okstra 0.108.0 → 0.110.0
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.
- package/README.kr.md +1 -1
- package/README.md +1 -1
- package/docs/kr/architecture.md +3 -3
- package/docs/kr/cli.md +2 -2
- package/docs/project-structure-overview.md +3 -3
- package/package.json +1 -1
- package/runtime/BUILD.json +2 -2
- package/runtime/prompts/profiles/_common-contract.md +1 -1
- package/runtime/python/okstra_ctl/graphify_cmd.py +225 -0
- package/runtime/python/okstra_ctl/resolve_task_key.py +15 -9
- package/runtime/python/okstra_ctl/worktree.py +14 -13
- package/runtime/python/okstra_project/__init__.py +2 -0
- package/runtime/python/okstra_project/state.py +36 -0
- package/runtime/python/okstra_vendor/__init__.py +41 -0
- package/runtime/python/okstra_vendor/graphify/.vendored-version +1 -0
- package/runtime/python/okstra_vendor/graphify/__init__.py +28 -0
- package/runtime/python/okstra_vendor/graphify/__main__.py +1371 -0
- package/runtime/python/okstra_vendor/graphify/analyze.py +540 -0
- package/runtime/python/okstra_vendor/graphify/benchmark.py +129 -0
- package/runtime/python/okstra_vendor/graphify/build.py +107 -0
- package/runtime/python/okstra_vendor/graphify/cache.py +169 -0
- package/runtime/python/okstra_vendor/graphify/cluster.py +137 -0
- package/runtime/python/okstra_vendor/graphify/detect.py +510 -0
- package/runtime/python/okstra_vendor/graphify/export.py +1014 -0
- package/runtime/python/okstra_vendor/graphify/extract.py +3277 -0
- package/runtime/python/okstra_vendor/graphify/hooks.py +220 -0
- package/runtime/python/okstra_vendor/graphify/ingest.py +297 -0
- package/runtime/python/okstra_vendor/graphify/manifest.py +4 -0
- package/runtime/python/okstra_vendor/graphify/report.py +175 -0
- package/runtime/python/okstra_vendor/graphify/security.py +203 -0
- package/runtime/python/okstra_vendor/graphify/serve.py +373 -0
- package/runtime/python/okstra_vendor/graphify/skill-aider.md +1184 -0
- package/runtime/python/okstra_vendor/graphify/skill-claw.md +1184 -0
- package/runtime/python/okstra_vendor/graphify/skill-codex.md +1242 -0
- package/runtime/python/okstra_vendor/graphify/skill-copilot.md +1268 -0
- package/runtime/python/okstra_vendor/graphify/skill-droid.md +1239 -0
- package/runtime/python/okstra_vendor/graphify/skill-kiro.md +1183 -0
- package/runtime/python/okstra_vendor/graphify/skill-opencode.md +1238 -0
- package/runtime/python/okstra_vendor/graphify/skill-trae.md +1208 -0
- package/runtime/python/okstra_vendor/graphify/skill-vscode.md +253 -0
- package/runtime/python/okstra_vendor/graphify/skill-windows.md +1245 -0
- package/runtime/python/okstra_vendor/graphify/skill.md +1319 -0
- package/runtime/python/okstra_vendor/graphify/transcribe.py +182 -0
- package/runtime/python/okstra_vendor/graphify/validate.py +72 -0
- package/runtime/python/okstra_vendor/graphify/watch.py +188 -0
- package/runtime/python/okstra_vendor/graphify/wiki.py +214 -0
- package/runtime/python/okstra_vendor/networkx/__init__.py +62 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/__init__.py +134 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/__init__.py +26 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clique.py +259 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/clustering_coefficient.py +71 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/connectivity.py +412 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/density.py +396 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/distance_measures.py +150 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/dominating_set.py +149 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/kcomponents.py +369 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/matching.py +44 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/maxcut.py +143 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/ramsey.py +53 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/steinertree.py +265 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_approx_clust_coeff.py +41 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_clique.py +112 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_connectivity.py +199 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_density.py +146 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_distance_measures.py +59 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_dominating_set.py +78 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_kcomponents.py +303 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_matching.py +8 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_maxcut.py +94 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_ramsey.py +31 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_steinertree.py +306 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_traveling_salesman.py +1014 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_treewidth.py +274 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/tests/test_vertex_cover.py +68 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/traveling_salesman.py +1508 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/treewidth.py +255 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/approximation/vertex_cover.py +83 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/__init__.py +5 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/connectivity.py +122 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/correlation.py +302 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/mixing.py +255 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/neighbor_degree.py +160 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/pairs.py +127 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/base_test.py +81 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_connectivity.py +143 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_correlation.py +122 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_mixing.py +174 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_neighbor_degree.py +107 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/assortativity/tests/test_pairs.py +87 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/asteroidal.py +164 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/__init__.py +88 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/basic.py +322 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/centrality.py +290 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/cluster.py +289 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/covering.py +57 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/edgelist.py +360 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/extendability.py +105 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/generators.py +603 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/link_analysis.py +316 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matching.py +590 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/matrix.py +232 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/projection.py +526 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/redundancy.py +112 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/spectral.py +69 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_basic.py +125 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_centrality.py +192 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_cluster.py +84 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_covering.py +33 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_edgelist.py +240 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_extendability.py +334 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_generators.py +407 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_link_analysis.py +218 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_matching.py +327 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_matrix.py +138 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_project.py +409 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_redundancy.py +35 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bipartite/tests/test_spectral_bipartivity.py +80 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/boundary.py +168 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/bridges.py +205 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/broadcasting.py +164 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/__init__.py +20 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness.py +591 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/betweenness_subset.py +236 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/closeness.py +282 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness.py +364 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_betweenness_subset.py +227 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/current_flow_closeness.py +96 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/degree_alg.py +150 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/dispersion.py +107 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/eigenvector.py +357 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/flow_matrix.py +130 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/group.py +787 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/harmonic.py +88 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/katz.py +331 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/laplacian.py +150 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/load.py +200 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/percolation.py +128 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/reaching.py +209 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/second_order.py +141 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/subgraph_alg.py +361 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_betweenness_centrality.py +923 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_betweenness_centrality_subset.py +354 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_closeness_centrality.py +274 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_betweenness_centrality.py +259 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_betweenness_centrality_subset.py +147 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_current_flow_closeness.py +43 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_degree_centrality.py +144 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_dispersion.py +73 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_eigenvector_centrality.py +186 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_group.py +277 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_harmonic_centrality.py +122 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_katz_centrality.py +345 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_laplacian_centrality.py +220 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_load_centrality.py +344 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_percolation_centrality.py +87 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_reaching.py +140 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_second_order_centrality.py +82 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_subgraph.py +110 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_trophic.py +302 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/tests/test_voterank.py +64 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/trophic.py +181 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/centrality/voterank_alg.py +95 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/chains.py +172 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/chordal.py +443 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/clique.py +818 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/cluster.py +732 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/coloring/__init__.py +4 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/coloring/equitable_coloring.py +505 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/coloring/greedy_coloring.py +565 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/coloring/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/coloring/tests/test_coloring.py +863 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/communicability_alg.py +163 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/__init__.py +28 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/asyn_fluid.py +153 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/bipartitions.py +354 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/centrality.py +171 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/community_utils.py +30 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/divisive.py +216 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/kclique.py +79 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/label_propagation.py +338 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/leiden.py +162 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/local.py +220 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/louvain.py +384 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/lukes.py +227 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/modularity_max.py +452 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/quality.py +347 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_asyn_fluid.py +147 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_bipartitions.py +157 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_centrality.py +85 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_divisive.py +106 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_kclique.py +91 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_label_propagation.py +241 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_leiden.py +138 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_local.py +76 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_louvain.py +264 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_lukes.py +152 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_modularity_max.py +340 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_quality.py +139 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/community/tests/test_utils.py +26 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/__init__.py +6 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/attracting.py +115 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/biconnected.py +394 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/connected.py +282 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/semiconnected.py +71 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/strongly_connected.py +359 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_attracting.py +70 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_biconnected.py +248 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_connected.py +138 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_semiconnected.py +55 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_strongly_connected.py +193 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/tests/test_weakly_connected.py +96 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/components/weakly_connected.py +196 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/__init__.py +11 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/connectivity.py +811 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/cuts.py +616 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/disjoint_paths.py +408 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_augmentation.py +1270 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/edge_kcomponents.py +592 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcomponents.py +220 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/kcutsets.py +235 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/stoerwagner.py +152 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/__init__.py +0 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_connectivity.py +421 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_cuts.py +309 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_disjoint_paths.py +249 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_edge_augmentation.py +502 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_edge_kcomponents.py +488 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_kcomponents.py +323 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_kcutsets.py +280 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/tests/test_stoer_wagner.py +102 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/connectivity/utils.py +88 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/core.py +588 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/covering.py +142 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/cuts.py +416 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/cycles.py +1234 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/d_separation.py +677 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/dag.py +1392 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/distance_measures.py +1095 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/distance_regular.py +272 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/dominance.py +142 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/dominating.py +268 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/efficiency_measures.py +167 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/euler.py +470 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/flow/__init__.py +11 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/flow/boykovkolmogorov.py +370 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/flow/capacityscaling.py +407 -0
- package/runtime/python/okstra_vendor/networkx/algorithms/flow/dinitz_alg.py +238 -0
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"""Algorithms to characterize the number of triangles in a graph."""
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from collections import Counter
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from itertools import chain, combinations
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import networkx as nx
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from networkx.utils import not_implemented_for
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__all__ = [
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"triangles",
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"all_triangles",
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"average_clustering",
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"clustering",
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"transitivity",
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"square_clustering",
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"generalized_degree",
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]
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@not_implemented_for("directed")
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@nx._dispatchable
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def triangles(G, nodes=None):
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"""Compute the number of triangles.
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Finds the number of triangles that include a node as one vertex.
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Parameters
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----------
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G : graph
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A networkx graph
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nodes : node, iterable of nodes, or None (default=None)
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If a singleton node, return the number of triangles for that node.
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If an iterable, compute the number of triangles for each of those nodes.
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If `None` (the default) compute the number of triangles for all nodes in `G`.
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Returns
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-------
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out : dict or int
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If `nodes` is a container of nodes, returns number of triangles keyed by node (dict).
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If `nodes` is a specific node, returns number of triangles for the node (int).
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Examples
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--------
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>>> G = nx.complete_graph(5)
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>>> print(nx.triangles(G, 0))
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>>> print(nx.triangles(G))
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{0: 6, 1: 6, 2: 6, 3: 6, 4: 6}
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>>> print(list(nx.triangles(G, [0, 1]).values()))
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[6, 6]
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The total number of unique triangles in `G` can be determined by summing
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the number of triangles for each node and dividing by 3 (because a given
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triangle gets counted three times, once for each of its nodes).
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>>> sum(nx.triangles(G).values()) // 3
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Notes
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-----
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Self loops are ignored.
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"""
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if nodes is not None:
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# If `nodes` represents a single node, return only its number of triangles
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return next(_triangles_and_degree_iter(G, nodes))[2] // 2
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# if `nodes` is a container of nodes, then return a
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# dictionary mapping node to number of triangles.
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return {v: t // 2 for v, d, t, _ in _triangles_and_degree_iter(G, nodes)}
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# if nodes is None, then compute triangles for the complete graph
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# dict used to avoid visiting the same nodes twice
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# this allows calculating/counting each triangle only once
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# iterate over the nodes in a graph
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for node, neighbors in G.adjacency():
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later_nbrs[node] = {n for n in neighbors if n not in later_nbrs and n != node}
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# instantiate Counter for each node to include isolated nodes
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# add 1 to the count if a nodes neighbor's neighbor is also a neighbor
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triangle_counts = Counter(dict.fromkeys(G, 0))
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for node1, neighbors in later_nbrs.items():
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for node2 in neighbors:
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third_nodes = neighbors & later_nbrs[node2]
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m = len(third_nodes)
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triangle_counts[node1] += m
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triangle_counts[node2] += m
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triangle_counts.update(third_nodes)
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return dict(triangle_counts)
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@not_implemented_for("multigraph")
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def _triangles_and_degree_iter(G, nodes=None):
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"""Return an iterator of (node, degree, triangles, generalized degree).
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This double counts triangles so you may want to divide by 2.
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See degree(), triangles() and generalized_degree() for definitions
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and details.
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"""
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if nodes is None:
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nodes_nbrs = G.adj.items()
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else:
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nodes_nbrs = ((n, G[n]) for n in G.nbunch_iter(nodes))
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for v, v_nbrs in nodes_nbrs:
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vs = set(v_nbrs) - {v}
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gen_degree = Counter(len(vs & (set(G[w]) - {w})) for w in vs)
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ntriangles = sum(k * val for k, val in gen_degree.items())
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yield (v, len(vs), ntriangles, gen_degree)
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@not_implemented_for("multigraph")
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def _weighted_triangles_and_degree_iter(G, nodes=None, weight="weight"):
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"""Return an iterator of (node, degree, weighted_triangles).
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Used for weighted clustering.
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Note: this returns the geometric average weight of edges in the triangle.
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Also, each triangle is counted twice (each direction).
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So you may want to divide by 2.
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"""
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import numpy as np
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if weight is None or G.number_of_edges() == 0:
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max_weight = 1
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max_weight = max(d.get(weight, 1) for u, v, d in G.edges(data=True))
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if nodes is None:
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nodes_nbrs = G.adj.items()
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nodes_nbrs = ((n, G[n]) for n in G.nbunch_iter(nodes))
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def wt(u, v):
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return G[u][v].get(weight, 1) / max_weight
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for i, nbrs in nodes_nbrs:
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inbrs = set(nbrs) - {i}
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weighted_triangles = 0
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seen = set()
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for j in inbrs:
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seen.add(j)
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# This avoids counting twice -- we double at the end.
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jnbrs = set(G[j]) - seen
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# Only compute the edge weight once, before the inner inner
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# loop.
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wij = wt(i, j)
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weighted_triangles += np.cbrt(
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[(wij * wt(j, k) * wt(k, i)) for k in inbrs & jnbrs]
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).sum()
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yield (i, len(inbrs), 2 * float(weighted_triangles))
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158
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+
|
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159
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+
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160
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+
@not_implemented_for("multigraph")
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161
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+
def _directed_triangles_and_degree_iter(G, nodes=None):
|
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+
"""Return an iterator of
|
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+
(node, total_degree, reciprocal_degree, directed_triangles).
|
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164
|
+
|
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165
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+
Used for directed clustering.
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166
|
+
Note that unlike `_triangles_and_degree_iter()`, this function counts
|
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167
|
+
directed triangles so does not count triangles twice.
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168
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+
|
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+
"""
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+
nodes_nbrs = ((n, G._pred[n], G._succ[n]) for n in G.nbunch_iter(nodes))
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+
|
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172
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+
for i, preds, succs in nodes_nbrs:
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+
ipreds = set(preds) - {i}
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|
+
isuccs = set(succs) - {i}
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175
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+
|
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176
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+
directed_triangles = 0
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177
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+
for j in chain(ipreds, isuccs):
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+
jpreds = set(G._pred[j]) - {j}
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+
jsuccs = set(G._succ[j]) - {j}
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+
directed_triangles += sum(
|
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+
1
|
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182
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+
for k in chain(
|
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+
(ipreds & jpreds),
|
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184
|
+
(ipreds & jsuccs),
|
|
185
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+
(isuccs & jpreds),
|
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186
|
+
(isuccs & jsuccs),
|
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187
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+
)
|
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188
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+
)
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+
dtotal = len(ipreds) + len(isuccs)
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+
dbidirectional = len(ipreds & isuccs)
|
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191
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+
yield (i, dtotal, dbidirectional, directed_triangles)
|
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+
|
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193
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+
|
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194
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+
@not_implemented_for("multigraph")
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195
|
+
def _directed_weighted_triangles_and_degree_iter(G, nodes=None, weight="weight"):
|
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+
"""Return an iterator of
|
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197
|
+
(node, total_degree, reciprocal_degree, directed_weighted_triangles).
|
|
198
|
+
|
|
199
|
+
Used for directed weighted clustering.
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200
|
+
Note that unlike `_weighted_triangles_and_degree_iter()`, this function counts
|
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201
|
+
directed triangles so does not count triangles twice.
|
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202
|
+
|
|
203
|
+
"""
|
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|
+
import numpy as np
|
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|
+
|
|
206
|
+
if weight is None or G.number_of_edges() == 0:
|
|
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+
max_weight = 1
|
|
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|
+
else:
|
|
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|
+
max_weight = max(d.get(weight, 1) for u, v, d in G.edges(data=True))
|
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+
|
|
211
|
+
nodes_nbrs = ((n, G._pred[n], G._succ[n]) for n in G.nbunch_iter(nodes))
|
|
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|
+
|
|
213
|
+
def wt(u, v):
|
|
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|
+
return G[u][v].get(weight, 1) / max_weight
|
|
215
|
+
|
|
216
|
+
for i, preds, succs in nodes_nbrs:
|
|
217
|
+
ipreds = set(preds) - {i}
|
|
218
|
+
isuccs = set(succs) - {i}
|
|
219
|
+
|
|
220
|
+
directed_triangles = 0
|
|
221
|
+
for j in ipreds:
|
|
222
|
+
jpreds = set(G._pred[j]) - {j}
|
|
223
|
+
jsuccs = set(G._succ[j]) - {j}
|
|
224
|
+
directed_triangles += np.cbrt(
|
|
225
|
+
[(wt(j, i) * wt(k, i) * wt(k, j)) for k in ipreds & jpreds]
|
|
226
|
+
).sum()
|
|
227
|
+
directed_triangles += np.cbrt(
|
|
228
|
+
[(wt(j, i) * wt(k, i) * wt(j, k)) for k in ipreds & jsuccs]
|
|
229
|
+
).sum()
|
|
230
|
+
directed_triangles += np.cbrt(
|
|
231
|
+
[(wt(j, i) * wt(i, k) * wt(k, j)) for k in isuccs & jpreds]
|
|
232
|
+
).sum()
|
|
233
|
+
directed_triangles += np.cbrt(
|
|
234
|
+
[(wt(j, i) * wt(i, k) * wt(j, k)) for k in isuccs & jsuccs]
|
|
235
|
+
).sum()
|
|
236
|
+
|
|
237
|
+
for j in isuccs:
|
|
238
|
+
jpreds = set(G._pred[j]) - {j}
|
|
239
|
+
jsuccs = set(G._succ[j]) - {j}
|
|
240
|
+
directed_triangles += np.cbrt(
|
|
241
|
+
[(wt(i, j) * wt(k, i) * wt(k, j)) for k in ipreds & jpreds]
|
|
242
|
+
).sum()
|
|
243
|
+
directed_triangles += np.cbrt(
|
|
244
|
+
[(wt(i, j) * wt(k, i) * wt(j, k)) for k in ipreds & jsuccs]
|
|
245
|
+
).sum()
|
|
246
|
+
directed_triangles += np.cbrt(
|
|
247
|
+
[(wt(i, j) * wt(i, k) * wt(k, j)) for k in isuccs & jpreds]
|
|
248
|
+
).sum()
|
|
249
|
+
directed_triangles += np.cbrt(
|
|
250
|
+
[(wt(i, j) * wt(i, k) * wt(j, k)) for k in isuccs & jsuccs]
|
|
251
|
+
).sum()
|
|
252
|
+
|
|
253
|
+
dtotal = len(ipreds) + len(isuccs)
|
|
254
|
+
dbidirectional = len(ipreds & isuccs)
|
|
255
|
+
yield (i, dtotal, dbidirectional, float(directed_triangles))
|
|
256
|
+
|
|
257
|
+
|
|
258
|
+
@not_implemented_for("directed")
|
|
259
|
+
@nx._dispatchable
|
|
260
|
+
def all_triangles(G, nbunch=None):
|
|
261
|
+
"""
|
|
262
|
+
Yields all unique triangles in an undirected graph.
|
|
263
|
+
|
|
264
|
+
A triangle is a set of three distinct nodes where each node is connected to
|
|
265
|
+
the other two.
|
|
266
|
+
|
|
267
|
+
Parameters
|
|
268
|
+
----------
|
|
269
|
+
G : NetworkX graph
|
|
270
|
+
An undirected graph.
|
|
271
|
+
|
|
272
|
+
nbunch : node, iterable of nodes, or None (default=None)
|
|
273
|
+
If a node or iterable of nodes, only triangles involving at least one
|
|
274
|
+
node in `nbunch` are yielded.
|
|
275
|
+
If ``None``, yields all unique triangles in the graph.
|
|
276
|
+
|
|
277
|
+
Yields
|
|
278
|
+
------
|
|
279
|
+
tuple
|
|
280
|
+
A tuple of three nodes forming a triangle ``(u, v, w)``.
|
|
281
|
+
|
|
282
|
+
Examples
|
|
283
|
+
--------
|
|
284
|
+
>>> G = nx.complete_graph(4)
|
|
285
|
+
>>> sorted([sorted(t) for t in all_triangles(G)])
|
|
286
|
+
[[0, 1, 2], [0, 1, 3], [0, 2, 3], [1, 2, 3]]
|
|
287
|
+
|
|
288
|
+
Notes
|
|
289
|
+
-----
|
|
290
|
+
This algorithm ensures each triangle is yielded once using an internal node ordering.
|
|
291
|
+
In multigraphs, triangles are identified by their unique set of nodes,
|
|
292
|
+
ignoring multiple edges between the same nodes. Self-loops are ignored.
|
|
293
|
+
Runs in ``O(m * d)`` time in the worst case, where ``m`` the number of edges
|
|
294
|
+
and ``d`` the maximum degree.
|
|
295
|
+
|
|
296
|
+
See Also
|
|
297
|
+
--------
|
|
298
|
+
:func:`~networkx.algorithms.triads.all_triads` : related function for directed graphs
|
|
299
|
+
"""
|
|
300
|
+
if nbunch is None:
|
|
301
|
+
nbunch = relevant_nodes = G
|
|
302
|
+
else:
|
|
303
|
+
nbunch = dict.fromkeys(G.nbunch_iter(nbunch))
|
|
304
|
+
relevant_nodes = chain(
|
|
305
|
+
nbunch,
|
|
306
|
+
(nbr for node in nbunch for nbr in G.neighbors(node) if nbr not in nbunch),
|
|
307
|
+
)
|
|
308
|
+
|
|
309
|
+
node_to_id = {node: i for i, node in enumerate(relevant_nodes)}
|
|
310
|
+
|
|
311
|
+
for u in nbunch:
|
|
312
|
+
u_id = node_to_id[u]
|
|
313
|
+
u_nbrs = G._adj[u].keys()
|
|
314
|
+
for v in u_nbrs:
|
|
315
|
+
v_id = node_to_id.get(v, -1)
|
|
316
|
+
if v_id <= u_id:
|
|
317
|
+
continue
|
|
318
|
+
v_nbrs = G._adj[v].keys()
|
|
319
|
+
for w in v_nbrs & u_nbrs:
|
|
320
|
+
if node_to_id.get(w, -1) > v_id:
|
|
321
|
+
yield u, v, w
|
|
322
|
+
|
|
323
|
+
|
|
324
|
+
@nx._dispatchable(edge_attrs="weight")
|
|
325
|
+
def average_clustering(G, nodes=None, weight=None, count_zeros=True):
|
|
326
|
+
r"""Compute the average clustering coefficient for the graph G.
|
|
327
|
+
|
|
328
|
+
The clustering coefficient for the graph is the average,
|
|
329
|
+
|
|
330
|
+
.. math::
|
|
331
|
+
|
|
332
|
+
C = \frac{1}{n}\sum_{v \in G} c_v,
|
|
333
|
+
|
|
334
|
+
where :math:`n` is the number of nodes in `G`.
|
|
335
|
+
|
|
336
|
+
Parameters
|
|
337
|
+
----------
|
|
338
|
+
G : graph
|
|
339
|
+
|
|
340
|
+
nodes : container of nodes, optional (default=all nodes in G)
|
|
341
|
+
Compute average clustering for nodes in this container.
|
|
342
|
+
|
|
343
|
+
weight : string or None, optional (default=None)
|
|
344
|
+
The edge attribute that holds the numerical value used as a weight.
|
|
345
|
+
If None, then each edge has weight 1.
|
|
346
|
+
|
|
347
|
+
count_zeros : bool
|
|
348
|
+
If False include only the nodes with nonzero clustering in the average.
|
|
349
|
+
|
|
350
|
+
Returns
|
|
351
|
+
-------
|
|
352
|
+
avg : float
|
|
353
|
+
Average clustering
|
|
354
|
+
|
|
355
|
+
Examples
|
|
356
|
+
--------
|
|
357
|
+
>>> G = nx.complete_graph(5)
|
|
358
|
+
>>> print(nx.average_clustering(G))
|
|
359
|
+
1.0
|
|
360
|
+
|
|
361
|
+
Notes
|
|
362
|
+
-----
|
|
363
|
+
This is a space saving routine; it might be faster
|
|
364
|
+
to use the clustering function to get a list and then take the average.
|
|
365
|
+
|
|
366
|
+
Self loops are ignored.
|
|
367
|
+
|
|
368
|
+
References
|
|
369
|
+
----------
|
|
370
|
+
.. [1] Generalizations of the clustering coefficient to weighted
|
|
371
|
+
complex networks by J. Saramäki, M. Kivelä, J.-P. Onnela,
|
|
372
|
+
K. Kaski, and J. Kertész, Physical Review E, 75 027105 (2007).
|
|
373
|
+
http://jponnela.com/web_documents/a9.pdf
|
|
374
|
+
.. [2] Marcus Kaiser, Mean clustering coefficients: the role of isolated
|
|
375
|
+
nodes and leafs on clustering measures for small-world networks.
|
|
376
|
+
https://arxiv.org/abs/0802.2512
|
|
377
|
+
"""
|
|
378
|
+
c = clustering(G, nodes, weight=weight).values()
|
|
379
|
+
if not count_zeros:
|
|
380
|
+
c = [v for v in c if abs(v) > 0]
|
|
381
|
+
return sum(c) / len(c)
|
|
382
|
+
|
|
383
|
+
|
|
384
|
+
@nx._dispatchable(edge_attrs="weight")
|
|
385
|
+
def clustering(G, nodes=None, weight=None):
|
|
386
|
+
r"""Compute the clustering coefficient for nodes.
|
|
387
|
+
|
|
388
|
+
For unweighted graphs, the clustering of a node :math:`u`
|
|
389
|
+
is the fraction of possible triangles through that node that exist,
|
|
390
|
+
|
|
391
|
+
.. math::
|
|
392
|
+
|
|
393
|
+
c_u = \frac{2 T(u)}{deg(u)(deg(u)-1)},
|
|
394
|
+
|
|
395
|
+
where :math:`T(u)` is the number of triangles through node :math:`u` and
|
|
396
|
+
:math:`deg(u)` is the degree of :math:`u`.
|
|
397
|
+
|
|
398
|
+
For weighted graphs, there are several ways to define clustering [1]_.
|
|
399
|
+
the one used here is defined
|
|
400
|
+
as the geometric average of the subgraph edge weights [2]_,
|
|
401
|
+
|
|
402
|
+
.. math::
|
|
403
|
+
|
|
404
|
+
c_u = \frac{1}{deg(u)(deg(u)-1))}
|
|
405
|
+
\sum_{vw} (\hat{w}_{uv} \hat{w}_{uw} \hat{w}_{vw})^{1/3}.
|
|
406
|
+
|
|
407
|
+
The edge weights :math:`\hat{w}_{uv}` are normalized by the maximum weight
|
|
408
|
+
in the network :math:`\hat{w}_{uv} = w_{uv}/\max(w)`.
|
|
409
|
+
|
|
410
|
+
The value of :math:`c_u` is assigned to 0 if :math:`deg(u) < 2`.
|
|
411
|
+
|
|
412
|
+
Additionally, this weighted definition has been generalized to support negative edge weights [3]_.
|
|
413
|
+
|
|
414
|
+
For directed graphs, the clustering is similarly defined as the fraction
|
|
415
|
+
of all possible directed triangles or geometric average of the subgraph
|
|
416
|
+
edge weights for unweighted and weighted directed graph respectively [4]_.
|
|
417
|
+
|
|
418
|
+
.. math::
|
|
419
|
+
|
|
420
|
+
c_u = \frac{T(u)}{2(deg^{tot}(u)(deg^{tot}(u)-1) - 2deg^{\leftrightarrow}(u))},
|
|
421
|
+
|
|
422
|
+
where :math:`T(u)` is the number of directed triangles through node
|
|
423
|
+
:math:`u`, :math:`deg^{tot}(u)` is the sum of in degree and out degree of
|
|
424
|
+
:math:`u` and :math:`deg^{\leftrightarrow}(u)` is the reciprocal degree of
|
|
425
|
+
:math:`u`.
|
|
426
|
+
|
|
427
|
+
|
|
428
|
+
Parameters
|
|
429
|
+
----------
|
|
430
|
+
G : graph
|
|
431
|
+
|
|
432
|
+
nodes : node, iterable of nodes, or None (default=None)
|
|
433
|
+
If a singleton node, return the number of triangles for that node.
|
|
434
|
+
If an iterable, compute the number of triangles for each of those nodes.
|
|
435
|
+
If `None` (the default) compute the number of triangles for all nodes in `G`.
|
|
436
|
+
|
|
437
|
+
weight : string or None, optional (default=None)
|
|
438
|
+
The edge attribute that holds the numerical value used as a weight.
|
|
439
|
+
If None, then each edge has weight 1.
|
|
440
|
+
|
|
441
|
+
Returns
|
|
442
|
+
-------
|
|
443
|
+
out : float, or dictionary
|
|
444
|
+
Clustering coefficient at specified nodes
|
|
445
|
+
|
|
446
|
+
Examples
|
|
447
|
+
--------
|
|
448
|
+
>>> G = nx.complete_graph(5)
|
|
449
|
+
>>> print(nx.clustering(G, 0))
|
|
450
|
+
1.0
|
|
451
|
+
>>> print(nx.clustering(G))
|
|
452
|
+
{0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0, 4: 1.0}
|
|
453
|
+
|
|
454
|
+
Notes
|
|
455
|
+
-----
|
|
456
|
+
Self loops are ignored.
|
|
457
|
+
|
|
458
|
+
References
|
|
459
|
+
----------
|
|
460
|
+
.. [1] Generalizations of the clustering coefficient to weighted
|
|
461
|
+
complex networks by J. Saramäki, M. Kivelä, J.-P. Onnela,
|
|
462
|
+
K. Kaski, and J. Kertész, Physical Review E, 75 027105 (2007).
|
|
463
|
+
http://jponnela.com/web_documents/a9.pdf
|
|
464
|
+
.. [2] Intensity and coherence of motifs in weighted complex
|
|
465
|
+
networks by J. P. Onnela, J. Saramäki, J. Kertész, and K. Kaski,
|
|
466
|
+
Physical Review E, 71(6), 065103 (2005).
|
|
467
|
+
.. [3] Generalization of Clustering Coefficients to Signed Correlation Networks
|
|
468
|
+
by G. Costantini and M. Perugini, PloS one, 9(2), e88669 (2014).
|
|
469
|
+
.. [4] Clustering in complex directed networks by G. Fagiolo,
|
|
470
|
+
Physical Review E, 76(2), 026107 (2007).
|
|
471
|
+
"""
|
|
472
|
+
if G.is_directed():
|
|
473
|
+
if weight is not None:
|
|
474
|
+
td_iter = _directed_weighted_triangles_and_degree_iter(G, nodes, weight)
|
|
475
|
+
clusterc = {
|
|
476
|
+
v: 0 if t == 0 else t / ((dt * (dt - 1) - 2 * db) * 2)
|
|
477
|
+
for v, dt, db, t in td_iter
|
|
478
|
+
}
|
|
479
|
+
else:
|
|
480
|
+
td_iter = _directed_triangles_and_degree_iter(G, nodes)
|
|
481
|
+
clusterc = {
|
|
482
|
+
v: 0 if t == 0 else t / ((dt * (dt - 1) - 2 * db) * 2)
|
|
483
|
+
for v, dt, db, t in td_iter
|
|
484
|
+
}
|
|
485
|
+
else:
|
|
486
|
+
# The formula 2*T/(d*(d-1)) from docs is t/(d*(d-1)) here b/c t==2*T
|
|
487
|
+
if weight is not None:
|
|
488
|
+
td_iter = _weighted_triangles_and_degree_iter(G, nodes, weight)
|
|
489
|
+
clusterc = {v: 0 if t == 0 else t / (d * (d - 1)) for v, d, t in td_iter}
|
|
490
|
+
else:
|
|
491
|
+
td_iter = _triangles_and_degree_iter(G, nodes)
|
|
492
|
+
clusterc = {v: 0 if t == 0 else t / (d * (d - 1)) for v, d, t, _ in td_iter}
|
|
493
|
+
if nodes in G:
|
|
494
|
+
# Return the value of the sole entry in the dictionary.
|
|
495
|
+
return clusterc[nodes]
|
|
496
|
+
return clusterc
|
|
497
|
+
|
|
498
|
+
|
|
499
|
+
@nx._dispatchable
|
|
500
|
+
def transitivity(G):
|
|
501
|
+
r"""Compute graph transitivity, the fraction of all possible triangles
|
|
502
|
+
present in G.
|
|
503
|
+
|
|
504
|
+
Possible triangles are identified by the number of "triads"
|
|
505
|
+
(two edges with a shared vertex).
|
|
506
|
+
|
|
507
|
+
The transitivity is
|
|
508
|
+
|
|
509
|
+
.. math::
|
|
510
|
+
|
|
511
|
+
T = 3\frac{\#triangles}{\#triads}.
|
|
512
|
+
|
|
513
|
+
Parameters
|
|
514
|
+
----------
|
|
515
|
+
G : graph
|
|
516
|
+
|
|
517
|
+
Returns
|
|
518
|
+
-------
|
|
519
|
+
out : float
|
|
520
|
+
Transitivity
|
|
521
|
+
|
|
522
|
+
Notes
|
|
523
|
+
-----
|
|
524
|
+
Self loops are ignored.
|
|
525
|
+
|
|
526
|
+
Examples
|
|
527
|
+
--------
|
|
528
|
+
>>> G = nx.complete_graph(5)
|
|
529
|
+
>>> print(nx.transitivity(G))
|
|
530
|
+
1.0
|
|
531
|
+
"""
|
|
532
|
+
triangles_contri = [
|
|
533
|
+
(t, d * (d - 1)) for v, d, t, _ in _triangles_and_degree_iter(G)
|
|
534
|
+
]
|
|
535
|
+
# If the graph is empty
|
|
536
|
+
if len(triangles_contri) == 0:
|
|
537
|
+
return 0
|
|
538
|
+
triangles, contri = map(sum, zip(*triangles_contri))
|
|
539
|
+
return 0 if triangles == 0 else triangles / contri
|
|
540
|
+
|
|
541
|
+
|
|
542
|
+
@nx._dispatchable
|
|
543
|
+
def square_clustering(G, nodes=None):
|
|
544
|
+
r"""Compute the squares clustering coefficient for nodes.
|
|
545
|
+
|
|
546
|
+
For each node return the fraction of possible squares that exist at
|
|
547
|
+
the node [1]_
|
|
548
|
+
|
|
549
|
+
.. math::
|
|
550
|
+
C_4(v) = \frac{ \sum_{u=1}^{k_v}
|
|
551
|
+
\sum_{w=u+1}^{k_v} q_v(u,w) }{ \sum_{u=1}^{k_v}
|
|
552
|
+
\sum_{w=u+1}^{k_v} [a_v(u,w) + q_v(u,w)]},
|
|
553
|
+
|
|
554
|
+
where :math:`q_v(u,w)` are the number of common neighbors of :math:`u` and
|
|
555
|
+
:math:`w` other than :math:`v` (ie squares), and :math:`a_v(u,w) = (k_u -
|
|
556
|
+
(1+q_v(u,w)+\theta_{uv})) + (k_w - (1+q_v(u,w)+\theta_{uw}))`, where
|
|
557
|
+
:math:`\theta_{uw} = 1` if :math:`u` and :math:`w` are connected and 0
|
|
558
|
+
otherwise. [2]_
|
|
559
|
+
|
|
560
|
+
Parameters
|
|
561
|
+
----------
|
|
562
|
+
G : graph
|
|
563
|
+
|
|
564
|
+
nodes : container of nodes, optional (default=all nodes in G)
|
|
565
|
+
Compute clustering for nodes in this container.
|
|
566
|
+
|
|
567
|
+
Returns
|
|
568
|
+
-------
|
|
569
|
+
c4 : dictionary
|
|
570
|
+
A dictionary keyed by node with the square clustering coefficient value.
|
|
571
|
+
|
|
572
|
+
Examples
|
|
573
|
+
--------
|
|
574
|
+
>>> G = nx.complete_graph(5)
|
|
575
|
+
>>> print(nx.square_clustering(G, 0))
|
|
576
|
+
1.0
|
|
577
|
+
>>> print(nx.square_clustering(G))
|
|
578
|
+
{0: 1.0, 1: 1.0, 2: 1.0, 3: 1.0, 4: 1.0}
|
|
579
|
+
|
|
580
|
+
Notes
|
|
581
|
+
-----
|
|
582
|
+
Self loops are ignored.
|
|
583
|
+
|
|
584
|
+
While :math:`C_3(v)` (triangle clustering) gives the probability that
|
|
585
|
+
two neighbors of node v are connected with each other, :math:`C_4(v)` is
|
|
586
|
+
the probability that two neighbors of node v share a common
|
|
587
|
+
neighbor different from v. This algorithm can be applied to both
|
|
588
|
+
bipartite and unipartite networks.
|
|
589
|
+
|
|
590
|
+
References
|
|
591
|
+
----------
|
|
592
|
+
.. [1] Pedro G. Lind, Marta C. González, and Hans J. Herrmann. 2005
|
|
593
|
+
Cycles and clustering in bipartite networks.
|
|
594
|
+
Physical Review E (72) 056127.
|
|
595
|
+
.. [2] Zhang, Peng et al. Clustering Coefficient and Community Structure of
|
|
596
|
+
Bipartite Networks. Physica A: Statistical Mechanics and its Applications 387.27 (2008): 6869–6875.
|
|
597
|
+
https://arxiv.org/abs/0710.0117v1
|
|
598
|
+
"""
|
|
599
|
+
if nodes is None:
|
|
600
|
+
node_iter = G
|
|
601
|
+
else:
|
|
602
|
+
node_iter = G.nbunch_iter(nodes)
|
|
603
|
+
clustering = {}
|
|
604
|
+
_G_adj = G._adj
|
|
605
|
+
|
|
606
|
+
class GAdj(dict):
|
|
607
|
+
"""Calculate (and cache) node neighbor sets excluding self-loops."""
|
|
608
|
+
|
|
609
|
+
def __missing__(self, v):
|
|
610
|
+
v_neighbors = self[v] = set(_G_adj[v])
|
|
611
|
+
v_neighbors.discard(v) # Ignore self-loops
|
|
612
|
+
return v_neighbors
|
|
613
|
+
|
|
614
|
+
G_adj = GAdj() # Values are sets of neighbors (no self-loops)
|
|
615
|
+
|
|
616
|
+
for v in node_iter:
|
|
617
|
+
v_neighbors = G_adj[v]
|
|
618
|
+
v_degrees_m1 = len(v_neighbors) - 1 # degrees[v] - 1 (used below)
|
|
619
|
+
if v_degrees_m1 <= 0:
|
|
620
|
+
# Can't form a square without at least two neighbors
|
|
621
|
+
clustering[v] = 0
|
|
622
|
+
continue
|
|
623
|
+
|
|
624
|
+
# Count squares with nodes u-v-w-x from the current node v.
|
|
625
|
+
# Terms of the denominator: potential = uw_degrees - uw_count - triangles - squares
|
|
626
|
+
# uw_degrees: degrees[u] + degrees[w] for each u-w combo
|
|
627
|
+
uw_degrees = 0
|
|
628
|
+
# uw_count: 1 for each u and 1 for each w for all combos (degrees * (degrees - 1))
|
|
629
|
+
uw_count = len(v_neighbors) * v_degrees_m1
|
|
630
|
+
# triangles: 1 for each edge where u-w or w-u are connected (i.e. triangles)
|
|
631
|
+
triangles = 0
|
|
632
|
+
# squares: the number of squares (also the numerator)
|
|
633
|
+
squares = 0
|
|
634
|
+
|
|
635
|
+
# Iterate over all neighbors
|
|
636
|
+
for u in v_neighbors:
|
|
637
|
+
u_neighbors = G_adj[u]
|
|
638
|
+
uw_degrees += len(u_neighbors) * v_degrees_m1
|
|
639
|
+
# P2 from https://arxiv.org/abs/2007.11111
|
|
640
|
+
p2 = len(u_neighbors & v_neighbors)
|
|
641
|
+
# triangles is C_3, sigma_4 from https://arxiv.org/abs/2007.11111
|
|
642
|
+
# This double-counts triangles compared to `triangles` function
|
|
643
|
+
triangles += p2
|
|
644
|
+
# squares is C_4, sigma_12 from https://arxiv.org/abs/2007.11111
|
|
645
|
+
# Include this term, b/c a neighbor u can also be a neighbor of neighbor x
|
|
646
|
+
squares += p2 * (p2 - 1) # Will divide by 2 later
|
|
647
|
+
|
|
648
|
+
# And iterate over all neighbors of neighbors.
|
|
649
|
+
# These nodes x may be the corners opposite v in squares u-v-w-x.
|
|
650
|
+
two_hop_neighbors = set.union(*(G_adj[u] for u in v_neighbors))
|
|
651
|
+
two_hop_neighbors -= v_neighbors # Neighbors already counted above
|
|
652
|
+
two_hop_neighbors.discard(v)
|
|
653
|
+
for x in two_hop_neighbors:
|
|
654
|
+
p2 = len(v_neighbors & G_adj[x])
|
|
655
|
+
squares += p2 * (p2 - 1) # Will divide by 2 later
|
|
656
|
+
|
|
657
|
+
squares //= 2
|
|
658
|
+
potential = uw_degrees - uw_count - triangles - squares
|
|
659
|
+
if potential > 0:
|
|
660
|
+
clustering[v] = squares / potential
|
|
661
|
+
else:
|
|
662
|
+
clustering[v] = 0
|
|
663
|
+
if nodes in G:
|
|
664
|
+
# Return the value of the sole entry in the dictionary.
|
|
665
|
+
return clustering[nodes]
|
|
666
|
+
return clustering
|
|
667
|
+
|
|
668
|
+
|
|
669
|
+
@not_implemented_for("directed")
|
|
670
|
+
@nx._dispatchable
|
|
671
|
+
def generalized_degree(G, nodes=None):
|
|
672
|
+
r"""Compute the generalized degree for nodes.
|
|
673
|
+
|
|
674
|
+
For each node, the generalized degree shows how many edges of given
|
|
675
|
+
triangle multiplicity the node is connected to. The triangle multiplicity
|
|
676
|
+
of an edge is the number of triangles an edge participates in. The
|
|
677
|
+
generalized degree of node :math:`i` can be written as a vector
|
|
678
|
+
:math:`\mathbf{k}_i=(k_i^{(0)}, \dotsc, k_i^{(N-2)})` where
|
|
679
|
+
:math:`k_i^{(j)}` is the number of edges attached to node :math:`i` that
|
|
680
|
+
participate in :math:`j` triangles.
|
|
681
|
+
|
|
682
|
+
Parameters
|
|
683
|
+
----------
|
|
684
|
+
G : graph
|
|
685
|
+
|
|
686
|
+
nodes : container of nodes, optional (default=all nodes in G)
|
|
687
|
+
Compute the generalized degree for nodes in this container.
|
|
688
|
+
|
|
689
|
+
Returns
|
|
690
|
+
-------
|
|
691
|
+
out : Counter, or dictionary of Counters
|
|
692
|
+
Generalized degree of specified nodes. The Counter is keyed by edge
|
|
693
|
+
triangle multiplicity.
|
|
694
|
+
|
|
695
|
+
Examples
|
|
696
|
+
--------
|
|
697
|
+
>>> G = nx.complete_graph(5)
|
|
698
|
+
>>> print(nx.generalized_degree(G, 0))
|
|
699
|
+
Counter({3: 4})
|
|
700
|
+
>>> print(nx.generalized_degree(G))
|
|
701
|
+
{0: Counter({3: 4}), 1: Counter({3: 4}), 2: Counter({3: 4}), 3: Counter({3: 4}), 4: Counter({3: 4})}
|
|
702
|
+
|
|
703
|
+
To recover the number of triangles attached to a node:
|
|
704
|
+
|
|
705
|
+
>>> k1 = nx.generalized_degree(G, 0)
|
|
706
|
+
>>> sum([k * v for k, v in k1.items()]) / 2 == nx.triangles(G, 0)
|
|
707
|
+
True
|
|
708
|
+
|
|
709
|
+
Notes
|
|
710
|
+
-----
|
|
711
|
+
Self loops are ignored.
|
|
712
|
+
|
|
713
|
+
In a network of N nodes, the highest triangle multiplicity an edge can have
|
|
714
|
+
is N-2.
|
|
715
|
+
|
|
716
|
+
The return value does not include a `zero` entry if no edges of a
|
|
717
|
+
particular triangle multiplicity are present.
|
|
718
|
+
|
|
719
|
+
The number of triangles node :math:`i` is attached to can be recovered from
|
|
720
|
+
the generalized degree :math:`\mathbf{k}_i=(k_i^{(0)}, \dotsc,
|
|
721
|
+
k_i^{(N-2)})` by :math:`(k_i^{(1)}+2k_i^{(2)}+\dotsc +(N-2)k_i^{(N-2)})/2`.
|
|
722
|
+
|
|
723
|
+
References
|
|
724
|
+
----------
|
|
725
|
+
.. [1] Networks with arbitrary edge multiplicities by V. Zlatić,
|
|
726
|
+
D. Garlaschelli and G. Caldarelli, EPL (Europhysics Letters),
|
|
727
|
+
Volume 97, Number 2 (2012).
|
|
728
|
+
https://iopscience.iop.org/article/10.1209/0295-5075/97/28005
|
|
729
|
+
"""
|
|
730
|
+
if nodes in G:
|
|
731
|
+
return next(_triangles_and_degree_iter(G, nodes))[3]
|
|
732
|
+
return {v: gd for v, d, t, gd in _triangles_and_degree_iter(G, nodes)}
|