> paths = ["ab", "abs", "ad"]
253
+ >>> T = nx.prefix_tree(paths)
254
+ >>> list(T.edges)
255
+ [(0, 1), (1, 2), (1, 4), (2, -1), (2, 3), (3, -1), (4, -1)]
256
+
257
+ The leaf nodes can be obtained as predecessors of the nil node.
258
+
259
+ >>> root, NIL = 0, -1
260
+ >>> list(T.predecessors(NIL))
261
+ [2, 3, 4]
262
+
263
+ To recover the original paths that generated the prefix tree,
264
+ traverse up the tree from the node `-1` to the node `0`::
265
+
266
+ >>> recovered = []
267
+ >>> for v in T.predecessors(NIL):
268
+ ... prefix = ""
269
+ ... while v != root:
270
+ ... prefix = str(T.nodes[v]["source"]) + prefix
271
+ ... v = next(T.predecessors(v)) # only one predecessor
272
+ ... recovered.append(prefix)
273
+ >>> sorted(recovered)
274
+ ['ab', 'abs', 'ad']
275
+ """
276
+
277
+ def _helper(paths, root, tree):
278
+ """Recursively create a trie from the given list of paths.
279
+
280
+ `paths` is a list of paths, each of which is itself a list of
281
+ nodes, relative to the given `root` (but not including it). This
282
+ list of paths will be interpreted as a tree-like structure, in
283
+ which two paths that share a prefix represent two branches of
284
+ the tree with the same initial segment.
285
+
286
+ `root` is the parent of the node at index 0 in each path.
287
+
288
+ `tree` is the "accumulator", the :class:`networkx.DiGraph`
289
+ representing the branching to which the new nodes and edges will
290
+ be added.
291
+
292
+ """
293
+ # For each path, remove the first node and make it a child of root.
294
+ # Any remaining paths then get processed recursively.
295
+ children = defaultdict(list)
296
+ for path in paths:
297
+ # If path is empty, we add an edge to the NIL node.
298
+ if not path:
299
+ tree.add_edge(root, NIL)
300
+ continue
301
+ child, *rest = path
302
+ # `child` may exist as the head of more than one path in `paths`.
303
+ children[child].append(rest)
304
+ # Add a node for each child, connect root, recurse to remaining paths
305
+ for child, remaining_paths in children.items():
306
+ # We relabel each child with an unused name.
307
+ new_name = len(tree) - 1
308
+ # The "source" node attribute stores the original node name.
309
+ tree.add_node(new_name, source=child)
310
+ tree.add_edge(root, new_name)
311
+ _helper(remaining_paths, new_name, tree)
312
+
313
+ # Initialize the prefix tree with a root node and a nil node.
314
+ tree = nx.DiGraph()
315
+ root = 0
316
+ tree.add_node(root, source=None)
317
+ NIL = -1
318
+ tree.add_node(NIL, source="NIL")
319
+ # Populate the tree.
320
+ _helper(paths, root, tree)
321
+ return tree
322
+
323
+
324
+ @py_random_state("seed")
325
+ @nx._dispatchable(graphs=None, returns_graph=True)
326
+ def random_labeled_tree(n, *, seed=None):
327
+ """Returns a labeled tree on `n` nodes chosen uniformly at random.
328
+
329
+ Generating uniformly distributed random Prüfer sequences and
330
+ converting them into the corresponding trees is a straightforward
331
+ method of generating uniformly distributed random labeled trees.
332
+ This function implements this method.
333
+
334
+ Parameters
335
+ ----------
336
+ n : int
337
+ The number of nodes, greater than zero.
338
+ seed : random_state
339
+ Indicator of random number generation state.
340
+ See :ref:`Randomness<randomness>`
341
+
342
+ Returns
343
+ -------
344
+ :class:`networkx.Graph`
345
+ A `networkx.Graph` with nodes in the set {0, …, *n* - 1}.
346
+
347
+ Raises
348
+ ------
349
+ NetworkXPointlessConcept
350
+ If `n` is zero (because the null graph is not a tree).
351
+
352
+ Examples
353
+ --------
354
+ >>> G = nx.random_labeled_tree(5, seed=42)
355
+ >>> nx.is_tree(G)
356
+ True
357
+ >>> G.edges
358
+ EdgeView([(0, 1), (0, 3), (0, 2), (2, 4)])
359
+
360
+ A tree with *arbitrarily directed* edges can be created by assigning
361
+ generated edges to a ``DiGraph``:
362
+
363
+ >>> DG = nx.DiGraph()
364
+ >>> DG.add_edges_from(G.edges)
365
+ >>> nx.is_tree(DG)
366
+ True
367
+ >>> DG.edges
368
+ OutEdgeView([(0, 1), (0, 3), (0, 2), (2, 4)])
369
+ """
370
+ # Cannot create a Prüfer sequence unless `n` is at least two.
371
+ if n == 0:
372
+ raise nx.NetworkXPointlessConcept("the null graph is not a tree")
373
+ if n == 1:
374
+ return nx.empty_graph(1)
375
+ return nx.from_prufer_sequence([seed.choice(range(n)) for i in range(n - 2)])
376
+
377
+
378
+ @py_random_state("seed")
379
+ @nx._dispatchable(graphs=None, returns_graph=True)
380
+ def random_labeled_rooted_tree(n, *, seed=None):
381
+ """Returns a labeled rooted tree with `n` nodes.
382
+
383
+ The returned tree is chosen uniformly at random from all labeled rooted trees.
384
+
385
+ Parameters
386
+ ----------
387
+ n : int
388
+ The number of nodes
389
+ seed : integer, random_state, or None (default)
390
+ Indicator of random number generation state.
391
+ See :ref:`Randomness<randomness>`.
392
+
393
+ Returns
394
+ -------
395
+ :class:`networkx.Graph`
396
+ A `networkx.Graph` with integer nodes 0 <= node <= `n` - 1.
397
+ The root of the tree is selected uniformly from the nodes.
398
+ The "root" graph attribute identifies the root of the tree.
399
+
400
+ Notes
401
+ -----
402
+ This function returns the result of :func:`random_labeled_tree`
403
+ with a randomly selected root.
404
+
405
+ Raises
406
+ ------
407
+ NetworkXPointlessConcept
408
+ If `n` is zero (because the null graph is not a tree).
409
+ """
410
+ t = random_labeled_tree(n, seed=seed)
411
+ t.graph["root"] = seed.randint(0, n - 1)
412
+ return t
413
+
414
+
415
+ @py_random_state("seed")
416
+ @nx._dispatchable(graphs=None, returns_graph=True)
417
+ def random_labeled_rooted_forest(n, *, seed=None):
418
+ """Returns a labeled rooted forest with `n` nodes.
419
+
420
+ The returned forest is chosen uniformly at random using a
421
+ generalization of Prüfer sequences [1]_ in the form described in [2]_.
422
+
423
+ Parameters
424
+ ----------
425
+ n : int
426
+ The number of nodes.
427
+ seed : random_state
428
+ See :ref:`Randomness<randomness>`.
429
+
430
+ Returns
431
+ -------
432
+ :class:`networkx.Graph`
433
+ A `networkx.Graph` with integer nodes 0 <= node <= `n` - 1.
434
+ The "roots" graph attribute is a set of integers containing the roots.
435
+
436
+ References
437
+ ----------
438
+ .. [1] Knuth, Donald E. "Another Enumeration of Trees."
439
+ Canadian Journal of Mathematics, 20 (1968): 1077-1086.
440
+ https://doi.org/10.4153/CJM-1968-104-8
441
+ .. [2] Rubey, Martin. "Counting Spanning Trees". Diplomarbeit
442
+ zur Erlangung des akademischen Grades Magister der
443
+ Naturwissenschaften an der Formal- und Naturwissenschaftlichen
444
+ Fakultät der Universität Wien. Wien, May 2000.
445
+ """
446
+
447
+ # Select the number of roots by iterating over the cumulative count of trees
448
+ # with at most k roots
449
+ def _select_k(n, seed):
450
+ r = seed.randint(0, (n + 1) ** (n - 1) - 1)
451
+ cum_sum = 0
452
+ for k in range(1, n):
453
+ cum_sum += (factorial(n - 1) * n ** (n - k)) // (
454
+ factorial(k - 1) * factorial(n - k)
455
+ )
456
+ if r < cum_sum:
457
+ return k
458
+
459
+ return n
460
+
461
+ F = nx.empty_graph(n)
462
+ if n == 0:
463
+ F.graph["roots"] = {}
464
+ return F
465
+ # Select the number of roots k
466
+ k = _select_k(n, seed)
467
+ if k == n:
468
+ F.graph["roots"] = set(range(n))
469
+ return F # Nothing to do
470
+ # Select the roots
471
+ roots = seed.sample(range(n), k)
472
+ # Nonroots
473
+ p = set(range(n)).difference(roots)
474
+ # Coding sequence
475
+ N = [seed.randint(0, n - 1) for i in range(n - k - 1)]
476
+ # Multiset of elements in N also in p
477
+ degree = Counter([x for x in N if x in p])
478
+ # Iterator over the elements of p with degree zero
479
+ iterator = iter(x for x in p if degree[x] == 0)
480
+ u = last = next(iterator)
481
+ # This loop is identical to that for Prüfer sequences,
482
+ # except that we can draw nodes only from p
483
+ for v in N:
484
+ F.add_edge(u, v)
485
+ degree[v] -= 1
486
+ if v < last and degree[v] == 0:
487
+ u = v
488
+ else:
489
+ last = u = next(iterator)
490
+
491
+ F.add_edge(u, roots[0])
492
+ F.graph["roots"] = set(roots)
493
+ return F
494
+
495
+
496
+ # The following functions support generation of unlabeled trees and forests.
497
+
498
+
499
+ def _to_nx(edges, n_nodes, root=None, roots=None):
500
+ """
501
+ Converts the (edges, n_nodes) input to a :class:`networkx.Graph`.
502
+ The (edges, n_nodes) input is a list of even length, where each pair
503
+ of consecutive integers represents an edge, and an integer `n_nodes`.
504
+ Integers in the list are elements of `range(n_nodes)`.
505
+
506
+ Parameters
507
+ ----------
508
+ edges : list of ints
509
+ The flattened list of edges of the graph.
510
+ n_nodes : int
511
+ The number of nodes of the graph.
512
+ root: int (default=None)
513
+ If not None, the "root" attribute of the graph will be set to this value.
514
+ roots: collection of ints (default=None)
515
+ If not None, he "roots" attribute of the graph will be set to this value.
516
+
517
+ Returns
518
+ -------
519
+ :class:`networkx.Graph`
520
+ The graph with `n_nodes` nodes and edges given by `edges`.
521
+ """
522
+ G = nx.empty_graph(n_nodes)
523
+ G.add_edges_from(edges)
524
+ if root is not None:
525
+ G.graph["root"] = root
526
+ if roots is not None:
527
+ G.graph["roots"] = roots
528
+ return G
529
+
530
+
531
+ def _num_rooted_trees(n, cache_trees):
532
+ """Returns the number of unlabeled rooted trees with `n` nodes.
533
+
534
+ See also https://oeis.org/A000081.
535
+
536
+ Parameters
537
+ ----------
538
+ n : int
539
+ The number of nodes
540
+ cache_trees : list of ints
541
+ The $i$-th element is the number of unlabeled rooted trees with $i$ nodes,
542
+ which is used as a cache (and is extended to length $n+1$ if needed)
543
+
544
+ Returns
545
+ -------
546
+ int
547
+ The number of unlabeled rooted trees with `n` nodes.
548
+ """
549
+ for n_i in range(len(cache_trees), n + 1):
550
+ cache_trees.append(
551
+ sum(
552
+ [
553
+ d * cache_trees[n_i - j * d] * cache_trees[d]
554
+ for d in range(1, n_i)
555
+ for j in range(1, (n_i - 1) // d + 1)
556
+ ]
557
+ )
558
+ // (n_i - 1)
559
+ )
560
+ return cache_trees[n]
561
+
562
+
563
+ def _select_jd_trees(n, cache_trees, seed):
564
+ """Returns a pair $(j,d)$ with a specific probability
565
+
566
+ Given $n$, returns a pair of positive integers $(j,d)$ with the probability
567
+ specified in formula (5) of Chapter 29 of [1]_.
568
+
569
+ Parameters
570
+ ----------
571
+ n : int
572
+ The number of nodes
573
+ cache_trees : list of ints
574
+ Cache for :func:`_num_rooted_trees`.
575
+ seed : random_state
576
+ See :ref:`Randomness<randomness>`.
577
+
578
+ Returns
579
+ -------
580
+ (int, int)
581
+ A pair of positive integers $(j,d)$ satisfying formula (5) of
582
+ Chapter 29 of [1]_.
583
+
584
+ References
585
+ ----------
586
+ .. [1] Nijenhuis, Albert, and Wilf, Herbert S.
587
+ "Combinatorial algorithms: for computers and calculators."
588
+ Academic Press, 1978.
589
+ https://doi.org/10.1016/C2013-0-11243-3
590
+ """
591
+ p = seed.randint(0, _num_rooted_trees(n, cache_trees) * (n - 1) - 1)
592
+ cumsum = 0
593
+ for d in range(n - 1, 0, -1):
594
+ for j in range(1, (n - 1) // d + 1):
595
+ cumsum += (
596
+ d
597
+ * _num_rooted_trees(n - j * d, cache_trees)
598
+ * _num_rooted_trees(d, cache_trees)
599
+ )
600
+ if p < cumsum:
601
+ return (j, d)
602
+
603
+
604
+ def _random_unlabeled_rooted_tree(n, cache_trees, seed):
605
+ """Returns an unlabeled rooted tree with `n` nodes.
606
+
607
+ Returns an unlabeled rooted tree with `n` nodes chosen uniformly
608
+ at random using the "RANRUT" algorithm from [1]_.
609
+ The tree is returned in the form: (list_of_edges, number_of_nodes)
610
+
611
+ Parameters
612
+ ----------
613
+ n : int
614
+ The number of nodes, greater than zero.
615
+ cache_trees : list ints
616
+ Cache for :func:`_num_rooted_trees`.
617
+ seed : random_state
618
+ See :ref:`Randomness<randomness>`.
619
+
620
+ Returns
621
+ -------
622
+ (list_of_edges, number_of_nodes) : list, int
623
+ A random unlabeled rooted tree with `n` nodes as a 2-tuple
624
+ ``(list_of_edges, number_of_nodes)``.
625
+ The root is node 0.
626
+
627
+ References
628
+ ----------
629
+ .. [1] Nijenhuis, Albert, and Wilf, Herbert S.
630
+ "Combinatorial algorithms: for computers and calculators."
631
+ Academic Press, 1978.
632
+ https://doi.org/10.1016/C2013-0-11243-3
633
+ """
634
+ if n == 1:
635
+ edges, n_nodes = [], 1
636
+ return edges, n_nodes
637
+ if n == 2:
638
+ edges, n_nodes = [(0, 1)], 2
639
+ return edges, n_nodes
640
+
641
+ j, d = _select_jd_trees(n, cache_trees, seed)
642
+ t1, t1_nodes = _random_unlabeled_rooted_tree(n - j * d, cache_trees, seed)
643
+ t2, t2_nodes = _random_unlabeled_rooted_tree(d, cache_trees, seed)
644
+ t12 = [(0, t2_nodes * i + t1_nodes) for i in range(j)]
645
+ t1.extend(t12)
646
+ for _ in range(j):
647
+ t1.extend((n1 + t1_nodes, n2 + t1_nodes) for n1, n2 in t2)
648
+ t1_nodes += t2_nodes
649
+
650
+ return t1, t1_nodes
651
+
652
+
653
+ @py_random_state("seed")
654
+ @nx._dispatchable(graphs=None, returns_graph=True)
655
+ def random_unlabeled_rooted_tree(n, *, number_of_trees=None, seed=None):
656
+ """Returns a number of unlabeled rooted trees uniformly at random
657
+
658
+ Returns one or more (depending on `number_of_trees`)
659
+ unlabeled rooted trees with `n` nodes drawn uniformly
660
+ at random.
661
+
662
+ Parameters
663
+ ----------
664
+ n : int
665
+ The number of nodes
666
+ number_of_trees : int or None (default)
667
+ If not None, this number of trees is generated and returned.
668
+ seed : integer, random_state, or None (default)
669
+ Indicator of random number generation state.
670
+ See :ref:`Randomness<randomness>`.
671
+
672
+ Returns
673
+ -------
674
+ :class:`networkx.Graph` or list of :class:`networkx.Graph`
675
+ A single `networkx.Graph` (or a list thereof, if `number_of_trees`
676
+ is specified) with nodes in the set {0, …, *n* - 1}.
677
+ The "root" graph attribute identifies the root of the tree.
678
+
679
+ Notes
680
+ -----
681
+ The trees are generated using the "RANRUT" algorithm from [1]_.
682
+ The algorithm needs to compute some counting functions
683
+ that are relatively expensive: in case several trees are needed,
684
+ it is advisable to use the `number_of_trees` optional argument
685
+ to reuse the counting functions.
686
+
687
+ Raises
688
+ ------
689
+ NetworkXPointlessConcept
690
+ If `n` is zero (because the null graph is not a tree).
691
+
692
+ References
693
+ ----------
694
+ .. [1] Nijenhuis, Albert, and Wilf, Herbert S.
695
+ "Combinatorial algorithms: for computers and calculators."
696
+ Academic Press, 1978.
697
+ https://doi.org/10.1016/C2013-0-11243-3
698
+ """
699
+ if n == 0:
700
+ raise nx.NetworkXPointlessConcept("the null graph is not a tree")
701
+ cache_trees = [0, 1] # initial cache of number of rooted trees
702
+ if number_of_trees is None:
703
+ return _to_nx(*_random_unlabeled_rooted_tree(n, cache_trees, seed), root=0)
704
+ return [
705
+ _to_nx(*_random_unlabeled_rooted_tree(n, cache_trees, seed), root=0)
706
+ for i in range(number_of_trees)
707
+ ]
708
+
709
+
710
+ def _num_rooted_forests(n, q, cache_forests):
711
+ """Returns the number of unlabeled rooted forests with `n` nodes, and with
712
+ no more than `q` nodes per tree. A recursive formula for this is (2) in
713
+ [1]_. This function is implemented using dynamic programming instead of
714
+ recursion.
715
+
716
+ Parameters
717
+ ----------
718
+ n : int
719
+ The number of nodes.
720
+ q : int
721
+ The maximum number of nodes for each tree of the forest.
722
+ cache_forests : list of ints
723
+ The $i$-th element is the number of unlabeled rooted forests with
724
+ $i$ nodes, and with no more than `q` nodes per tree; this is used
725
+ as a cache (and is extended to length `n` + 1 if needed).
726
+
727
+ Returns
728
+ -------
729
+ int
730
+ The number of unlabeled rooted forests with `n` nodes with no more than
731
+ `q` nodes per tree.
732
+
733
+ References
734
+ ----------
735
+ .. [1] Wilf, Herbert S. "The uniform selection of free trees."
736
+ Journal of Algorithms 2.2 (1981): 204-207.
737
+ https://doi.org/10.1016/0196-6774(81)90021-3
738
+ """
739
+ for n_i in range(len(cache_forests), n + 1):
740
+ q_i = min(n_i, q)
741
+ cache_forests.append(
742
+ sum(
743
+ [
744
+ d * cache_forests[n_i - j * d] * cache_forests[d - 1]
745
+ for d in range(1, q_i + 1)
746
+ for j in range(1, n_i // d + 1)
747
+ ]
748
+ )
749
+ // n_i
750
+ )
751
+
752
+ return cache_forests[n]
753
+
754
+
755
+ def _select_jd_forests(n, q, cache_forests, seed):
756
+ """Given `n` and `q`, returns a pair of positive integers $(j,d)$
757
+ such that $j\\leq d$, with probability satisfying (F1) of [1]_.
758
+
759
+ Parameters
760
+ ----------
761
+ n : int
762
+ The number of nodes.
763
+ q : int
764
+ The maximum number of nodes for each tree of the forest.
765
+ cache_forests : list of ints
766
+ Cache for :func:`_num_rooted_forests`.
767
+ seed : random_state
768
+ See :ref:`Randomness<randomness>`.
769
+
770
+ Returns
771
+ -------
772
+ (int, int)
773
+ A pair of positive integers $(j,d)$
774
+
775
+ References
776
+ ----------
777
+ .. [1] Wilf, Herbert S. "The uniform selection of free trees."
778
+ Journal of Algorithms 2.2 (1981): 204-207.
779
+ https://doi.org/10.1016/0196-6774(81)90021-3
780
+ """
781
+ p = seed.randint(0, _num_rooted_forests(n, q, cache_forests) * n - 1)
782
+ cumsum = 0
783
+ for d in range(q, 0, -1):
784
+ for j in range(1, n // d + 1):
785
+ cumsum += (
786
+ d
787
+ * _num_rooted_forests(n - j * d, q, cache_forests)
788
+ * _num_rooted_forests(d - 1, q, cache_forests)
789
+ )
790
+ if p < cumsum:
791
+ return (j, d)
792
+
793
+
794
+ def _random_unlabeled_rooted_forest(n, q, cache_trees, cache_forests, seed):
795
+ """Returns an unlabeled rooted forest with `n` nodes, and with no more
796
+ than `q` nodes per tree, drawn uniformly at random. It is an implementation
797
+ of the algorithm "Forest" of [1]_.
798
+
799
+ Parameters
800
+ ----------
801
+ n : int
802
+ The number of nodes.
803
+ q : int
804
+ The maximum number of nodes per tree.
805
+ cache_trees :
806
+ Cache for :func:`_num_rooted_trees`.
807
+ cache_forests :
808
+ Cache for :func:`_num_rooted_forests`.
809
+ seed : random_state
810
+ See :ref:`Randomness<randomness>`.
811
+
812
+ Returns
813
+ -------
814
+ (edges, n, r) : (list, int, list)
815
+ The forest (edges, n) and a list r of root nodes.
816
+
817
+ References
818
+ ----------
819
+ .. [1] Wilf, Herbert S. "The uniform selection of free trees."
820
+ Journal of Algorithms 2.2 (1981): 204-207.
821
+ https://doi.org/10.1016/0196-6774(81)90021-3
822
+ """
823
+ if n == 0:
824
+ return ([], 0, [])
825
+
826
+ j, d = _select_jd_forests(n, q, cache_forests, seed)
827
+ t1, t1_nodes, r1 = _random_unlabeled_rooted_forest(
828
+ n - j * d, q, cache_trees, cache_forests, seed
829
+ )
830
+ t2, t2_nodes = _random_unlabeled_rooted_tree(d, cache_trees, seed)
831
+ for _ in range(j):
832
+ r1.append(t1_nodes)
833
+ t1.extend((n1 + t1_nodes, n2 + t1_nodes) for n1, n2 in t2)
834
+ t1_nodes += t2_nodes
835
+ return t1, t1_nodes, r1
836
+
837
+
838
+ @py_random_state("seed")
839
+ @nx._dispatchable(graphs=None, returns_graph=True)
840
+ def random_unlabeled_rooted_forest(n, *, q=None, number_of_forests=None, seed=None):
841
+ """Returns a forest or list of forests selected at random.
842
+
843
+ Returns one or more (depending on `number_of_forests`)
844
+ unlabeled rooted forests with `n` nodes, and with no more than
845
+ `q` nodes per tree, drawn uniformly at random.
846
+ The "roots" graph attribute identifies the roots of the forest.
847
+
848
+ Parameters
849
+ ----------
850
+ n : int
851
+ The number of nodes
852
+ q : int or None (default)
853
+ The maximum number of nodes per tree.
854
+ number_of_forests : int or None (default)
855
+ If not None, this number of forests is generated and returned.
856
+ seed : integer, random_state, or None (default)
857
+ Indicator of random number generation state.
858
+ See :ref:`Randomness<randomness>`.
859
+
860
+ Returns
861
+ -------
862
+ :class:`networkx.Graph` or list of :class:`networkx.Graph`
863
+ A single `networkx.Graph` (or a list thereof, if `number_of_forests`
864
+ is specified) with nodes in the set {0, …, *n* - 1}.
865
+ The "roots" graph attribute is a set containing the roots
866
+ of the trees in the forest.
867
+
868
+ Notes
869
+ -----
870
+ This function implements the algorithm "Forest" of [1]_.
871
+ The algorithm needs to compute some counting functions
872
+ that are relatively expensive: in case several trees are needed,
873
+ it is advisable to use the `number_of_forests` optional argument
874
+ to reuse the counting functions.
875
+
876
+ Raises
877
+ ------
878
+ ValueError
879
+ If `n` is non-zero but `q` is zero.
880
+
881
+ References
882
+ ----------
883
+ .. [1] Wilf, Herbert S. "The uniform selection of free trees."
884
+ Journal of Algorithms 2.2 (1981): 204-207.
885
+ https://doi.org/10.1016/0196-6774(81)90021-3
886
+ """
887
+ if q is None:
888
+ q = n
889
+ if q == 0 and n != 0:
890
+ raise ValueError("q must be a positive integer if n is positive.")
891
+
892
+ cache_trees = [0, 1] # initial cache of number of rooted trees
893
+ cache_forests = [1] # initial cache of number of rooted forests
894
+
895
+ if number_of_forests is None:
896
+ g, nodes, rs = _random_unlabeled_rooted_forest(
897
+ n, q, cache_trees, cache_forests, seed
898
+ )
899
+ return _to_nx(g, nodes, roots=set(rs))
900
+
901
+ res = []
902
+ for i in range(number_of_forests):
903
+ g, nodes, rs = _random_unlabeled_rooted_forest(
904
+ n, q, cache_trees, cache_forests, seed
905
+ )
906
+ res.append(_to_nx(g, nodes, roots=set(rs)))
907
+ return res
908
+
909
+
910
+ def _num_trees(n, cache_trees):
911
+ """Returns the number of unlabeled trees with `n` nodes.
912
+
913
+ See also https://oeis.org/A000055.
914
+
915
+ Parameters
916
+ ----------
917
+ n : int
918
+ The number of nodes.
919
+ cache_trees : list of ints
920
+ Cache for :func:`_num_rooted_trees`.
921
+
922
+ Returns
923
+ -------
924
+ int
925
+ The number of unlabeled trees with `n` nodes.
926
+ """
927
+ r = _num_rooted_trees(n, cache_trees) - sum(
928
+ [
929
+ _num_rooted_trees(j, cache_trees) * _num_rooted_trees(n - j, cache_trees)
930
+ for j in range(1, n // 2 + 1)
931
+ ]
932
+ )
933
+ if n % 2 == 0:
934
+ r += comb(_num_rooted_trees(n // 2, cache_trees) + 1, 2)
935
+ return r
936
+
937
+
938
+ def _bicenter(n, cache, seed):
939
+ """Returns a bi-centroidal tree on `n` nodes drawn uniformly at random.
940
+
941
+ This function implements the algorithm Bicenter of [1]_.
942
+
943
+ Parameters
944
+ ----------
945
+ n : int
946
+ The number of nodes (must be even).
947
+ cache : list of ints.
948
+ Cache for :func:`_num_rooted_trees`.
949
+ seed : random_state
950
+ See :ref:`Randomness<randomness>`
951
+
952
+ Returns
953
+ -------
954
+ (edges, n)
955
+ The tree as a list of edges and number of nodes.
956
+
957
+ References
958
+ ----------
959
+ .. [1] Wilf, Herbert S. "The uniform selection of free trees."
960
+ Journal of Algorithms 2.2 (1981): 204-207.
961
+ https://doi.org/10.1016/0196-6774(81)90021-3
962
+ """
963
+ t, t_nodes = _random_unlabeled_rooted_tree(n // 2, cache, seed)
964
+ if seed.randint(0, _num_rooted_trees(n // 2, cache)) == 0:
965
+ t2, t2_nodes = t, t_nodes
966
+ else:
967
+ t2, t2_nodes = _random_unlabeled_rooted_tree(n // 2, cache, seed)
968
+ t.extend([(n1 + (n // 2), n2 + (n // 2)) for n1, n2 in t2])
969
+ t.append((0, n // 2))
970
+ return t, t_nodes + t2_nodes
971
+
972
+
973
+ def _random_unlabeled_tree(n, cache_trees, cache_forests, seed):
974
+ """Returns a tree on `n` nodes drawn uniformly at random.
975
+ It implements the Wilf's algorithm "Free" of [1]_.
976
+
977
+ Parameters
978
+ ----------
979
+ n : int
980
+ The number of nodes, greater than zero.
981
+ cache_trees : list of ints
982
+ Cache for :func:`_num_rooted_trees`.
983
+ cache_forests : list of ints
984
+ Cache for :func:`_num_rooted_forests`.
985
+ seed : random_state
986
+ Indicator of random number generation state.
987
+ See :ref:`Randomness<randomness>`
988
+
989
+ Returns
990
+ -------
991
+ (edges, n)
992
+ The tree as a list of edges and number of nodes.
993
+
994
+ References
995
+ ----------
996
+ .. [1] Wilf, Herbert S. "The uniform selection of free trees."
997
+ Journal of Algorithms 2.2 (1981): 204-207.
998
+ https://doi.org/10.1016/0196-6774(81)90021-3
999
+ """
1000
+ if n % 2 == 1:
1001
+ p = 0
1002
+ else:
1003
+ p = comb(_num_rooted_trees(n // 2, cache_trees) + 1, 2)
1004
+ if seed.randint(0, _num_trees(n, cache_trees) - 1) < p:
1005
+ return _bicenter(n, cache_trees, seed)
1006
+ else:
1007
+ f, n_f, r = _random_unlabeled_rooted_forest(
1008
+ n - 1, (n - 1) // 2, cache_trees, cache_forests, seed
1009
+ )
1010
+ for i in r:
1011
+ f.append((i, n_f))
1012
+ return f, n_f + 1
1013
+
1014
+
1015
+ @py_random_state("seed")
1016
+ @nx._dispatchable(graphs=None, returns_graph=True)
1017
+ def random_unlabeled_tree(n, *, number_of_trees=None, seed=None):
1018
+ """Returns a tree or list of trees chosen randomly.
1019
+
1020
+ Returns one or more (depending on `number_of_trees`)
1021
+ unlabeled trees with `n` nodes drawn uniformly at random.
1022
+
1023
+ Parameters
1024
+ ----------
1025
+ n : int
1026
+ The number of nodes
1027
+ number_of_trees : int or None (default)
1028
+ If not None, this number of trees is generated and returned.
1029
+ seed : integer, random_state, or None (default)
1030
+ Indicator of random number generation state.
1031
+ See :ref:`Randomness<randomness>`.
1032
+
1033
+ Returns
1034
+ -------
1035
+ :class:`networkx.Graph` or list of :class:`networkx.Graph`
1036
+ A single `networkx.Graph` (or a list thereof, if
1037
+ `number_of_trees` is specified) with nodes in the set {0, …, *n* - 1}.
1038
+
1039
+ Raises
1040
+ ------
1041
+ NetworkXPointlessConcept
1042
+ If `n` is zero (because the null graph is not a tree).
1043
+
1044
+ Notes
1045
+ -----
1046
+ This function generates an unlabeled tree uniformly at random using
1047
+ Wilf's algorithm "Free" of [1]_. The algorithm needs to
1048
+ compute some counting functions that are relatively expensive:
1049
+ in case several trees are needed, it is advisable to use the
1050
+ `number_of_trees` optional argument to reuse the counting
1051
+ functions.
1052
+
1053
+ References
1054
+ ----------
1055
+ .. [1] Wilf, Herbert S. "The uniform selection of free trees."
1056
+ Journal of Algorithms 2.2 (1981): 204-207.
1057
+ https://doi.org/10.1016/0196-6774(81)90021-3
1058
+ """
1059
+ if n == 0:
1060
+ raise nx.NetworkXPointlessConcept("the null graph is not a tree")
1061
+
1062
+ cache_trees = [0, 1] # initial cache of number of rooted trees
1063
+ cache_forests = [1] # initial cache of number of rooted forests
1064
+ if number_of_trees is None:
1065
+ return _to_nx(*_random_unlabeled_tree(n, cache_trees, cache_forests, seed))
1066
+ else:
1067
+ return [
1068
+ _to_nx(*_random_unlabeled_tree(n, cache_trees, cache_forests, seed))
1069
+ for i in range(number_of_trees)
1070
+ ]