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 +1,604 @@
1
+ """Laws of one component and one law kind, evaluated over members or pairs."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ import functools
7
+ from collections.abc import Callable, Mapping, Sequence
8
+
9
+ import numpy as np
10
+ import numpy.typing as npt
11
+ from sage.all__sagemath_symbolics import SR, Expression
12
+
13
+ from ...errors import ValidationError
14
+ from ...specs import CallSpec, LayoutSpec, NoiseProcessSpec, RunStateSpec, WienerBlockSpec
15
+ from ...specs._jump_channels_spec import _JumpChannelsSpec
16
+ from ...types import Array, Indices
17
+ from ..types import OptionalPairs, ReadFunction, ReadKind
18
+ from ._base import BaseKernel
19
+ from ._edge_search import EdgeSearch
20
+ from ._expression_printer import ExpressionPrinter
21
+ from ._output_spec import OutputSpec
22
+ from ._pair_search import PairSearch
23
+ from ._random_stream import RandomStream
24
+ from ._reference_spec import PairsSearch, ReferenceSpec
25
+
26
+ MODES = {'periodic': 0, 'zero-flux': 1, 'fixed': 2}
27
+
28
+
29
+ LATTICE_BOUNDARIES = {'periodic': 'periodic', 'zero-flux': 'reflecting', 'fixed': 'fixed'}
30
+
31
+
32
+ class LawKernel(BaseKernel):
33
+ """Laws of one component and one law kind, evaluated over members or pairs.
34
+
35
+ Args:
36
+ owner:
37
+ The path of the component that returned the laws.
38
+
39
+ time:
40
+ The time symbol.
41
+
42
+ references:
43
+ A mapping from every symbol the laws may use to the component it stands for.
44
+
45
+ rows:
46
+ The number of evaluation indices in member mode.
47
+
48
+ layout_states:
49
+ The layout of the state vector, used to build the values passed to callables.
50
+
51
+ layout_parameters:
52
+ The layout of the parameter vector, used to build the values passed to callables.
53
+
54
+ pairs:
55
+ The neighbour search of a pair interaction, or the edges of an interaction over neighbours, or `None` for
56
+ member mode.
57
+
58
+ outputs:
59
+ The outputs of the laws.
60
+
61
+ names:
62
+ A mapping from the name a relative function reads to the dotted name of the variable.
63
+
64
+ stream:
65
+ The random stream a function with `random=True` receives, or `None` for a kernel without one.
66
+
67
+ Attributes:
68
+ values_:
69
+ The number of evaluation indices, the pairs in pair mode, and one array of values per output, of the last
70
+ run.
71
+ """
72
+
73
+ values_: tuple[int, OptionalPairs, list[Array]]
74
+
75
+ def __init__(
76
+ self,
77
+ owner: str,
78
+ time: Expression,
79
+ references: Mapping[Expression, ReferenceSpec],
80
+ rows: int,
81
+ layout_states: LayoutSpec,
82
+ *,
83
+ layout_parameters: LayoutSpec,
84
+ pairs: PairsSearch | None = None,
85
+ outputs: Sequence[OutputSpec] = (),
86
+ names: Mapping[str, str] | None = None,
87
+ stream: RandomStream | None = None,
88
+ ) -> None:
89
+ self.owner = owner
90
+ self.time = time
91
+ self.references = references
92
+ self.rows = rows
93
+ self.layout_states = layout_states
94
+ self.layout_parameters = layout_parameters
95
+ self.pairs = pairs
96
+ self.outputs = outputs
97
+ self.names = names
98
+ self.stream = stream
99
+
100
+ @functools.cached_property
101
+ def _plan(self) -> tuple[list[tuple[int, int]], list[Expression]]:
102
+ """Return the slot of every output among the compiled expressions, and the expressions, found once.
103
+
104
+ Outputs that call the same function on the same arguments share one slot.
105
+ """
106
+ slots: list[tuple[int, int]] = []
107
+ expressions: list[Expression] = []
108
+ calls: dict[tuple[int, tuple[Expression, ...]], tuple[int, int]] = {}
109
+ for output in self.outputs:
110
+ key = (id(output.function), output.arguments) if output.arguments is not None else None
111
+ if key is not None and key in calls:
112
+ slots.append(calls[key])
113
+ continue
114
+ parts = [output.expression] if output.expression is not None else list(output.arguments or ())
115
+ slots.append((len(expressions), len(parts)))
116
+ if key is not None:
117
+ calls[key] = slots[-1]
118
+ expressions.extend(parts)
119
+ return slots, expressions
120
+
121
+ @functools.cached_property
122
+ def _slots(self) -> list[tuple[int, int]]:
123
+ """Start and count of the compiled values of every output."""
124
+ return self._plan[0]
125
+
126
+ @functools.cached_property
127
+ def _arguments(self) -> list[Expression]:
128
+ """Symbols the compiled expressions read besides time, sorted by name."""
129
+ return sorted(
130
+ {item for expression in self._plan[1] for item in SR(expression).variables()} - {self.time},
131
+ key=str,
132
+ )
133
+
134
+ @functools.cached_property
135
+ def _function(self) -> Callable[..., object] | None:
136
+ """NumPy function of the symbolic outputs and the arguments of calls, or `None` without expressions."""
137
+ expressions = self._plan[1]
138
+ if not expressions:
139
+ return None
140
+ printer = ExpressionPrinter(time=self.time, compiled=True).check().prepare(self._arguments)
141
+ return ExpressionPrinter._function_of(printer.run(expressions).code_)
142
+
143
+ @functools.cached_property
144
+ def _readers(self) -> dict[Expression, ReadFunction]:
145
+ """Reader of every symbol resolved so far."""
146
+ return {}
147
+
148
+ @functools.cached_property
149
+ def _applied(self) -> dict[int, Array]:
150
+ """Values of the global operators applied in the current evaluation, cleared when an evaluation starts."""
151
+ return {}
152
+
153
+ @functools.cached_property
154
+ def _argument_readers(self) -> list[ReadFunction]:
155
+ """Readers of the arguments of the compiled function, in order."""
156
+ return [self._reader(item) for item in self._arguments]
157
+
158
+ def _check(self) -> None:
159
+ """Check that the outputs read only declared symbols, and neighbour symbols only inside a reduction.
160
+
161
+ Raises:
162
+ ValidationError:
163
+ If an output reads an undeclared symbol, or a neighbour symbol outside a neighbourhood reduction.
164
+ """
165
+ used = set(self._arguments)
166
+ unknown = used - set(self.references)
167
+ if unknown:
168
+ names = ', '.join(sorted(map(str, unknown)))
169
+ error_msg = (
170
+ f'A law of {self.owner} uses the symbols {names}, which are not declared. Declare them with `state` '
171
+ 'or `parameter` and use them through the namespace `s` that `laws` receives.'
172
+ )
173
+ raise ValidationError(error_msg)
174
+ others = sorted(str(item) for item in used if self.references[item].source is ReadKind.OTHER)
175
+ if others:
176
+ error_msg = (
177
+ f'A law of {self.owner} reads the neighbour symbols {", ".join(others)} outside a reduction. Read '
178
+ '`s.other` inside `neighbors`, which reduces over the neighbours of every member, or inside a '
179
+ 'reduction over the group.'
180
+ )
181
+ raise ValidationError(error_msg)
182
+
183
+ @property
184
+ def arguments(self) -> list[Expression]:
185
+ """Symbols the outputs read, in the order the compiled function takes them after time."""
186
+ return list(self._arguments)
187
+
188
+ def gather(self, t: float, x: Array, p: Array) -> list[object]:
189
+ """Return the values of the symbols the outputs read, for every evaluation index of a member kernel.
190
+
191
+ Args:
192
+ t:
193
+ The time.
194
+
195
+ x:
196
+ The state vector.
197
+
198
+ p:
199
+ The parameter vector, extended with the reductions when the kernel reads them.
200
+
201
+ Returns:
202
+ values:
203
+ One value or one array of values per symbol of `arguments`.
204
+ """
205
+ self._applied.clear()
206
+ return [read(x, p, None, t) for read in self._argument_readers]
207
+
208
+ def read(self, symbol: Expression, t: float, x: Array, p: Array) -> object:
209
+ """Return the values of one symbol the kernel knows, for every evaluation index of a member kernel.
210
+
211
+ Args:
212
+ symbol:
213
+ A symbol of `references`, such as an operand symbol of a derived read.
214
+
215
+ t:
216
+ The time.
217
+
218
+ x:
219
+ The state vector.
220
+
221
+ p:
222
+ The parameter vector, extended with the reductions when the kernel reads them.
223
+
224
+ Returns:
225
+ values:
226
+ One value or one array of values.
227
+ """
228
+ self._applied.clear()
229
+ return self._reader(symbol)(x, p, None, t)
230
+
231
+ @property
232
+ def has_python_functions(self) -> bool:
233
+ """Whether an output is computed by a function, either a callable law or a `Call`."""
234
+ return any(output.function is not None for output in self.outputs)
235
+
236
+ def _gather_around(
237
+ self,
238
+ reference: ReferenceSpec,
239
+ x: Array,
240
+ p: Array,
241
+ pairs: tuple[Indices, Indices] | None,
242
+ t: float,
243
+ ) -> object:
244
+ """Return the values of a symbol read at neighbouring sites or derived by a global operator."""
245
+ if reference.source is ReadKind.NEIGHBOR:
246
+ return reference.shifted.read(reference.column_of(x, p), p)
247
+ read = reference.derived
248
+ if id(read) not in self._applied:
249
+ values = [self._gather(item, x, p, pairs, t) for item in read.symbols]
250
+ operand = read.operand_values(t, values, reference.entry.rows)
251
+ self._applied[id(read)] = read.run(RunStateSpec(t, operand, p)).values_
252
+ return self._applied[id(read)]
253
+
254
+ def _reader(self, symbol: Expression) -> ReadFunction:
255
+ """Return the function that reads the values of a symbol for every evaluation index, resolved once."""
256
+ if symbol in self._readers:
257
+ return self._readers[symbol]
258
+ reference = self.references[symbol]
259
+ source = reference.source
260
+ read: ReadFunction
261
+ if source is ReadKind.DERIVED or source is ReadKind.NEIGHBOR:
262
+ if source is ReadKind.DERIVED:
263
+ for item in reference.derived.symbols:
264
+ self._reader(item)
265
+
266
+ def read(x: Array, p: Array, pairs: OptionalPairs, t: float) -> object:
267
+ return self._gather_around(reference, x, p, pairs, t)
268
+
269
+ elif source is ReadKind.SINGLE or (source is ReadKind.REDUCED and reference.entry.members is None):
270
+ read = self._single_reader(reference.is_state, reference.index)
271
+ else:
272
+ read = self._member_reader(reference)
273
+ self._readers[symbol] = read
274
+ return read
275
+
276
+ def _member_reader(self, reference: ReferenceSpec) -> ReadFunction:
277
+ """Return the function that reads a member symbol, indexed by the pairs of a pair kernel."""
278
+ is_state, members, source = reference.is_state, reference.members, reference.source
279
+ search = self.pairs if isinstance(self.pairs, PairSearch) else None
280
+ images = search is not None and reference.entry == search.second and is_state
281
+ column = reference.column
282
+
283
+ def read(x: Array, p: Array, pairs: OptionalPairs, t: float) -> Array:
284
+ values = (x if is_state else p)[members]
285
+ if source is ReadKind.MEMBER or pairs is None:
286
+ return values
287
+ first, second = pairs
288
+ if source is ReadKind.FIRST:
289
+ return values[first]
290
+ if images and search is not None:
291
+ return search.second_images(x, first, second)[:, column]
292
+ return values[second]
293
+
294
+ return read
295
+
296
+ def _gather(
297
+ self,
298
+ symbol: Expression,
299
+ x: Array,
300
+ p: Array,
301
+ pairs: OptionalPairs,
302
+ t: float = 0.0,
303
+ ) -> object:
304
+ """Return the values of a symbol for every evaluation index."""
305
+ return self._reader(symbol)(x, p, pairs, t)
306
+
307
+ @property
308
+ def reads_reductions(self) -> bool:
309
+ """Whether an output reads a reduction, directly or through the operand of a derived read."""
310
+ return any(self._reads_reduction(item) for item in self.arguments)
311
+
312
+ def _reads_reduction(self, item: Expression) -> bool:
313
+ """Check whether a symbol reads a reduction, directly or through the operand of a derived read."""
314
+ reference = self.references[item]
315
+ if reference.source is ReadKind.REDUCED:
316
+ return True
317
+ if reference.source is ReadKind.DERIVED:
318
+ return any(self._reads_reduction(symbol) for symbol in reference.derived.symbols)
319
+ return False
320
+
321
+ def _run(self, inputs: RunStateSpec | None) -> None:
322
+ """Set the number of evaluation indices, the pairs in pair mode, and one array of values per output."""
323
+ state = self._state_of(inputs)
324
+ t, x, p = state.t, state.x, state.p
325
+ self._applied.clear()
326
+ pairs = self.pairs.run(state).pairs_ if self.pairs is not None else None
327
+ size = len(pairs[0]) if pairs is not None else self.rows
328
+ computed: list[npt.ArrayLike] = []
329
+ if self._function is not None:
330
+ computed = ExpressionPrinter._values_of(
331
+ self._function(t, *[read(x, p, pairs, t) for read in self._argument_readers]),
332
+ )
333
+ values: list[Array] = []
334
+ function_results: dict[tuple[int, int], Array] = {}
335
+ for output, (start, count) in zip(self.outputs, self._slots, strict=True):
336
+ if output.expression is not None:
337
+ values.append(self._broadcast(computed[start], size))
338
+ continue
339
+ key = (id(output.function), start)
340
+ if key not in function_results:
341
+ arguments = [
342
+ np.broadcast_to(np.asarray(value, dtype=float), (size,))
343
+ for value in computed[start : start + count]
344
+ ]
345
+ function_results[key] = self._call(output, t, x, p, size=size, arguments=arguments)
346
+ values.append(function_results[key][:, output.component])
347
+ self.values_ = size, pairs, values
348
+
349
+ def _named_values(self, x: Array, p: Array, *, relative: bool) -> dict[str, object]:
350
+ """Return the value of every state and parameter, by dotted name or by the name in the component."""
351
+ values: dict[str, object] = {**self.layout_states.values(x), **self.layout_parameters.values(p)}
352
+ if not relative:
353
+ return values
354
+ return {name: values[path] for name, path in (self.names or {}).items() if path in values}
355
+
356
+ def _keywords(self, output: OutputSpec) -> dict[str, np.random.Generator]:
357
+ """Return the keyword arguments of a function: the random stream when it asks for it."""
358
+ if not output.random:
359
+ return {}
360
+ if self.stream is None:
361
+ error_msg = f'A function of {self.owner} asks for the random stream, which this kind of law does not take.'
362
+ raise ValidationError(error_msg)
363
+ return {'rng': self.stream.generator}
364
+
365
+ def _call(self, output: OutputSpec, t: float, x: Array, p: Array, *, size: int, arguments: list[Array]) -> Array:
366
+ """Return the result of a function as one row per evaluation index and one column per component."""
367
+ function: Callable[..., object] | None = output.function
368
+ if function is None:
369
+ error_msg = f'The output of {self.owner} computed by a function holds no function.'
370
+ raise ValidationError(error_msg)
371
+ keywords = self._keywords(output)
372
+ if output.arguments is not None and not output.vectorized:
373
+ rows = [
374
+ np.atleast_1d(np.asarray(function(t, *row, **keywords), dtype=float))
375
+ for row in zip(*arguments, strict=True)
376
+ ]
377
+ result = np.asarray(rows, dtype=float).reshape(size, -1) if rows else np.zeros((0, output.components))
378
+ return np.broadcast_to(result, (size, output.components))
379
+ if output.arguments is not None:
380
+ result = np.asarray(function(t, *arguments, **keywords), dtype=float)
381
+ else:
382
+ values = self._named_values(x, p, relative=output.relative)
383
+ result = np.asarray(function(t, values, **keywords), dtype=float)
384
+ if result.size == size * output.components:
385
+ return result.reshape(size, output.components)
386
+ return np.broadcast_to(result.reshape(-1)[: output.components], (size, output.components))
387
+
388
+ def _change_function(self, value: object) -> Callable[[float, Array, Array], Array]:
389
+ """Return the function that gives the change of a jump for every evaluation index."""
390
+ relative = isinstance(value, CallSpec) and value.relative
391
+ function = value.function if isinstance(value, CallSpec) else value
392
+ if not callable(function) or (isinstance(value, CallSpec) and value.arguments):
393
+ error_msg = (
394
+ f'A change of a jump of {self.owner} is {value!r}. Give a number, a function `f(t, values)`, or '
395
+ '`CallSpec(f, relative=True)`.'
396
+ )
397
+ raise ValidationError(error_msg)
398
+ rows = self.rows
399
+
400
+ def change(t: float, x: Array, p: Array) -> Array:
401
+ values = self._named_values(x, p, relative=relative)
402
+ return np.broadcast_to(np.asarray(function(t, values), dtype=float), (rows,))
403
+
404
+ return change
405
+
406
+ @staticmethod
407
+ def _single_reader(is_state: bool, index: int) -> ReadFunction:
408
+ """Return the function that reads one component shared by every evaluation index."""
409
+ if is_state:
410
+ return lambda x, p, pairs, t: x[index]
411
+ return lambda x, p, pairs, t: p[index]
412
+
413
+ @staticmethod
414
+ def _broadcast(value: npt.ArrayLike, size: int) -> Array:
415
+ """Return the values of an output as one float per evaluation index."""
416
+ if np.ndim(value) == 0:
417
+ return np.full(size, value, dtype=float)
418
+ return np.broadcast_to(np.asarray(value, dtype=float), (size,))
419
+
420
+ @staticmethod
421
+ def _lower_noise(kernels: list['LawKernel']) -> tuple[Indices, Indices, int, tuple[WienerBlockSpec, ...]]:
422
+ """Return the state and the Wiener process of every amplitude of noise kernels, with the processes they draw.
423
+
424
+ Processes are numbered in order of first use. An output without a named process takes one new process per
425
+ evaluation index, so noise without named processes draws one process per amplitude in evaluation order.
426
+
427
+ Args:
428
+ kernels:
429
+ The noise kernels in evaluation order.
430
+
431
+ Returns:
432
+ rows:
433
+ One state index per amplitude.
434
+
435
+ columns:
436
+ One process index per amplitude.
437
+
438
+ processes:
439
+ The number of processes.
440
+
441
+ blocks:
442
+ The blocks of correlated processes with their covariance factors.
443
+ """
444
+ rows: list[Indices] = []
445
+ columns: list[Indices] = []
446
+ local: dict[object, Indices] = {}
447
+ starts: dict[object, int] = {}
448
+ blocks: list[WienerBlockSpec] = []
449
+ counter = [0, -1]
450
+ for kernel in kernels:
451
+ for item in kernel.outputs:
452
+ if item.target is None:
453
+ error_msg = f'A noise output of {kernel.owner} has no target.'
454
+ raise ValidationError(error_msg)
455
+ indices = LawKernel._member_indices(item.target, kernel.rows, kernel.pairs)
456
+ rows.append(indices)
457
+ columns.append(
458
+ LawKernel._process_columns(
459
+ item.process,
460
+ indices.size,
461
+ counter=counter,
462
+ local=local,
463
+ starts=starts,
464
+ blocks=blocks,
465
+ ),
466
+ )
467
+ empty = np.zeros(0, dtype=np.intp)
468
+ return (
469
+ np.concatenate([empty, *rows]).astype(np.intp),
470
+ np.concatenate([empty, *columns]).astype(np.intp),
471
+ counter[0],
472
+ tuple(blocks),
473
+ )
474
+
475
+ @staticmethod
476
+ def _process_columns(
477
+ process: NoiseProcessSpec | None,
478
+ size: int,
479
+ *,
480
+ counter: list[int],
481
+ local: dict[object, Indices],
482
+ starts: dict[object, int],
483
+ blocks: list[WienerBlockSpec],
484
+ ) -> Indices:
485
+ """Return the process of every evaluation index of a noise output, numbering new processes in `counter`.
486
+
487
+ `counter` holds the number of processes so far and the column of the silent process, -1 until one links.
488
+ """
489
+ if process is None:
490
+ counter[0] += size
491
+ return np.arange(counter[0] - size, counter[0], dtype=np.intp)
492
+ if process.key not in starts and (process.links is not None or process.dimension):
493
+ starts[process.key] = counter[0]
494
+ if process.factor is not None and process.links is None:
495
+ blocks.append(WienerBlockSpec(counter[0], process.dimension, process.factor))
496
+ counter[0] += process.dimension
497
+ if process.links is not None:
498
+ links = process.links
499
+ if np.all(links >= 0):
500
+ return (starts[process.key] + links).astype(np.intp)
501
+ if counter[1] < 0:
502
+ counter[1] = counter[0]
503
+ blocks.append(WienerBlockSpec(counter[0], 1, np.zeros((1, 1))))
504
+ counter[0] += 1
505
+ return np.where(links >= 0, starts[process.key] + links, counter[1]).astype(np.intp)
506
+ if process.dimension:
507
+ return np.full(size, starts[process.key] + process.index, dtype=np.intp)
508
+ if process.key not in local:
509
+ counter[0] += size
510
+ local[process.key] = np.arange(counter[0] - size, counter[0], dtype=np.intp)
511
+ if local[process.key].size != size:
512
+ error_msg = (
513
+ f'The noise process {process.key!r} drives members of groups of different sizes. Name one process per '
514
+ 'group.'
515
+ )
516
+ raise ValidationError(error_msg)
517
+ return local[process.key]
518
+
519
+ @staticmethod
520
+ def _jump_channels(
521
+ kernels: list['LawKernel'],
522
+ changes: Mapping[int, list[tuple[ReferenceSpec, object]]],
523
+ ) -> tuple[_JumpChannelsSpec, ...]:
524
+ """Return the channels of every jump law of jump kernels.
525
+
526
+ Args:
527
+ kernels:
528
+ The jump kernels in evaluation order.
529
+
530
+ changes:
531
+ The changes of every jump output, keyed by the output's identity.
532
+
533
+ Returns:
534
+ channels:
535
+ One set of channels per jump law.
536
+ """
537
+ channels, offset = [], 0
538
+ for kernel in kernels:
539
+ for item in kernel.outputs:
540
+ law_changes = changes[id(item)]
541
+ targets = np.array(
542
+ [LawKernel._member_indices(reference, kernel.rows, kernel.pairs) for reference, _ in law_changes],
543
+ dtype=np.intp,
544
+ ).reshape(len(law_changes), kernel.rows)
545
+ increments = np.array(
546
+ [increment if isinstance(increment, float) else np.nan for _, increment in law_changes],
547
+ dtype=float,
548
+ )
549
+ functions = tuple(
550
+ None if isinstance(increment, float) else kernel._change_function(increment)
551
+ for _, increment in law_changes
552
+ )
553
+ channels.append(
554
+ _JumpChannelsSpec(offset, targets, increments, functions if any(functions) else ()),
555
+ )
556
+ offset += kernel.rows
557
+ return tuple(channels)
558
+
559
+ @staticmethod
560
+ def _member_indices(reference: ReferenceSpec, rows: int, pairs: PairsSearch | None = None) -> Indices:
561
+ """Return the flat index of a target component for every evaluation index of a member or edge kernel.
562
+
563
+ Args:
564
+ reference:
565
+ The target component.
566
+
567
+ rows:
568
+ The number of evaluation indices of the kernel.
569
+
570
+ pairs:
571
+ The edges of an edge kernel, whose ends targets of the source and target roles index, or `None`.
572
+
573
+ Returns:
574
+ indices:
575
+ One flat index per evaluation index.
576
+
577
+ Raises:
578
+ ValidationError:
579
+ A target of an end of an edge lies on a network whose edges change.
580
+ """
581
+ if reference.source is ReadKind.MEMBER:
582
+ return reference.flat_indices
583
+ if reference.source in {ReadKind.FIRST, ReadKind.SECOND} and isinstance(pairs, EdgeSearch):
584
+ if pairs.source is not None:
585
+ error_msg = (
586
+ f'A law targets {reference.entry.name} at an end of the edges of a network whose edges change, '
587
+ 'whose ends a fixed channel cannot follow. Target the edge member, or the node through its own '
588
+ 'laws.'
589
+ )
590
+ raise ValidationError(error_msg)
591
+ ends = pairs.sources if reference.source is ReadKind.FIRST else pairs.targets
592
+ return (reference.entry.start + ends * reference.entry.columns + reference.column).astype(np.intp)
593
+ if reference.source is ReadKind.NEIGHBOR:
594
+ if reference.shifted.entry is not None:
595
+ error_msg = (
596
+ f'A law targets {reference.entry.name} at the members of hyperedges that change during a run, '
597
+ 'whose members a fixed channel cannot follow. Write a rate or an update in place of a jump.'
598
+ )
599
+ raise ValidationError(error_msg)
600
+ table = np.asarray(reference.shifted.table, dtype=np.intp)
601
+ inside = table < reference.entry.rows
602
+ flat = reference.entry.start + table * reference.entry.columns + reference.column
603
+ return np.where(inside, flat, -1).astype(np.intp)
604
+ return np.full(rows, reference.entry.start + reference.column, dtype=np.intp)
@@ -0,0 +1,67 @@
1
+ """Define the learning problem spec."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ from collections.abc import Mapping
7
+ from dataclasses import dataclass, field
8
+
9
+ from ...core.laws import GradientStepLaw
10
+ from ..types import TracedFunction
11
+ from ._base_problem_spec import BaseProblemSpec
12
+ from ._problem_spec import ProblemSpec
13
+
14
+
15
+ @dataclass(frozen=True)
16
+ class LearningProblemSpec(BaseProblemSpec):
17
+ """Problem of a system that trains the adaptive parameters of a nested system by gradient steps, once per epoch.
18
+
19
+ Its states are the trained parameters, named by their paths from the root, and its parameters are the
20
+ hyperparameters of the optimizer. The nested system is compiled to its own problem, a discrete map or ordinary
21
+ differential equations, which the solver unrolls over the sequences of the dataset.
22
+
23
+ Args:
24
+ inner:
25
+ The problem of the nested system, compiled by the JAX backend.
26
+
27
+ model:
28
+ The path of the nested system.
29
+
30
+ training:
31
+ The path of the interaction that returns the law.
32
+
33
+ law:
34
+ The gradient-step law.
35
+
36
+ trained:
37
+ The names of the trained parameters in the states of the inner problem, in the order of the states.
38
+
39
+ hyperparameters:
40
+ A mapping from the name of every hyperparameter of the optimizer to its name in the parameters.
41
+
42
+ step:
43
+ The pure JAX function `f(t, x, p)` of the inner problem, its update or its drift.
44
+
45
+ measures:
46
+ A mapping from `'loss'` and the label of every metric to the pure JAX function `o(t, x, p)` of its value.
47
+
48
+ Examples:
49
+ >>> import numpy as np
50
+ >>> from skcomplex.types import FormKind
51
+ >>> from skcomplex.engine._utils import symbol
52
+ >>> from skcomplex.specs import LayoutSpec
53
+ >>> from skcomplex.engine.problems import LearningProblemSpec
54
+ >>> layout = LayoutSpec(())
55
+ >>> problem = LearningProblemSpec(FormKind.LEARNING, layout, layout, np.zeros(0), np.zeros(0), symbol('t'))
56
+ >>> problem.form.value, problem.trained
57
+ ('learning by gradient steps', ())
58
+ """
59
+
60
+ inner: ProblemSpec | None = field(default=None, repr=False)
61
+ model: str = ''
62
+ training: str = ''
63
+ law: GradientStepLaw | None = field(default=None, repr=False)
64
+ trained: tuple[str, ...] = ()
65
+ hyperparameters: Mapping[str, str] = field(default_factory=dict)
66
+ step: TracedFunction | None = field(default=None, repr=False)
67
+ measures: Mapping[str, TracedFunction] = field(default_factory=dict, repr=False)