scikit-complexity 0.2.0__py3-none-any.whl

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  1. scikit_complexity-0.2.0.dist-info/METADATA +317 -0
  2. scikit_complexity-0.2.0.dist-info/RECORD +1748 -0
  3. scikit_complexity-0.2.0.dist-info/WHEEL +4 -0
  4. scikit_complexity-0.2.0.dist-info/entry_points.txt +4 -0
  5. scikit_complexity-0.2.0.dist-info/licenses/LICENSE +21 -0
  6. skcomplex/__init__.py +1 -0
  7. skcomplex/analysis/__init__.py +101 -0
  8. skcomplex/analysis/_alignment.py +263 -0
  9. skcomplex/analysis/_automata.py +658 -0
  10. skcomplex/analysis/_base.py +841 -0
  11. skcomplex/analysis/_clusters.py +298 -0
  12. skcomplex/analysis/_coarse_grain.py +183 -0
  13. skcomplex/analysis/_collapse.py +318 -0
  14. skcomplex/analysis/_complexity.py +129 -0
  15. skcomplex/analysis/_computational_mechanics.py +220 -0
  16. skcomplex/analysis/_correlation.py +364 -0
  17. skcomplex/analysis/_defects.py +111 -0
  18. skcomplex/analysis/_discovery.py +101 -0
  19. skcomplex/analysis/_displacement.py +135 -0
  20. skcomplex/analysis/_distribution.py +327 -0
  21. skcomplex/analysis/_domains.py +220 -0
  22. skcomplex/analysis/_embedding.py +235 -0
  23. skcomplex/analysis/_emergence.py +503 -0
  24. skcomplex/analysis/_entropy.py +425 -0
  25. skcomplex/analysis/_ergodicity.py +228 -0
  26. skcomplex/analysis/_events.py +301 -0
  27. skcomplex/analysis/_fit.py +368 -0
  28. skcomplex/analysis/_groups.py +205 -0
  29. skcomplex/analysis/_information.py +488 -0
  30. skcomplex/analysis/_invariants.py +409 -0
  31. skcomplex/analysis/_irreversibility.py +421 -0
  32. skcomplex/analysis/_kramers_moyal.py +104 -0
  33. skcomplex/analysis/_large_deviations.py +378 -0
  34. skcomplex/analysis/_linearization.py +231 -0
  35. skcomplex/analysis/_local_information.py +166 -0
  36. skcomplex/analysis/_loops.py +394 -0
  37. skcomplex/analysis/_lyapunov.py +342 -0
  38. skcomplex/analysis/_markov.py +303 -0
  39. skcomplex/analysis/_mode_decomposition.py +209 -0
  40. skcomplex/analysis/_motifs.py +239 -0
  41. skcomplex/analysis/_neighbors.py +303 -0
  42. skcomplex/analysis/_networks.py +286 -0
  43. skcomplex/analysis/_operator.py +312 -0
  44. skcomplex/analysis/_partial_information.py +118 -0
  45. skcomplex/analysis/_passage.py +244 -0
  46. skcomplex/analysis/_recurrence.py +202 -0
  47. skcomplex/analysis/_reservoirs.py +387 -0
  48. skcomplex/analysis/_rolling.py +168 -0
  49. skcomplex/analysis/_scaling.py +370 -0
  50. skcomplex/analysis/_sections.py +225 -0
  51. skcomplex/analysis/_signatures.py +250 -0
  52. skcomplex/analysis/_sparse_identification.py +398 -0
  53. skcomplex/analysis/_spectrum.py +164 -0
  54. skcomplex/analysis/_stability.py +547 -0
  55. skcomplex/analysis/_surrogates.py +127 -0
  56. skcomplex/analysis/_symbolic.py +639 -0
  57. skcomplex/analysis/types.py +43 -0
  58. skcomplex/base.py +159 -0
  59. skcomplex/core/__init__.py +1 -0
  60. skcomplex/core/base.py +150 -0
  61. skcomplex/core/elements/__init__.py +21 -0
  62. skcomplex/core/elements/_base.py +84 -0
  63. skcomplex/core/elements/_compartment.py +52 -0
  64. skcomplex/core/elements/_density.py +52 -0
  65. skcomplex/core/elements/_element.py +80 -0
  66. skcomplex/core/elements/_field.py +192 -0
  67. skcomplex/core/elements/_group.py +241 -0
  68. skcomplex/core/elements/_lattice.py +115 -0
  69. skcomplex/core/elements/_point.py +66 -0
  70. skcomplex/core/interactions/__init__.py +89 -0
  71. skcomplex/core/interactions/_advection.py +134 -0
  72. skcomplex/core/interactions/_base.py +361 -0
  73. skcomplex/core/interactions/_cascade.py +195 -0
  74. skcomplex/core/interactions/_choice.py +320 -0
  75. skcomplex/core/interactions/_conservation.py +164 -0
  76. skcomplex/core/interactions/_coupling.py +741 -0
  77. skcomplex/core/interactions/_crossing.py +136 -0
  78. skcomplex/core/interactions/_diffusion.py +99 -0
  79. skcomplex/core/interactions/_encounter.py +201 -0
  80. skcomplex/core/interactions/_euler_lagrange.py +183 -0
  81. skcomplex/core/interactions/_evolution.py +520 -0
  82. skcomplex/core/interactions/_feedback.py +79 -0
  83. skcomplex/core/interactions/_gradient.py +293 -0
  84. skcomplex/core/interactions/_grouping.py +399 -0
  85. skcomplex/core/interactions/_hamiltonian.py +191 -0
  86. skcomplex/core/interactions/_hyperedge.py +96 -0
  87. skcomplex/core/interactions/_imitation.py +357 -0
  88. skcomplex/core/interactions/_impulse.py +133 -0
  89. skcomplex/core/interactions/_interaction.py +58 -0
  90. skcomplex/core/interactions/_jump.py +201 -0
  91. skcomplex/core/interactions/_life_cycle.py +424 -0
  92. skcomplex/core/interactions/_local_rule.py +134 -0
  93. skcomplex/core/interactions/_map.py +239 -0
  94. skcomplex/core/interactions/_matching.py +701 -0
  95. skcomplex/core/interactions/_movement.py +377 -0
  96. skcomplex/core/interactions/_neighbor.py +88 -0
  97. skcomplex/core/interactions/_optimization.py +206 -0
  98. skcomplex/core/interactions/_pair.py +82 -0
  99. skcomplex/core/interactions/_pair_coupling.py +169 -0
  100. skcomplex/core/interactions/_rate.py +240 -0
  101. skcomplex/core/interactions/_reaction.py +466 -0
  102. skcomplex/core/interactions/_reinforcement.py +226 -0
  103. skcomplex/core/interactions/_relaxation.py +103 -0
  104. skcomplex/core/interactions/_sampling.py +177 -0
  105. skcomplex/core/interactions/_satisfiability.py +145 -0
  106. skcomplex/core/interactions/_sign_adjustment.py +222 -0
  107. skcomplex/core/interactions/_topology.py +215 -0
  108. skcomplex/core/interactions/_training.py +184 -0
  109. skcomplex/core/interactions/_transfer.py +669 -0
  110. skcomplex/core/interactions/_transition.py +427 -0
  111. skcomplex/core/laws/__init__.py +60 -0
  112. skcomplex/core/laws/_base.py +194 -0
  113. skcomplex/core/laws/_bilinear.py +91 -0
  114. skcomplex/core/laws/_boundary.py +59 -0
  115. skcomplex/core/laws/_cascade.py +79 -0
  116. skcomplex/core/laws/_crossing.py +87 -0
  117. skcomplex/core/laws/_dissipator.py +79 -0
  118. skcomplex/core/laws/_drive.py +56 -0
  119. skcomplex/core/laws/_emission.py +81 -0
  120. skcomplex/core/laws/_encounter.py +96 -0
  121. skcomplex/core/laws/_equation.py +105 -0
  122. skcomplex/core/laws/_extremal.py +94 -0
  123. skcomplex/core/laws/_flux.py +108 -0
  124. skcomplex/core/laws/_fractional_noise.py +65 -0
  125. skcomplex/core/laws/_generator.py +66 -0
  126. skcomplex/core/laws/_gradient_step.py +89 -0
  127. skcomplex/core/laws/_jump.py +137 -0
  128. skcomplex/core/laws/_local_rule.py +92 -0
  129. skcomplex/core/laws/_match.py +321 -0
  130. skcomplex/core/laws/_noise.py +125 -0
  131. skcomplex/core/laws/_rate.py +82 -0
  132. skcomplex/core/laws/_rule.py +82 -0
  133. skcomplex/core/laws/_sample.py +65 -0
  134. skcomplex/core/laws/_transfer.py +165 -0
  135. skcomplex/core/laws/_transition.py +77 -0
  136. skcomplex/core/laws/_update.py +121 -0
  137. skcomplex/core/laws/utils/__init__.py +142 -0
  138. skcomplex/core/laws/utils/_agents.py +127 -0
  139. skcomplex/core/laws/utils/_components.py +63 -0
  140. skcomplex/core/laws/utils/_conditions.py +198 -0
  141. skcomplex/core/laws/utils/_contractions.py +74 -0
  142. skcomplex/core/laws/utils/_delays.py +170 -0
  143. skcomplex/core/laws/utils/_history.py +167 -0
  144. skcomplex/core/laws/utils/_local_operators.py +68 -0
  145. skcomplex/core/laws/utils/_lookups.py +40 -0
  146. skcomplex/core/laws/utils/_moments.py +122 -0
  147. skcomplex/core/laws/utils/_operators.py +237 -0
  148. skcomplex/core/laws/utils/_phase.py +126 -0
  149. skcomplex/core/laws/utils/_pointwise.py +160 -0
  150. skcomplex/core/laws/utils/_reductions.py +942 -0
  151. skcomplex/core/laws/utils/_signals.py +214 -0
  152. skcomplex/core/laws/utils/_tables.py +4 -0
  153. skcomplex/core/laws/utils/_tensors.py +235 -0
  154. skcomplex/core/spaces/__init__.py +52 -0
  155. skcomplex/core/spaces/_adjacency.py +34 -0
  156. skcomplex/core/spaces/_base.py +218 -0
  157. skcomplex/core/spaces/_box.py +41 -0
  158. skcomplex/core/spaces/_cayley.py +352 -0
  159. skcomplex/core/spaces/_cone.py +65 -0
  160. skcomplex/core/spaces/_continuous.py +93 -0
  161. skcomplex/core/spaces/_continuous_time.py +27 -0
  162. skcomplex/core/spaces/_discrete_time.py +53 -0
  163. skcomplex/core/spaces/_generator.py +51 -0
  164. skcomplex/core/spaces/_lattice.py +194 -0
  165. skcomplex/core/spaces/_lattice_neighborhood.py +50 -0
  166. skcomplex/core/spaces/_memory.py +45 -0
  167. skcomplex/core/spaces/_mesh.py +71 -0
  168. skcomplex/core/spaces/_moore.py +49 -0
  169. skcomplex/core/spaces/_nearest.py +41 -0
  170. skcomplex/core/spaces/_network.py +256 -0
  171. skcomplex/core/spaces/_phase.py +136 -0
  172. skcomplex/core/spaces/_radius.py +40 -0
  173. skcomplex/core/spaces/_static_time.py +34 -0
  174. skcomplex/core/spaces/_triangular.py +37 -0
  175. skcomplex/core/spaces/_von_neumann.py +51 -0
  176. skcomplex/core/specs/__init__.py +25 -0
  177. skcomplex/core/specs/_census_record_spec.py +72 -0
  178. skcomplex/core/specs/_census_spec.py +40 -0
  179. skcomplex/core/specs/_compiled_agents_spec.py +62 -0
  180. skcomplex/core/specs/_compiled_element_spec.py +59 -0
  181. skcomplex/core/specs/_compiled_interaction_spec.py +33 -0
  182. skcomplex/core/specs/_lattice_context_spec.py +40 -0
  183. skcomplex/core/specs/_lattice_state_spec.py +49 -0
  184. skcomplex/core/specs/_node_spec.py +64 -0
  185. skcomplex/core/specs/_operator_view_spec.py +135 -0
  186. skcomplex/core/specs/_scenario_spec.py +45 -0
  187. skcomplex/core/specs/_subsystem_spec.py +24 -0
  188. skcomplex/core/system.py +140 -0
  189. skcomplex/core/types.py +249 -0
  190. skcomplex/engine/__init__.py +5 -0
  191. skcomplex/engine/_utils.py +278 -0
  192. skcomplex/engine/backends/__init__.py +13 -0
  193. skcomplex/engine/backends/_base.py +329 -0
  194. skcomplex/engine/backends/_jax.py +285 -0
  195. skcomplex/engine/backends/_numba.py +601 -0
  196. skcomplex/engine/backends/_numba_components.py +67 -0
  197. skcomplex/engine/backends/_numba_loops.py +163 -0
  198. skcomplex/engine/backends/_numba_neighbours.py +435 -0
  199. skcomplex/engine/backends/_numba_printer.py +1023 -0
  200. skcomplex/engine/backends/_numba_stencils.py +66 -0
  201. skcomplex/engine/backends/_numpy.py +215 -0
  202. skcomplex/engine/compile/__init__.py +27 -0
  203. skcomplex/engine/compile/_base.py +582 -0
  204. skcomplex/engine/compile/_bound_renewal_spec.py +47 -0
  205. skcomplex/engine/compile/_compilation.py +351 -0
  206. skcomplex/engine/compile/_compile.py +100 -0
  207. skcomplex/engine/compile/_complex.py +216 -0
  208. skcomplex/engine/compile/_draw_lowering.py +373 -0
  209. skcomplex/engine/compile/_field_lowering.py +1668 -0
  210. skcomplex/engine/compile/_flows.py +691 -0
  211. skcomplex/engine/compile/_forms.py +48 -0
  212. skcomplex/engine/compile/_laws.py +42 -0
  213. skcomplex/engine/compile/_learning_compiler.py +481 -0
  214. skcomplex/engine/compile/_member_reductions.py +206 -0
  215. skcomplex/engine/compile/_members.py +244 -0
  216. skcomplex/engine/compile/_observables.py +940 -0
  217. skcomplex/engine/compile/_observer.py +185 -0
  218. skcomplex/engine/compile/_pass_compiler.py +1534 -0
  219. skcomplex/engine/compile/_probe.py +78 -0
  220. skcomplex/engine/compile/_renewal_law.py +70 -0
  221. skcomplex/engine/compile/passes/__init__.py +34 -0
  222. skcomplex/engine/compile/passes/_agents.py +111 -0
  223. skcomplex/engine/compile/passes/_agents_problem.py +143 -0
  224. skcomplex/engine/compile/passes/_census.py +808 -0
  225. skcomplex/engine/compile/passes/_check_fractional_noise.py +107 -0
  226. skcomplex/engine/compile/passes/_collect.py +31 -0
  227. skcomplex/engine/compile/passes/_compile_encounters.py +301 -0
  228. skcomplex/engine/compile/passes/_complex.py +198 -0
  229. skcomplex/engine/compile/passes/_conserved_noise.py +224 -0
  230. skcomplex/engine/compile/passes/_core.py +116 -0
  231. skcomplex/engine/compile/passes/_declare_renewals.py +84 -0
  232. skcomplex/engine/compile/passes/_draws.py +29 -0
  233. skcomplex/engine/compile/passes/_encounter_functions.py +60 -0
  234. skcomplex/engine/compile/passes/_encounter_jacobian.py +25 -0
  235. skcomplex/engine/compile/passes/_encounter_problem.py +32 -0
  236. skcomplex/engine/compile/passes/_events.py +204 -0
  237. skcomplex/engine/compile/passes/_expand_flows.py +32 -0
  238. skcomplex/engine/compile/passes/_field_functions.py +647 -0
  239. skcomplex/engine/compile/passes/_field_jacobian.py +38 -0
  240. skcomplex/engine/compile/passes/_field_problem.py +106 -0
  241. skcomplex/engine/compile/passes/_flatten.py +339 -0
  242. skcomplex/engine/compile/passes/_flows_problem.py +29 -0
  243. skcomplex/engine/compile/passes/_form.py +82 -0
  244. skcomplex/engine/compile/passes/_fractional_form.py +172 -0
  245. skcomplex/engine/compile/passes/_fractional_problem.py +91 -0
  246. skcomplex/engine/compile/passes/_functions.py +485 -0
  247. skcomplex/engine/compile/passes/_hilbert_space_error.py +10 -0
  248. skcomplex/engine/compile/passes/_hyperedges.py +598 -0
  249. skcomplex/engine/compile/passes/_jacobian.py +38 -0
  250. skcomplex/engine/compile/passes/_kernels.py +407 -0
  251. skcomplex/engine/compile/passes/_lattices.py +818 -0
  252. skcomplex/engine/compile/passes/_layout.py +667 -0
  253. skcomplex/engine/compile/passes/_lower_fields.py +225 -0
  254. skcomplex/engine/compile/passes/_lower_flows.py +28 -0
  255. skcomplex/engine/compile/passes/_markov.py +329 -0
  256. skcomplex/engine/compile/passes/_mask_requests.py +121 -0
  257. skcomplex/engine/compile/passes/_members.py +30 -0
  258. skcomplex/engine/compile/passes/_noise.py +196 -0
  259. skcomplex/engine/compile/passes/_operator_compiler.py +843 -0
  260. skcomplex/engine/compile/passes/_orders.py +409 -0
  261. skcomplex/engine/compile/passes/_owners.py +90 -0
  262. skcomplex/engine/compile/passes/_particles.py +69 -0
  263. skcomplex/engine/compile/passes/_plan.py +130 -0
  264. skcomplex/engine/compile/passes/_problem.py +802 -0
  265. skcomplex/engine/compile/passes/_reduction_lowering.py +1193 -0
  266. skcomplex/engine/compile/passes/_reductions.py +84 -0
  267. skcomplex/engine/compile/passes/_renewal_problem.py +357 -0
  268. skcomplex/engine/compile/passes/_request_jumps.py +51 -0
  269. skcomplex/engine/compile/passes/_residences.py +140 -0
  270. skcomplex/engine/compile/passes/_rows.py +162 -0
  271. skcomplex/engine/compile/passes/_set_renewals_apart.py +29 -0
  272. skcomplex/engine/compile/passes/_set_rules_apart.py +28 -0
  273. skcomplex/engine/compile/passes/_specs.py +1317 -0
  274. skcomplex/engine/compile/passes/_split_requests.py +44 -0
  275. skcomplex/engine/compile/passes/_topology_functions.py +265 -0
  276. skcomplex/engine/compile/passes/_topology_problem.py +27 -0
  277. skcomplex/engine/compile/passes/_towards.py +66 -0
  278. skcomplex/engine/compile/passes/_unpack_matches.py +29 -0
  279. skcomplex/engine/compile/passes/_unpack_renewals.py +41 -0
  280. skcomplex/engine/problems/__init__.py +61 -0
  281. skcomplex/engine/problems/_base.py +150 -0
  282. skcomplex/engine/problems/_base_problem_spec.py +153 -0
  283. skcomplex/engine/problems/_block_spec.py +48 -0
  284. skcomplex/engine/problems/_born_spec.py +24 -0
  285. skcomplex/engine/problems/_cascade_kernel.py +134 -0
  286. skcomplex/engine/problems/_collision_kernel.py +147 -0
  287. skcomplex/engine/problems/_compiled_delay_spec.py +21 -0
  288. skcomplex/engine/problems/_compiled_request_spec.py +46 -0
  289. skcomplex/engine/problems/_control_problem_spec.py +90 -0
  290. skcomplex/engine/problems/_declarations_spec.py +126 -0
  291. skcomplex/engine/problems/_delayed_state_spec.py +50 -0
  292. skcomplex/engine/problems/_diffusive_limit_spec.py +50 -0
  293. skcomplex/engine/problems/_draw_kernel.py +128 -0
  294. skcomplex/engine/problems/_drive_kernel.py +65 -0
  295. skcomplex/engine/problems/_dynamics_spec.py +28 -0
  296. skcomplex/engine/problems/_edge_row_search.py +78 -0
  297. skcomplex/engine/problems/_edge_search.py +64 -0
  298. skcomplex/engine/problems/_encounter_kernel.py +200 -0
  299. skcomplex/engine/problems/_event_kernel.py +70 -0
  300. skcomplex/engine/problems/_expression_printer.py +410 -0
  301. skcomplex/engine/problems/_extremal_kernel.py +125 -0
  302. skcomplex/engine/problems/_field_operator_kernel.py +105 -0
  303. skcomplex/engine/problems/_finite_volume_kernel.py +423 -0
  304. skcomplex/engine/problems/_flow_term_spec.py +45 -0
  305. skcomplex/engine/problems/_frame_spec.py +105 -0
  306. skcomplex/engine/problems/_jacobian_kernel.py +575 -0
  307. skcomplex/engine/problems/_kernel_spec.py +130 -0
  308. skcomplex/engine/problems/_kinetic_problem_spec.py +23 -0
  309. skcomplex/engine/problems/_law_kernel.py +604 -0
  310. skcomplex/engine/problems/_learning_problem_spec.py +67 -0
  311. skcomplex/engine/problems/_linear_term_spec.py +50 -0
  312. skcomplex/engine/problems/_loop_term_spec.py +44 -0
  313. skcomplex/engine/problems/_lowered_kernels_spec.py +59 -0
  314. skcomplex/engine/problems/_markov_kernel.py +68 -0
  315. skcomplex/engine/problems/_metric_search.py +155 -0
  316. skcomplex/engine/problems/_monte_carlo_kernel.py +213 -0
  317. skcomplex/engine/problems/_neighborhood_kernel.py +594 -0
  318. skcomplex/engine/problems/_noise_term_spec.py +26 -0
  319. skcomplex/engine/problems/_observed_spec.py +22 -0
  320. skcomplex/engine/problems/_operator_kernel.py +102 -0
  321. skcomplex/engine/problems/_operator_lowering.py +323 -0
  322. skcomplex/engine/problems/_operator_problem_spec.py +138 -0
  323. skcomplex/engine/problems/_output_spec.py +78 -0
  324. skcomplex/engine/problems/_pair_search.py +86 -0
  325. skcomplex/engine/problems/_partials_spec.py +27 -0
  326. skcomplex/engine/problems/_partition_spec.py +39 -0
  327. skcomplex/engine/problems/_printed_spec.py +24 -0
  328. skcomplex/engine/problems/_problem_functions_spec.py +102 -0
  329. skcomplex/engine/problems/_problem_spec.py +365 -0
  330. skcomplex/engine/problems/_random_stream.py +49 -0
  331. skcomplex/engine/problems/_record_spec.py +22 -0
  332. skcomplex/engine/problems/_recorded_spec.py +21 -0
  333. skcomplex/engine/problems/_reduction_kernel.py +254 -0
  334. skcomplex/engine/problems/_reduction_schedule_spec.py +97 -0
  335. skcomplex/engine/problems/_reference_spec.py +114 -0
  336. skcomplex/engine/problems/_relation_spec.py +29 -0
  337. skcomplex/engine/problems/_renewal_kernel.py +250 -0
  338. skcomplex/engine/problems/_request_spec.py +27 -0
  339. skcomplex/engine/problems/_rule_kernel.py +227 -0
  340. skcomplex/engine/problems/_set_symbol_spec.py +28 -0
  341. skcomplex/engine/problems/_source_loader.py +113 -0
  342. skcomplex/engine/problems/_static_search.py +42 -0
  343. skcomplex/engine/problems/_steps.py +39 -0
  344. skcomplex/engine/problems/_sweep_spec.py +26 -0
  345. skcomplex/engine/problems/_symmetry_spec.py +29 -0
  346. skcomplex/engine/problems/_too_dense.py +8 -0
  347. skcomplex/engine/problems/_topology_kernel.py +589 -0
  348. skcomplex/engine/problems/_transfer_network.py +4 -0
  349. skcomplex/engine/problems/_transfer_network_spec.py +50 -0
  350. skcomplex/engine/problems/_transfer_state_spec.py +68 -0
  351. skcomplex/engine/runtime/__init__.py +22 -0
  352. skcomplex/engine/runtime/_as_fast_as_possible.py +17 -0
  353. skcomplex/engine/runtime/_base.py +137 -0
  354. skcomplex/engine/runtime/_conservation.py +125 -0
  355. skcomplex/engine/runtime/_invariants.py +100 -0
  356. skcomplex/engine/runtime/_real_time.py +55 -0
  357. skcomplex/engine/runtime/_recorder.py +84 -0
  358. skcomplex/engine/runtime/_simulations.py +665 -0
  359. skcomplex/engine/runtime/_trajectories.py +314 -0
  360. skcomplex/engine/solvers/__init__.py +95 -0
  361. skcomplex/engine/solvers/_base.py +372 -0
  362. skcomplex/engine/solvers/_caputo.py +194 -0
  363. skcomplex/engine/solvers/_collocation.py +334 -0
  364. skcomplex/engine/solvers/_convolution.py +155 -0
  365. skcomplex/engine/solvers/_cosimulation.py +400 -0
  366. skcomplex/engine/solvers/_crank_nicolson.py +32 -0
  367. skcomplex/engine/solvers/_defaults.py +34 -0
  368. skcomplex/engine/solvers/_etdrk4.py +86 -0
  369. skcomplex/engine/solvers/_euler_maruyama.py +161 -0
  370. skcomplex/engine/solvers/_event_locator.py +249 -0
  371. skcomplex/engine/solvers/_external.py +94 -0
  372. skcomplex/engine/solvers/_fractional_abm.py +126 -0
  373. skcomplex/engine/solvers/_fractional_euler_maruyama.py +322 -0
  374. skcomplex/engine/solvers/_gillespie.py +135 -0
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  1620. skcomplex/models/social/segregation/_resident_view.py +13 -0
  1621. skcomplex/models/social/segregation/_schelling.py +75 -0
  1622. skcomplex/models/social/spreading/__init__.py +37 -0
  1623. skcomplex/models/social/spreading/_cascades.py +118 -0
  1624. skcomplex/models/social/spreading/_exposure.py +166 -0
  1625. skcomplex/models/social/spreading/_growing_word.py +55 -0
  1626. skcomplex/models/social/spreading/_growing_word_view.py +13 -0
  1627. skcomplex/models/social/spreading/_growth.py +52 -0
  1628. skcomplex/models/social/spreading/_infective.py +55 -0
  1629. skcomplex/models/social/spreading/_listeners.py +41 -0
  1630. skcomplex/models/social/spreading/_participant.py +50 -0
  1631. skcomplex/models/social/spreading/_rumour_contacts.py +81 -0
  1632. skcomplex/models/social/spreading/_rumours.py +57 -0
  1633. skcomplex/models/social/spreading/_simplicial.py +120 -0
  1634. skcomplex/models/social/spreading/_simplicial_infection.py +64 -0
  1635. skcomplex/models/social/spreading/_threshold_activation.py +50 -0
  1636. skcomplex/models/social/spreading/_threshold_node_view.py +13 -0
  1637. skcomplex/models/social/spreading/_writing.py +86 -0
  1638. skcomplex/models/types.py +10 -0
  1639. skcomplex/specs/__init__.py +198 -0
  1640. skcomplex/specs/_accelerated_spec.py +46 -0
  1641. skcomplex/specs/_agent_snapshot_spec.py +34 -0
  1642. skcomplex/specs/_agent_state_spec.py +26 -0
  1643. skcomplex/specs/_arguments_spec.py +60 -0
  1644. skcomplex/specs/_axis_spec.py +59 -0
  1645. skcomplex/specs/_base_record_spec.py +16 -0
  1646. skcomplex/specs/_base_spec.py +73 -0
  1647. skcomplex/specs/_base_structure_spec.py +173 -0
  1648. skcomplex/specs/_batch_matching_spec.py +23 -0
  1649. skcomplex/specs/_breakpoints_spec.py +58 -0
  1650. skcomplex/specs/_call_spec.py +64 -0
  1651. skcomplex/specs/_capacity_rows_spec.py +120 -0
  1652. skcomplex/specs/_cardinality_spec.py +58 -0
  1653. skcomplex/specs/_cascade_record_spec.py +36 -0
  1654. skcomplex/specs/_clamp_spec.py +54 -0
  1655. skcomplex/specs/_clause_spec.py +42 -0
  1656. skcomplex/specs/_compiled_flow_spec.py +20 -0
  1657. skcomplex/specs/_composed_rule_spec.py +33 -0
  1658. skcomplex/specs/_continuous_matching_spec.py +48 -0
  1659. skcomplex/specs/_control_solution_spec.py +54 -0
  1660. skcomplex/specs/_control_spec.py +21 -0
  1661. skcomplex/specs/_covariance_adaptation_spec.py +25 -0
  1662. skcomplex/specs/_dataset_spec.py +85 -0
  1663. skcomplex/specs/_delay_spec.py +27 -0
  1664. skcomplex/specs/_dialect_spec.py +207 -0
  1665. skcomplex/specs/_differential_evolution_spec.py +33 -0
  1666. skcomplex/specs/_direction_spec.py +44 -0
  1667. skcomplex/specs/_draw_spec.py +273 -0
  1668. skcomplex/specs/_entry_spec.py +403 -0
  1669. skcomplex/specs/_event_record_spec.py +37 -0
  1670. skcomplex/specs/_evolution_strategy_spec.py +25 -0
  1671. skcomplex/specs/_extremal_record_spec.py +32 -0
  1672. skcomplex/specs/_fractional_rows_spec.py +33 -0
  1673. skcomplex/specs/_fractional_state_spec.py +30 -0
  1674. skcomplex/specs/_held_reduction_spec.py +29 -0
  1675. skcomplex/specs/_hilbert_spec.py +75 -0
  1676. skcomplex/specs/_hyperedge_reduction_spec.py +38 -0
  1677. skcomplex/specs/_issue_spec.py +52 -0
  1678. skcomplex/specs/_iterative_matching_spec.py +39 -0
  1679. skcomplex/specs/_jump_channels_spec.py +40 -0
  1680. skcomplex/specs/_jump_path_spec.py +29 -0
  1681. skcomplex/specs/_layer_spec.py +47 -0
  1682. skcomplex/specs/_layout_spec.py +158 -0
  1683. skcomplex/specs/_local_operator_spec.py +72 -0
  1684. skcomplex/specs/_lookup_spec.py +33 -0
  1685. skcomplex/specs/_loop_spec.py +17 -0
  1686. skcomplex/specs/_lowered_functions_spec.py +71 -0
  1687. skcomplex/specs/_match_spec.py +37 -0
  1688. skcomplex/specs/_matrix_law_spec.py +31 -0
  1689. skcomplex/specs/_move_spec.py +69 -0
  1690. skcomplex/specs/_neighbor_read_spec.py +83 -0
  1691. skcomplex/specs/_neighbor_reduction_spec.py +39 -0
  1692. skcomplex/specs/_network_rows_spec.py +124 -0
  1693. skcomplex/specs/_network_snapshot_spec.py +61 -0
  1694. skcomplex/specs/_noise_process_spec.py +41 -0
  1695. skcomplex/specs/_objective_spec.py +39 -0
  1696. skcomplex/specs/_observable_spec.py +79 -0
  1697. skcomplex/specs/_operator_spec.py +170 -0
  1698. skcomplex/specs/_orders_spec.py +16 -0
  1699. skcomplex/specs/_outer_totalistic_spec.py +38 -0
  1700. skcomplex/specs/_owners_spec.py +28 -0
  1701. skcomplex/specs/_pair_read_spec.py +38 -0
  1702. skcomplex/specs/_parameter_spec.py +81 -0
  1703. skcomplex/specs/_parameters_spec.py +26 -0
  1704. skcomplex/specs/_particle_swarm_spec.py +33 -0
  1705. skcomplex/specs/_partner_spec.py +98 -0
  1706. skcomplex/specs/_partner_switch_spec.py +39 -0
  1707. skcomplex/specs/_phase_spec.py +61 -0
  1708. skcomplex/specs/_phases_schedule_spec.py +59 -0
  1709. skcomplex/specs/_plan_spec.py +18 -0
  1710. skcomplex/specs/_planned_partition_spec.py +30 -0
  1711. skcomplex/specs/_queue_spec.py +46 -0
  1712. skcomplex/specs/_radius_spec.py +66 -0
  1713. skcomplex/specs/_random_search_spec.py +51 -0
  1714. skcomplex/specs/_read_spec.py +45 -0
  1715. skcomplex/specs/_reduction_spec.py +48 -0
  1716. skcomplex/specs/_renewal_record_spec.py +49 -0
  1717. skcomplex/specs/_requirement_spec.py +32 -0
  1718. skcomplex/specs/_role_spec.py +54 -0
  1719. skcomplex/specs/_run_result_spec.py +52 -0
  1720. skcomplex/specs/_run_state_spec.py +41 -0
  1721. skcomplex/specs/_sampled_draw_spec.py +32 -0
  1722. skcomplex/specs/_sampler_spec.py +57 -0
  1723. skcomplex/specs/_samples_spec.py +29 -0
  1724. skcomplex/specs/_schedule_spec.py +17 -0
  1725. skcomplex/specs/_sector_spec.py +31 -0
  1726. skcomplex/specs/_segment_spec.py +21 -0
  1727. skcomplex/specs/_series_spec.py +29 -0
  1728. skcomplex/specs/_signature_spec.py +55 -0
  1729. skcomplex/specs/_snapshots_spec.py +56 -0
  1730. skcomplex/specs/_stable_matching_spec.py +58 -0
  1731. skcomplex/specs/_state_spec.py +138 -0
  1732. skcomplex/specs/_step_spec.py +39 -0
  1733. skcomplex/specs/_structure_state_spec.py +30 -0
  1734. skcomplex/specs/_support_spec.py +76 -0
  1735. skcomplex/specs/_symmetry_spec.py +59 -0
  1736. skcomplex/specs/_table_spec.py +42 -0
  1737. skcomplex/specs/_table_values_spec.py +36 -0
  1738. skcomplex/specs/_tensor_spec.py +197 -0
  1739. skcomplex/specs/_topology_request_spec.py +97 -0
  1740. skcomplex/specs/_totalistic_spec.py +37 -0
  1741. skcomplex/specs/_unknown_spec.py +22 -0
  1742. skcomplex/specs/_validation_report_spec.py +62 -0
  1743. skcomplex/specs/_variable_spec.py +124 -0
  1744. skcomplex/specs/_visual_spec.py +30 -0
  1745. skcomplex/specs/_weight_spec.py +16 -0
  1746. skcomplex/specs/_wiener_block_spec.py +31 -0
  1747. skcomplex/specs/_wiener_process_spec.py +54 -0
  1748. skcomplex/types.py +140 -0
@@ -0,0 +1,741 @@
1
+ """Define coupling, which gives every member a reduction over other members of a function of both of them."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ from collections.abc import Callable, Sequence
7
+ from types import SimpleNamespace
8
+ from typing import Annotated, cast
9
+
10
+ import numpy as np
11
+ import numpy.typing as npt
12
+ import scipy.sparse
13
+ from sage.all__sagemath_symbolics import SR, Expression, arctan2, cos, oo, sin
14
+ from sage.modules.free_module_element import FreeModuleElement
15
+ from sage.sets.real_set import RealSet
16
+
17
+ from ...errors import ValidationError
18
+ from ...specs import BaseSpec, ClampSpec, ParameterSpec, RadiusSpec, RoleSpec
19
+ from ...types import Array
20
+ from ..laws import BaseLaw, RateLaw, RuleLaw, UpdateLaw
21
+ from ..laws.utils import count, delayed, hyperedges, maximum, minimum, neighbors, shift_member, total
22
+ from ..spaces import BaseNeighborhood
23
+ from ..types import AgentCombination, AgentViewProtocol, Combination, ModelViewProtocol, NamespaceFunction, Target
24
+ from ._neighbor import NeighborInteraction
25
+
26
+ MODES = ('edges', 'group', 'next', 'hyperedges')
27
+ MIN_SIZE = 2
28
+ REDUCTIONS = ('sum', 'mean', 'max', 'min', 'normalized-mean', 'circular-mean')
29
+ SUMS = ('sum', 'mean')
30
+ EXTREMES = ('max', 'min')
31
+ FORMS = ('rate', 'map', 'agent')
32
+ ENDS = ('source', 'target')
33
+
34
+ type Weights = str | npt.ArrayLike | scipy.sparse.sparray | NamespaceFunction | None
35
+ type Part = Callable[[Target, Target], Target]
36
+
37
+
38
+ class CouplingInteraction(NeighborInteraction):
39
+ """Coupling of every member to other members, through a reduction over them of a function of both members.
40
+
41
+ Every member `i` gets the reduction over other members `j` of `function(namespace)`, where `namespace.member` reads
42
+ the states of `i`, `namespace.other` those of `j`, `namespace.edge` the member of the edge group that joins them, or
43
+ `None`, and the namespace also holds the parameters and the time `t`. The function is the difference `x_j - x_i` of
44
+ the state `read` by default. The members `j` are, by `mode`:
45
+
46
+ - `'edges'`: the neighbours of `i` along the edges of its lattice or network, or within the `neighborhood`.
47
+ - `'group'`: every other member of the group, or every member of the group `source` when it is given.
48
+
49
+ In the mode `'group'` the roles may also bind separate elements. A target that lists elements couples every element
50
+ to the other elements of the list, a single target element is a hub that reduces over every member of the group
51
+ `source`, and a source that is one element or a list of elements couples every member of the target to them. The
52
+ reduction over separate elements is written out term by term.
53
+ - `'next'`: the next member of the group in member order, the first after the last.
54
+ - `'hyperedges'`: the other members of every hyperedge around `i` of `size` members, or of every size, on a network
55
+ with hyperedges. The function then reads `namespace.member`, `namespace.others`, the other members of one
56
+ hyperedge in its order, and `namespace.members`, all its members, which reductions over them read, and the
57
+ reduction runs over the hyperedges around `i`. The default function is the sum over the other members of the
58
+ difference of `read`.
59
+
60
+ With `include_self`, the reduction also runs over `j = i`. Every term `f_ij` has a weight `w_ij`: on edges, the
61
+ state `weights` of the edge group, which a subclass binds with a second role, over the group, the entry `W_ij` of
62
+ the matrix `weights` or of the shaped parameter of the interaction that `weights` names, which a subclass declares,
63
+ and in every mode a callable `weights(namespace)` of the namespace of the term, such as an
64
+ indicator of the states of both members. The reductions are `'sum'`, `sum_j w_ij f_ij`, `'mean'`, the sum divided
65
+ by the number of members `j`, `'max'` and `'min'`, the largest and smallest `w_ij f_ij`, `'normalized-mean'`,
66
+ `sum_j w_ij f_ij / sum_j w_ij`, and `'circular-mean'`, the angle `arctan2(sum_j w_ij sin f_ij, sum_j w_ij cos
67
+ f_ij)`. The state `read` of `j` is read `delay` earlier, and the one of `i` shifted by the phase lag `lag`, when
68
+ they are not 0.
69
+
70
+ In the form `'rate'` the reduction adds to the rate of the state `write`, and in the form `'map'` it sets the next
71
+ value of `write` every step of discrete time to `combine(namespace, reduction)`, where `namespace.member` reads the
72
+ states of `i` and the namespace holds the parameters and the time, or to the reduction itself by default. The sum
73
+ and the mean of the rate on the edges of a lattice or network run once per edge along both directions, and every
74
+ other coupling runs once per member. On a `FieldElement`, a rate that is a constant times the difference of the
75
+ ends becomes that constant times the field's Laplacian times its squared spacing, and on a lattice the other end is
76
+ read across the field's boundary conditions, so beyond fixed edges it reads the fixed value.
77
+
78
+ In the form `'agent'` the target is a group of agents, and every agent runs the coupling in its own activation in
79
+ the phase `phase`. Every `RadiusSpec` of `radii` gives the vector `function(agent, other, model)` of every other
80
+ agent of the source group, or of the target group, within its radius, reduced by its sum or mean. Only the radii
81
+ of the highest priority that hold another agent count, and their reductions add up. The states `write` of the
82
+ agent form a vector `v`, which becomes `combine(agent, model, reduction, priority)`, or `v` plus the reduction by
83
+ default, where `reduction` and `priority` are `None` when no radius holds another agent. `clamp` then bounds the
84
+ angle the vector turns and its norm.
85
+
86
+ Args:
87
+ label:
88
+ The label of the interaction, unique among the parts of its system.
89
+
90
+ target:
91
+ The path of the group of the members, or in the mode `'group'` the path of one element or the paths of
92
+ separate elements.
93
+
94
+ source:
95
+ The path of the group, the element, or the paths of the separate elements of the other members in the mode
96
+ `'group'`, or `None` for the members of the target.
97
+
98
+ read:
99
+ The name of the state that the default function, the delay, and the lag read.
100
+
101
+ write:
102
+ The name of the state that the coupling changes, or the names of the components of the vector of the agent
103
+ form.
104
+
105
+ function:
106
+ The term of one other member, a callable of the namespace, or `None` for the difference of `read`.
107
+
108
+ reduce:
109
+ `'sum'`, `'mean'`, `'max'`, `'min'`, `'normalized-mean'`, or `'circular-mean'`.
110
+
111
+ mode:
112
+ `'edges'`, `'group'`, `'next'`, or `'hyperedges'`.
113
+
114
+ size:
115
+ The number of members of the hyperedges of the mode `'hyperedges'`, or `None` for every size.
116
+
117
+ weights:
118
+ The name of the state of the edge group in the mode `'edges'`, a matrix with one row per member and one
119
+ column per other member or the name of a parameter of the interaction declared
120
+ `ParameterSpec(shape=('target', 'source'))` in the mode `'group'`, a callable of the namespace of a term in
121
+ any mode, or `None` for no weights.
122
+
123
+ include_self:
124
+ Whether the reduction also runs over the member itself.
125
+
126
+ lag:
127
+ The phase lag added to the state `read` of the member.
128
+
129
+ delay:
130
+ The delay of the state `read` of the other member, 0 for none.
131
+
132
+ form:
133
+ `'rate'`, `'map'`, or `'agent'`.
134
+
135
+ combine:
136
+ The next value in the form `'map'`, a callable of the namespace of the member and the reduction, or in the
137
+ form `'agent'` a callable of the agent, the model view, the reduction, and its priority, or `None` for the
138
+ default.
139
+
140
+ neighborhood:
141
+ The neighbourhood of the mode `'edges'`, such as `RadiusNeighborhood(1.0)` in a continuous space, or `None`
142
+ for the edges of the lattice or network.
143
+
144
+ layer:
145
+ The layer of the network whose edges the interaction runs on, or `None` for the graph of the network.
146
+
147
+ radii:
148
+ The terms of the agent form over the radii around an agent.
149
+
150
+ clamp:
151
+ The clamp of the turn and the norm of the vector of the agent form, or `None`.
152
+
153
+ phase:
154
+ The phase of the step the agent and the map forms run in, or `None` for the default phase.
155
+
156
+ Raises:
157
+ ValidationError:
158
+ A variant is unknown, the function or the combination is not callable, the weights, the source, the
159
+ reduction, or the neighbourhood do not suit the mode and the form, or the radii, the clamp, the phase, or
160
+ the written states do not suit the form, raised by `check`.
161
+
162
+ Examples:
163
+ >>> from types import SimpleNamespace
164
+ >>> from sage.all__sagemath_symbolics import sin, var
165
+ >>> from skcomplex.core.interactions import CouplingInteraction
166
+ >>> source, target = SimpleNamespace(theta=var('a')), SimpleNamespace(theta=var('b'))
167
+ >>> sine = lambda s: sin(s.other.theta - s.member.theta)
168
+ >>> coupling = CouplingInteraction('coupling', target='oscillators', read='theta', write='theta', function=sine)
169
+ >>> [law.value for law in coupling.check().prepare().run(SimpleNamespace(source=source, target=target)).laws_]
170
+ [sin(a - b), sin(-a + b)]
171
+ """
172
+
173
+ def __init__(
174
+ self,
175
+ label: str,
176
+ *,
177
+ target: Annotated[str | Sequence[str], RoleSpec()],
178
+ source: Annotated[str | Sequence[str] | None, RoleSpec(optional=True)] = None,
179
+ read: str = 'x',
180
+ write: str | Sequence[str] = 'x',
181
+ function: NamespaceFunction | None = None,
182
+ reduce: str = 'sum',
183
+ mode: str = 'edges',
184
+ size: int | None = None,
185
+ weights: Weights = None,
186
+ include_self: bool = False,
187
+ lag: Annotated[float, ParameterSpec()] = 0.0,
188
+ delay: Annotated[float, ParameterSpec(domain=RealSet.closed_open(0, oo))] = 0.0,
189
+ form: str = 'rate',
190
+ combine: Combination | AgentCombination | None = None,
191
+ neighborhood: BaseNeighborhood | None = None,
192
+ layer: str | None = None,
193
+ radii: Sequence[RadiusSpec] = (),
194
+ clamp: ClampSpec | None = None,
195
+ phase: str | None = None,
196
+ ) -> None:
197
+ super().__init__(label, layer=layer)
198
+ self.target = target
199
+ self.source = source
200
+ self.read = read
201
+ self.write = write
202
+ self.function = function
203
+ self.reduce = reduce
204
+ self.mode = mode
205
+ self.size = size
206
+ self.weights = weights
207
+ self.include_self = include_self
208
+ self.lag = lag
209
+ self.delay = delay
210
+ self.form = form
211
+ self.combine = combine
212
+ self.neighborhood = neighborhood
213
+ self.radii = radii
214
+ self.clamp = clamp
215
+ self.phase = phase
216
+
217
+ def _check_variants(self) -> None:
218
+ """Raise an error for an unknown mode, reduction, or form, or a function or combination that is not callable."""
219
+ self._check_variant('mode', self.mode, MODES, (BaseSpec,))
220
+ for name, value, known in (
221
+ ('reduce', self.reduce, REDUCTIONS),
222
+ ('form', self.form, FORMS),
223
+ ):
224
+ if value not in known:
225
+ error_msg = f'The {name} of coupling is {value!r}. Use one of {", ".join(known)}.'
226
+ raise ValidationError(error_msg)
227
+ for role, item in (('function', self.function), ('combine', self.combine)):
228
+ if item is not None and not callable(item):
229
+ error_msg = f'The {role} of coupling must be callable or None, but it is {item!r}.'
230
+ raise ValidationError(error_msg)
231
+
232
+ def _check_reduction(self) -> None:
233
+ """Raise an error for a source outside the mode group, or a reduction that its mode cannot run."""
234
+ if self.source is not None and self.mode != 'group':
235
+ error_msg = f'The source {self.source!r} of coupling needs the mode group, but the mode is {self.mode!r}.'
236
+ raise ValidationError(error_msg)
237
+ if not isinstance(self.target, str) and self.mode != 'group':
238
+ error_msg = (
239
+ f'The coupling of the separate elements {self.target!r} needs the mode group, not {self.mode!r}.'
240
+ )
241
+ raise ValidationError(error_msg)
242
+ if self.mode == 'next' and self.reduce not in SUMS:
243
+ error_msg = f'The coupling to the next member reduces by sum or mean, not {self.reduce!r}.'
244
+ raise ValidationError(error_msg)
245
+ if self.reduce in EXTREMES and self.mode == 'group' and self._excludes_self() and isinstance(self.target, str):
246
+ error_msg = (
247
+ f'The {self.reduce} of coupling over its own group runs over every member. Pass include_self=True or '
248
+ 'a separate source group.'
249
+ )
250
+ raise ValidationError(error_msg)
251
+ if self.reduce in EXTREMES and (self._has_matrix() or self._names_matrix()):
252
+ error_msg = f'The {self.reduce} of coupling takes no matrix of weights. Give the weights as a callable.'
253
+ raise ValidationError(error_msg)
254
+
255
+ def _check_structure(self) -> None:
256
+ """Raise an error for weights or a neighbourhood that do not suit the mode and the form."""
257
+ if self.neighborhood is not None and (
258
+ self.mode != 'edges' or not isinstance(self.neighborhood, BaseNeighborhood)
259
+ ):
260
+ error_msg = f'The neighbourhood {self.neighborhood!r} of coupling needs a neighbourhood in the mode edges.'
261
+ raise ValidationError(error_msg)
262
+ if isinstance(self.weights, str) and not self._is_per_edge() and not self._names_matrix():
263
+ error_msg = (
264
+ f'The weights {self.weights!r} of coupling name a state of the edges, which only the sum or mean rate '
265
+ 'on the edges of a lattice or network reads, or a shaped parameter in the mode group. Give a matrix '
266
+ 'in the mode group, or a callable.'
267
+ )
268
+ raise ValidationError(error_msg)
269
+ if self._names_matrix() and (self._excludes_self() or not isinstance(self.target, str) or self._is_separate()):
270
+ error_msg = (
271
+ f'The weights {self.weights!r} of coupling name a shaped parameter, whose matrix product runs over '
272
+ 'every member of a group. Pass include_self=True or a separate source group, and bind groups.'
273
+ )
274
+ raise ValidationError(error_msg)
275
+ if self._has_matrix() and self.mode != 'group':
276
+ error_msg = 'A matrix of weights of coupling needs the mode group. Name an edge state on the edges.'
277
+ raise ValidationError(error_msg)
278
+
279
+ def _check_hyperedges(self) -> None:
280
+ """Raise an error for a size outside the mode hyperedges, or a setting the mode hyperedges does not take."""
281
+ if self.size is not None and (
282
+ self.mode != 'hyperedges'
283
+ or isinstance(self.size, bool)
284
+ or not isinstance(self.size, int)
285
+ or self.size < MIN_SIZE
286
+ ):
287
+ error_msg = (
288
+ f'The size {self.size!r} of coupling needs the mode hyperedges and a whole number of 2 or more, but '
289
+ f'the mode is {self.mode!r}.'
290
+ )
291
+ raise ValidationError(error_msg)
292
+ if self.mode == 'hyperedges' and (self.include_self or self._is_nonzero('delay') or self.form == 'agent'):
293
+ error_msg = (
294
+ 'The coupling over hyperedges takes no include_self, no delay, and no agent form. Couple the member '
295
+ 'to itself with another interaction.'
296
+ )
297
+ raise ValidationError(error_msg)
298
+
299
+ def _check_agent(self) -> None:
300
+ """Raise an error for radii, a clamp, or several written states outside the agent form, or no radii."""
301
+ if self.form != 'agent':
302
+ if self.radii or self.clamp is not None or not isinstance(self.write, str):
303
+ error_msg = (
304
+ f'The coupling {self.label!r} takes radii, a clamp, and several written states in the agent form '
305
+ f'only, but its form is {self.form!r}.'
306
+ )
307
+ raise ValidationError(error_msg)
308
+ if self.phase is not None and self.form != 'map':
309
+ error_msg = (
310
+ f'The coupling {self.label!r} takes a phase in the agent and the map forms, but its form is '
311
+ f'{self.form!r}.'
312
+ )
313
+ raise ValidationError(error_msg)
314
+ return
315
+ if not self.radii or not isinstance(self.target, str):
316
+ error_msg = f'The agent form of coupling {self.label!r} needs one group of agents and at least one radius.'
317
+ raise ValidationError(error_msg)
318
+ for spec in self.radii:
319
+ spec.check()
320
+ if self.clamp is not None:
321
+ self.clamp.check()
322
+
323
+ def _check(self) -> None:
324
+ """Raise an error for unknown variants, functions that cannot be called, or weights that do not suit the mode.
325
+
326
+ Raises:
327
+ ValidationError:
328
+ A variant is unknown, the function or the combination is not callable, or the weights, the source, the
329
+ reduction, or the neighbourhood do not suit the mode and the form.
330
+ """
331
+ super()._check()
332
+ self._check_variants()
333
+ self._check_reduction()
334
+ self._check_structure()
335
+ self._check_hyperedges()
336
+ self._check_agent()
337
+
338
+ def _get_written(self) -> str:
339
+ """Return the name of the one state that the symbolic forms write."""
340
+ return cast(str, self.write)
341
+
342
+ def _has_matrix(self) -> bool:
343
+ """Return whether the weights are a matrix."""
344
+ return self.weights is not None and not isinstance(self.weights, str) and not callable(self.weights)
345
+
346
+ def _names_matrix(self) -> bool:
347
+ """Return whether the weights name a shaped parameter of the interaction in the mode group."""
348
+ return isinstance(self.weights, str) and self.mode == 'group'
349
+
350
+ def _is_separate(self) -> bool:
351
+ """Return whether the source lists separate elements."""
352
+ return self.source is not None and not isinstance(self.source, str)
353
+
354
+ def _excludes_self(self) -> bool:
355
+ """Return whether a reduction over the own group leaves the member out."""
356
+ return self.source is None and not self.include_self
357
+
358
+ def _is_nonzero(self, name: str) -> bool:
359
+ """Return whether a parameter, read under the name `_get_parameter` returns, has a value other than 0."""
360
+ return bool(getattr(self, self._get_parameter(name)) != 0)
361
+
362
+ def _is_per_edge(self) -> bool:
363
+ """Return whether the coupling is a rate written once per edge of a lattice or network."""
364
+ return self.mode == 'edges' and self.form == 'rate' and self.neighborhood is None and self.reduce in SUMS
365
+
366
+ def _parameters(self, namespace: SimpleNamespace) -> dict[str, object]:
367
+ """Return the parameters and the time of a namespace, without the ends and the edge."""
368
+ ends = {self._get_role(end) for end in (*ENDS, 'edge')}
369
+ return {name: value for name, value in vars(namespace).items() if name not in ends}
370
+
371
+ def _get_term(
372
+ self,
373
+ namespace: SimpleNamespace,
374
+ member: SimpleNamespace,
375
+ other: SimpleNamespace,
376
+ edge: SimpleNamespace | None = None,
377
+ ) -> Target:
378
+ """Return the term of one other member, with the delay and the lag applied to the read state."""
379
+ member_values, other_values = dict(vars(member)), dict(vars(other))
380
+ if self._is_nonzero('delay'):
381
+ other_values[self.read] = delayed(other_values[self.read], self._get_parameter_symbol('delay', namespace))
382
+ if self._is_nonzero('lag'):
383
+ member_values[self.read] = member_values[self.read] + self._get_parameter_symbol('lag', namespace)
384
+ if self.function is None:
385
+ return other_values[self.read] - member_values[self.read]
386
+ return self.function(
387
+ SimpleNamespace(
388
+ **self._parameters(namespace),
389
+ member=SimpleNamespace(**member_values),
390
+ other=SimpleNamespace(**other_values),
391
+ edge=edge,
392
+ ),
393
+ )
394
+
395
+ def _get_weight(
396
+ self,
397
+ namespace: SimpleNamespace,
398
+ member: SimpleNamespace,
399
+ other: SimpleNamespace,
400
+ edge: SimpleNamespace | None = None,
401
+ ) -> Target:
402
+ """Return the weight of the term of one other member from callable weights, or 1 for other weights."""
403
+ if not callable(self.weights):
404
+ return SR(1)
405
+ return self.weights(SimpleNamespace(**self._parameters(namespace), member=member, other=other, edge=edge))
406
+
407
+ def _get_matrix(self, namespace: SimpleNamespace) -> npt.ArrayLike | scipy.sparse.sparray | Expression | None:
408
+ """Return the matrix of weights, with a zero diagonal unless the member is included, or `None`.
409
+
410
+ Weights that name a shaped parameter give the symbol of that parameter.
411
+ """
412
+ if self._names_matrix():
413
+ name = cast(str, self.weights)
414
+ if not hasattr(namespace, name):
415
+ error_msg = (
416
+ f'The weights {name!r} of coupling {self.label!r} name no parameter of the interaction. Declare '
417
+ f"it as `ParameterSpec(shape=('target', 'source'))`."
418
+ )
419
+ raise ValidationError(error_msg)
420
+ return cast(Expression, getattr(namespace, name))
421
+ if not self._has_matrix():
422
+ return None
423
+ weights = cast(npt.ArrayLike | scipy.sparse.sparray, self.weights)
424
+ if not self._excludes_self():
425
+ return weights
426
+ if scipy.sparse.issparse(weights):
427
+ matrix = scipy.sparse.csr_array(weights, dtype=float)
428
+ matrix.setdiag(0)
429
+ matrix.eliminate_zeros()
430
+ return matrix
431
+ matrix = np.array(weights, dtype=float)
432
+ np.fill_diagonal(matrix, 0.0)
433
+ return matrix
434
+
435
+ @staticmethod
436
+ def _map(value: Target, operation: Callable[[Expression], Expression]) -> Target:
437
+ """Return an operation applied to an expression, or to every component of a vector."""
438
+ if isinstance(value, FreeModuleElement):
439
+ return value.parent()([operation(SR(item)) for item in value])
440
+ return operation(SR(value))
441
+
442
+ @staticmethod
443
+ def _shifted(member: SimpleNamespace) -> SimpleNamespace:
444
+ """Return the namespace of the next member of the group in member order."""
445
+ return SimpleNamespace(
446
+ **{
447
+ name: CouplingInteraction._map(value, lambda item: shift_member(item, 1))
448
+ for name, value in vars(member).items()
449
+ if isinstance(value, Expression | FreeModuleElement)
450
+ },
451
+ )
452
+
453
+ def _get_reduced(self, total_of: Callable[[Part], Target], number: Target) -> Target:
454
+ """Return the reduction from sums of parts of the weighted terms and the number of members, by reduction."""
455
+ if self.reduce == 'sum':
456
+ return total_of(lambda value, weight: weight * value)
457
+ if self.reduce == 'mean':
458
+ return total_of(lambda value, weight: weight * value) / number
459
+ if self.reduce == 'normalized-mean':
460
+ return total_of(lambda value, weight: weight * value) / total_of(lambda value, weight: weight)
461
+ sines = total_of(lambda value, weight: weight * sin(value))
462
+ return arctan2(sines, total_of(lambda value, weight: weight * cos(value)))
463
+
464
+ def _get_group_total(self, namespace: SimpleNamespace, part: Part) -> Target:
465
+ """Return the sum of a part of the weighted term over the other members of the group."""
466
+ source, target = getattr(namespace, self._get_role('source')), self._get_member(namespace, 'target')
467
+ matrix = self._get_matrix(namespace)
468
+ value, weight = self._get_term(namespace, target, source), self._get_weight(namespace, target, source)
469
+ reduction = self._map(part(value, weight), lambda item: total(item, over=source, weights=matrix))
470
+ if self._excludes_self() and matrix is None:
471
+ reduction = reduction - part(
472
+ self._get_term(namespace, target, target),
473
+ self._get_weight(namespace, target, target),
474
+ )
475
+ return reduction
476
+
477
+ @staticmethod
478
+ def _get_extreme(values: list[Target], extreme: Callable[..., Expression]) -> Target:
479
+ """Return the largest or smallest of several values, component by component for vectors."""
480
+ if len(values) == 1:
481
+ return values[0]
482
+ first = values[0]
483
+ if isinstance(first, FreeModuleElement):
484
+ columns = zip(*[list(value) for value in values], strict=True)
485
+ return first.parent()([extreme(*[SR(item) for item in column]) for column in columns])
486
+ return extreme(*[SR(value) for value in values])
487
+
488
+ @staticmethod
489
+ def _get_sum(pairs: list[tuple[Target, Target]], part: Part) -> Target:
490
+ """Return the sum of a part of the weighted terms of separate elements."""
491
+ parts = [part(value, weight) for value, weight in pairs]
492
+ return sum(parts[1:], parts[0])
493
+
494
+ def _get_separate_reduction(self, namespace: SimpleNamespace) -> Target:
495
+ """Return the reduction over the separate elements of `namespace.source`, written out term by term."""
496
+ if self._has_matrix():
497
+ error_msg = (
498
+ 'A matrix of weights of coupling needs groups. Give the weights of separate elements as a callable.'
499
+ )
500
+ raise ValidationError(error_msg)
501
+ target = self._get_member(namespace, 'target')
502
+ others = [*getattr(namespace, self._get_role('source')), *([target] if self.include_self else [])]
503
+ pairs = [
504
+ (self._get_term(namespace, target, other), self._get_weight(namespace, target, other)) for other in others
505
+ ]
506
+ if not pairs:
507
+ error_msg = f'The coupling {self.label!r} of separate elements has no other element. Bind two or more.'
508
+ raise ValidationError(error_msg)
509
+ if self.reduce in EXTREMES:
510
+ extreme = maximum if self.reduce == 'max' else minimum
511
+ return self._get_extreme([value * weight for value, weight in pairs], extreme)
512
+ return self._get_reduced(lambda part: self._get_sum(pairs, part), SR(len(pairs)))
513
+
514
+ def _get_group_reduction(self, namespace: SimpleNamespace) -> Target:
515
+ """Return the reduction over every other member of the group, or every member of the source group."""
516
+ source, target = getattr(namespace, self._get_role('source')), self._get_member(namespace, 'target')
517
+ if isinstance(source, tuple):
518
+ return self._get_separate_reduction(namespace)
519
+ if self.reduce in EXTREMES:
520
+ extreme = maximum if self.reduce == 'max' else minimum
521
+ value = self._get_term(namespace, target, source) * self._get_weight(namespace, target, source)
522
+ return self._map(value, lambda item: extreme(item, over=source))
523
+ number = count(over=source) - (1 if self._excludes_self() else 0)
524
+ return self._get_reduced(lambda part: self._get_group_total(namespace, part), number)
525
+
526
+ def _get_next_reduction(self, namespace: SimpleNamespace) -> Target:
527
+ """Return the reduction over the next member of the group."""
528
+ target = self._get_member(namespace, 'target')
529
+ shifted = self._shifted(target)
530
+ reduction = self._get_term(namespace, target, shifted) * self._get_weight(namespace, target, shifted)
531
+ if self.include_self:
532
+ own = self._get_term(namespace, target, target) * self._get_weight(namespace, target, target)
533
+ reduction = reduction + own
534
+ return reduction / 2 if self.reduce == 'mean' and self.include_self else reduction
535
+
536
+ def _get_neighbor_total(self, namespace: SimpleNamespace, part: Part) -> Target:
537
+ """Return the sum of a part of the weighted term over the neighbours and the member itself."""
538
+ source, target = getattr(namespace, self._get_role('source')), self._get_member(namespace, 'target')
539
+ value, weight = self._get_term(namespace, target, source), self._get_weight(namespace, target, source)
540
+ reduction = self._map(part(value, weight), lambda item: neighbors(item, over=self.neighborhood))
541
+ return reduction + part(self._get_term(namespace, target, target), self._get_weight(namespace, target, target))
542
+
543
+ def _get_neighbor_reduction(self, namespace: SimpleNamespace) -> Target:
544
+ """Return the reduction over the neighbours of the member."""
545
+ source, target = getattr(namespace, self._get_role('source')), self._get_member(namespace, 'target')
546
+ term = self._get_term(namespace, target, source)
547
+ weight = self._get_weight(namespace, target, source) if callable(self.weights) else None
548
+ if not self.include_self:
549
+ return self._map(
550
+ term,
551
+ lambda item: neighbors(item, over=self.neighborhood, reduce=self.reduce, weight=weight),
552
+ )
553
+ if self.reduce in EXTREMES:
554
+ extreme = maximum if self.reduce == 'max' else minimum
555
+ others = neighbors(term, over=self.neighborhood, reduce=self.reduce, weight=weight)
556
+ own = self._get_term(namespace, target, target) * self._get_weight(namespace, target, target)
557
+ return extreme(others, own)
558
+ number = neighbors(SR(1), over=self.neighborhood, reduce='count') + 1
559
+ return self._get_reduced(lambda part: self._get_neighbor_total(namespace, part), number)
560
+
561
+ def _get_hyperedge_term(self, namespace: SimpleNamespace, around: SimpleNamespace) -> Target:
562
+ """Return the term of one hyperedge around a member, with the lag applied to the read state of the member."""
563
+ member = around.member
564
+ if self._is_nonzero('lag'):
565
+ lag = self._get_parameter_symbol('lag', namespace)
566
+ member = SimpleNamespace(**{**vars(member), self.read: getattr(member, self.read) + lag})
567
+ if self.function is None:
568
+ members = around.members
569
+ own = getattr(around.member, self.read)
570
+ others = total(getattr(members, self.read), over=members) - own
571
+ return others - (count(over=members) - 1) * getattr(member, self.read)
572
+ return self.function(SimpleNamespace(**self._parameters(namespace), **{**vars(around), 'member': member}))
573
+
574
+ def _get_hyperedge_reduction(self, namespace: SimpleNamespace) -> Target:
575
+ """Return the reduction over the hyperedges around the member.
576
+
577
+ Args:
578
+ namespace:
579
+ The namespace of the states and parameters of the interaction.
580
+
581
+ Returns:
582
+ reduction:
583
+ The reduction over the hyperedges around the member.
584
+
585
+ Raises:
586
+ ValidationError:
587
+ The members live on no network with hyperedges.
588
+ """
589
+ target = self._get_member(namespace, 'target')
590
+ others, members = getattr(target, 'others', None), getattr(target, 'members', None)
591
+ if others is None or members is None:
592
+ error_msg = (
593
+ f'The coupling {self.label!r} over hyperedges binds {self.target!r}, whose members live on no network '
594
+ 'with hyperedges. Give the group a network space with hyperedges.'
595
+ )
596
+ raise ValidationError(error_msg)
597
+ if self.size is not None:
598
+ others = others[: self.size - 1]
599
+ around = SimpleNamespace(member=target, others=others, members=members)
600
+ term = self._get_hyperedge_term(namespace, around)
601
+ weight = None
602
+ if callable(self.weights):
603
+ weight = self.weights(SimpleNamespace(**self._parameters(namespace), **vars(around)))
604
+ return self._map(term, lambda item: hyperedges(item, reduce=self.reduce, size=self.size, weight=weight))
605
+
606
+ def _get_reduction(self, namespace: SimpleNamespace) -> Target:
607
+ """Return the reduction that one member gets, by mode."""
608
+ if self.mode == 'hyperedges':
609
+ return self._get_hyperedge_reduction(namespace)
610
+ if self.mode == 'group':
611
+ return self._get_group_reduction(namespace)
612
+ if self.mode == 'next':
613
+ return self._get_next_reduction(namespace)
614
+ if self.mode == 'edges':
615
+ return self._get_neighbor_reduction(namespace)
616
+ raise self._get_variant_error(self.mode, 'mode', '_get_reduction')
617
+
618
+ def _get_edge_term(self, namespace: SimpleNamespace, member: SimpleNamespace, other: SimpleNamespace) -> Target:
619
+ """Return the term one end of an edge gets from the other end, weighted and divided for a mean."""
620
+ edge = getattr(namespace, self._get_role('edge'), None)
621
+ term = self._get_term(namespace, member, other, edge)
622
+ if isinstance(self.weights, str):
623
+ term = term * getattr(edge, self.weights)
624
+ elif callable(self.weights):
625
+ term = term * self._get_weight(namespace, member, other, edge)
626
+ if self.reduce == 'mean':
627
+ term = term / (member.degree + int(self.include_self))
628
+ return term
629
+
630
+ def _get_edge_laws(self, namespace: SimpleNamespace) -> list[BaseLaw]:
631
+ """Return the rates of both ends of an edge, with the rate of the member itself when it is included."""
632
+ source, target = getattr(namespace, self._get_role('source')), self._get_member(namespace, 'target')
633
+ laws: list[BaseLaw] = [
634
+ RateLaw(getattr(target, self._get_written()), self._get_edge_term(namespace, target, source)),
635
+ RateLaw(getattr(source, self._get_written()), self._get_edge_term(namespace, source, target)),
636
+ ]
637
+ if self.include_self:
638
+ own = self._get_term(namespace, target, target) * self._get_weight(namespace, target, target)
639
+ divisor = target.degree + 1 if self.reduce == 'mean' else 1
640
+ laws.append(RateLaw(getattr(target, self._get_written()), own / divisor))
641
+ return laws
642
+
643
+ @staticmethod
644
+ def _get_bound(agent: AgentViewProtocol, bound: float | str) -> float:
645
+ """Return a bound given as a number or as the name of a parameter of the agent."""
646
+ return float(cast(float, getattr(agent, bound))) if isinstance(bound, str) else float(bound)
647
+
648
+ def _get_agent_reduction(
649
+ self,
650
+ agent: AgentViewProtocol,
651
+ model: ModelViewProtocol,
652
+ ) -> tuple[Array | None, int | None]:
653
+ """Return the sum of the reduced terms of the radii of the highest priority that hold another agent."""
654
+ groups = set(model.groups(self._get_role('source' if self.source is not None else 'target')))
655
+ found: dict[float, list[AgentViewProtocol]] = {}
656
+ levels: dict[int, list[Array]] = {}
657
+ for spec in self.radii:
658
+ radius = self._get_bound(agent, spec.radius)
659
+ if radius not in found:
660
+ found[radius] = [other for other in agent.neighbors(radius=radius) if other.group in groups]
661
+ others = found[radius]
662
+ if not others:
663
+ continue
664
+ terms = np.array([np.asarray(spec.function(agent, other, model), dtype=float) for other in others])
665
+ levels.setdefault(spec.priority, []).append(
666
+ terms.mean(axis=0) if spec.reduce == 'mean' else terms.sum(axis=0),
667
+ )
668
+ if not levels:
669
+ return None, None
670
+ priority = max(levels)
671
+ return np.sum(levels[priority], axis=0), priority
672
+
673
+ @staticmethod
674
+ def _turn(current: Array, value: Array, max_angle: float) -> Array:
675
+ """Return a vector turned from the current direction toward its own by at most an angle, keeping its norm."""
676
+ norm, size = float(np.linalg.norm(value)), float(np.linalg.norm(current))
677
+ if norm == 0 or size == 0:
678
+ return value
679
+ direction, facing = value / norm, current / size
680
+ angle = float(np.arccos(np.clip(facing @ direction, -1.0, 1.0)))
681
+ if angle <= max_angle:
682
+ return value
683
+ if angle == np.pi:
684
+ direction = np.eye(len(facing))[int(np.argmin(np.abs(facing)))]
685
+ normal = direction - (facing @ direction) * facing
686
+ normal = normal / np.linalg.norm(normal)
687
+ return norm * (np.cos(max_angle) * facing + np.sin(max_angle) * normal)
688
+
689
+ def _get_clamped(self, agent: AgentViewProtocol, current: Array, value: Array) -> Array:
690
+ """Return a new vector with its turn and its norm clamped."""
691
+ clamp = self.clamp
692
+ if clamp is None:
693
+ return value
694
+ if clamp.max_angle is not None:
695
+ value = self._turn(current, value, self._get_bound(agent, clamp.max_angle))
696
+ norm = float(np.linalg.norm(value))
697
+ if norm == 0:
698
+ return value
699
+ low = 0.0 if clamp.min_norm is None else self._get_bound(agent, clamp.min_norm)
700
+ high = np.inf if clamp.max_norm is None else self._get_bound(agent, clamp.max_norm)
701
+ return value * min(max(norm, low), high) / norm
702
+
703
+ def _update_member(self, agent: AgentViewProtocol, model: ModelViewProtocol) -> None:
704
+ """Set the written states of one agent to the clamped combination of the reduction over its radii."""
705
+ if not agent.alive:
706
+ return
707
+ names = [self.write] if isinstance(self.write, str) else list(self.write)
708
+ current = np.array([float(cast(float, getattr(agent, name))) for name in names])
709
+ reduction, priority = self._get_agent_reduction(agent, model)
710
+ if self.combine is not None:
711
+ combine = cast(AgentCombination, self.combine)
712
+ value = np.asarray(combine(agent, model, reduction, priority), dtype=float)
713
+ else:
714
+ value = current if reduction is None else current + reduction
715
+ for name, item in zip(names, self._get_clamped(agent, current, value), strict=True):
716
+ setattr(agent, name, float(item))
717
+
718
+ def _get_laws(self, namespace: SimpleNamespace) -> list[BaseLaw]:
719
+ """Return the rates of both ends of every edge, or the rate or next value of every member.
720
+
721
+ Args:
722
+ namespace:
723
+ The namespace of an edge, with the ends `source` and `target`.
724
+
725
+ Returns:
726
+ laws:
727
+ The laws of the coupling.
728
+ """
729
+ if self.form == 'agent':
730
+ return [RuleLaw(self._update_member, phase=self.phase, members=self._get_role('target'))]
731
+ if self._is_per_edge():
732
+ return self._get_edge_laws(namespace)
733
+ target = self._get_member(namespace, 'target')
734
+ reduction = self._get_reduction(namespace)
735
+ if self.form == 'rate':
736
+ return [RateLaw(getattr(target, self._get_written()), reduction)]
737
+ state = getattr(target, self._get_written())
738
+ if self.combine is None:
739
+ return [UpdateLaw(state, reduction, phase=self.phase)]
740
+ member = SimpleNamespace(**self._parameters(namespace), member=target)
741
+ return [UpdateLaw(state, cast(Combination, self.combine)(member, reduction), phase=self.phase)]