scikit-complexity 0.2.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1748) hide show
  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
  375. skcomplex/engine/solvers/_gradient_descent.py +353 -0
  376. skcomplex/engine/solvers/_grunwald_letnikov.py +83 -0
  377. skcomplex/engine/solvers/_heun.py +89 -0
  378. skcomplex/engine/solvers/_history.py +184 -0
  379. skcomplex/engine/solvers/_horizon_error.py +10 -0
  380. skcomplex/engine/solvers/_imex2.py +40 -0
  381. skcomplex/engine/solvers/_imex_euler.py +35 -0
  382. skcomplex/engine/solvers/_jump_trajectories.py +98 -0
  383. skcomplex/engine/solvers/_kinetics.py +242 -0
  384. skcomplex/engine/solvers/_l1.py +91 -0
  385. skcomplex/engine/solvers/_lammps.py +745 -0
  386. skcomplex/engine/solvers/_lammps_fix_spec.py +41 -0
  387. skcomplex/engine/solvers/_lattice.py +79 -0
  388. skcomplex/engine/solvers/_lindblad.py +70 -0
  389. skcomplex/engine/solvers/_maps.py +105 -0
  390. skcomplex/engine/solvers/_mesa.py +1624 -0
  391. skcomplex/engine/solvers/_milstein.py +93 -0
  392. skcomplex/engine/solvers/_monte_carlo.py +43 -0
  393. skcomplex/engine/solvers/_operator.py +212 -0
  394. skcomplex/engine/solvers/_optimal_control.py +368 -0
  395. skcomplex/engine/solvers/_pontryagin.py +298 -0
  396. skcomplex/engine/solvers/_renewal.py +90 -0
  397. skcomplex/engine/solvers/_renewals.py +190 -0
  398. skcomplex/engine/solvers/_rk4.py +263 -0
  399. skcomplex/engine/solvers/_root.py +176 -0
  400. skcomplex/engine/solvers/_rows.py +49 -0
  401. skcomplex/engine/solvers/_scipy_ode.py +602 -0
  402. skcomplex/engine/solvers/_sde.py +164 -0
  403. skcomplex/engine/solvers/_semi_lagrangian.py +213 -0
  404. skcomplex/engine/solvers/_solver.py +159 -0
  405. skcomplex/engine/solvers/_split.py +394 -0
  406. skcomplex/engine/solvers/_ssprk.py +147 -0
  407. skcomplex/engine/solvers/_strang_splitting.py +178 -0
  408. skcomplex/engine/solvers/_unitary.py +68 -0
  409. skcomplex/engine/solvers/_velocity_verlet.py +171 -0
  410. skcomplex/engine/solvers/_yoshida4.py +242 -0
  411. skcomplex/engine/types.py +90 -0
  412. skcomplex/engine/viz/__init__.py +35 -0
  413. skcomplex/engine/viz/_agents.py +223 -0
  414. skcomplex/engine/viz/_axes.py +146 -0
  415. skcomplex/engine/viz/_base.py +365 -0
  416. skcomplex/engine/viz/_bodies.py +334 -0
  417. skcomplex/engine/viz/_cayley.py +133 -0
  418. skcomplex/engine/viz/_expectation.py +208 -0
  419. skcomplex/engine/viz/_histograms.py +218 -0
  420. skcomplex/engine/viz/_images.py +307 -0
  421. skcomplex/engine/viz/_matrices.py +141 -0
  422. skcomplex/engine/viz/_meshes.py +149 -0
  423. skcomplex/engine/viz/_points.py +238 -0
  424. skcomplex/engine/viz/_rerun.py +527 -0
  425. skcomplex/engine/viz/_rings.py +127 -0
  426. skcomplex/engine/viz/_scalars.py +129 -0
  427. skcomplex/engine/viz/_sites.py +228 -0
  428. skcomplex/errors.py +112 -0
  429. skcomplex/experiments/__init__.py +36 -0
  430. skcomplex/experiments/_base.py +373 -0
  431. skcomplex/experiments/_basin_stability.py +153 -0
  432. skcomplex/experiments/_calibration.py +194 -0
  433. skcomplex/experiments/_experiment.py +327 -0
  434. skcomplex/experiments/_grid.py +36 -0
  435. skcomplex/experiments/_latin_hypercube.py +44 -0
  436. skcomplex/experiments/_morris.py +50 -0
  437. skcomplex/experiments/_one_at_a_time.py +28 -0
  438. skcomplex/experiments/_orbit_diagram.py +146 -0
  439. skcomplex/experiments/_random.py +44 -0
  440. skcomplex/experiments/_results.py +148 -0
  441. skcomplex/experiments/_rows.py +45 -0
  442. skcomplex/experiments/_saltelli.py +50 -0
  443. skcomplex/experiments/_sensitivity.py +122 -0
  444. skcomplex/experiments/_sobol.py +43 -0
  445. skcomplex/experiments/specs/__init__.py +1 -0
  446. skcomplex/experiments/specs/_task_spec.py +78 -0
  447. skcomplex/experiments/types.py +14 -0
  448. skcomplex/models/__init__.py +18 -0
  449. skcomplex/models/_catalog.py +243 -0
  450. skcomplex/models/_model_catalog.py +270 -0
  451. skcomplex/models/_model_entry.py +170 -0
  452. skcomplex/models/_model_listing.py +38 -0
  453. skcomplex/models/biology/__init__.py +1 -0
  454. skcomplex/models/biology/collective_behaviour/__init__.py +48 -0
  455. skcomplex/models/biology/collective_behaviour/_alarm.py +99 -0
  456. skcomplex/models/biology/collective_behaviour/_ant.py +101 -0
  457. skcomplex/models/biology/collective_behaviour/_ant_view.py +24 -0
  458. skcomplex/models/biology/collective_behaviour/_boid.py +104 -0
  459. skcomplex/models/biology/collective_behaviour/_boid_view.py +25 -0
  460. skcomplex/models/biology/collective_behaviour/_branch.py +41 -0
  461. skcomplex/models/biology/collective_behaviour/_decisions.py +149 -0
  462. skcomplex/models/biology/collective_behaviour/_flight.py +52 -0
  463. skcomplex/models/biology/collective_behaviour/_flocking.py +75 -0
  464. skcomplex/models/biology/collective_behaviour/_flocks.py +169 -0
  465. skcomplex/models/biology/collective_behaviour/_foraging.py +232 -0
  466. skcomplex/models/biology/collective_behaviour/_ground.py +67 -0
  467. skcomplex/models/biology/collective_behaviour/_leadership.py +207 -0
  468. skcomplex/models/biology/collective_behaviour/_morse_potential.py +87 -0
  469. skcomplex/models/biology/collective_behaviour/_pheromone.py +55 -0
  470. skcomplex/models/biology/collective_behaviour/_rats.py +41 -0
  471. skcomplex/models/biology/collective_behaviour/_schooling.py +102 -0
  472. skcomplex/models/biology/collective_behaviour/_self_propulsion.py +64 -0
  473. skcomplex/models/biology/collective_behaviour/_shoal_member_view.py +25 -0
  474. skcomplex/models/biology/collective_behaviour/_swimming.py +66 -0
  475. skcomplex/models/biology/collective_behaviour/_trail_choice.py +105 -0
  476. skcomplex/models/biology/collective_behaviour/_trails.py +245 -0
  477. skcomplex/models/biology/collective_behaviour/_walker.py +97 -0
  478. skcomplex/models/biology/collective_behaviour/_walker_view.py +23 -0
  479. skcomplex/models/biology/common/__init__.py +3 -0
  480. skcomplex/models/biology/common/excitable/__init__.py +7 -0
  481. skcomplex/models/biology/common/excitable/_fitzhugh_nagumo.py +121 -0
  482. skcomplex/models/biology/common/kinetics/__init__.py +7 -0
  483. skcomplex/models/biology/common/kinetics/_michaelis_menten.py +137 -0
  484. skcomplex/models/biology/common/networks/__init__.py +9 -0
  485. skcomplex/models/biology/common/networks/_edge_draw.py +95 -0
  486. skcomplex/models/biology/common/networks/_weighted_edge.py +48 -0
  487. skcomplex/models/biology/common/pharmacokinetics/__init__.py +7 -0
  488. skcomplex/models/biology/common/pharmacokinetics/_dosing.py +125 -0
  489. skcomplex/models/biology/common/populations/__init__.py +19 -0
  490. skcomplex/models/biology/common/populations/_exponential_growth.py +66 -0
  491. skcomplex/models/biology/common/populations/_gompertz_growth.py +75 -0
  492. skcomplex/models/biology/common/populations/_growth.py +176 -0
  493. skcomplex/models/biology/common/populations/_logistic_growth.py +92 -0
  494. skcomplex/models/biology/common/populations/_mortality.py +69 -0
  495. skcomplex/models/biology/common/populations/_population.py +41 -0
  496. skcomplex/models/biology/common/populations/_power_law_growth.py +71 -0
  497. skcomplex/models/biology/common/stigmergy/__init__.py +7 -0
  498. skcomplex/models/biology/common/stigmergy/_evaporation.py +95 -0
  499. skcomplex/models/biology/ecology/__init__.py +128 -0
  500. skcomplex/models/biology/ecology/_abundance.py +52 -0
  501. skcomplex/models/biology/ecology/_agent_predation.py +170 -0
  502. skcomplex/models/biology/ecology/_cell_quota.py +163 -0
  503. skcomplex/models/biology/ecology/_clustering.py +96 -0
  504. skcomplex/models/biology/ecology/_communities.py +234 -0
  505. skcomplex/models/biology/ecology/_competition.py +95 -0
  506. skcomplex/models/biology/ecology/_cow.py +49 -0
  507. skcomplex/models/biology/ecology/_cow_view.py +15 -0
  508. skcomplex/models/biology/ecology/_emotion_marks.py +65 -0
  509. skcomplex/models/biology/ecology/_factories.py +322 -0
  510. skcomplex/models/biology/ecology/_forager.py +116 -0
  511. skcomplex/models/biology/ecology/_forager_view.py +25 -0
  512. skcomplex/models/biology/ecology/_fronts.py +128 -0
  513. skcomplex/models/biology/ecology/_generalized_lotka_volterra.py +66 -0
  514. skcomplex/models/biology/ecology/_grass.py +96 -0
  515. skcomplex/models/biology/ecology/_grass_view.py +17 -0
  516. skcomplex/models/biology/ecology/_grazing.py +66 -0
  517. skcomplex/models/biology/ecology/_habitat_patch.py +49 -0
  518. skcomplex/models/biology/ecology/_herding.py +84 -0
  519. skcomplex/models/biology/ecology/_higher_order.py +102 -0
  520. skcomplex/models/biology/ecology/_hopping.py +68 -0
  521. skcomplex/models/biology/ecology/_instability.py +180 -0
  522. skcomplex/models/biology/ecology/_linear_growth.py +70 -0
  523. skcomplex/models/biology/ecology/_meadow.py +102 -0
  524. skcomplex/models/biology/ecology/_microbe.py +47 -0
  525. skcomplex/models/biology/ecology/_microbial_communities.py +90 -0
  526. skcomplex/models/biology/ecology/_mutualism.py +81 -0
  527. skcomplex/models/biology/ecology/_neutral.py +144 -0
  528. skcomplex/models/biology/ecology/_neutral_replacement.py +54 -0
  529. skcomplex/models/biology/ecology/_organism.py +63 -0
  530. skcomplex/models/biology/ecology/_organism_view.py +15 -0
  531. skcomplex/models/biology/ecology/_parasitism.py +78 -0
  532. skcomplex/models/biology/ecology/_pasture.py +83 -0
  533. skcomplex/models/biology/ecology/_pasture_view.py +16 -0
  534. skcomplex/models/biology/ecology/_pioneer_growth.py +101 -0
  535. skcomplex/models/biology/ecology/_plant.py +56 -0
  536. skcomplex/models/biology/ecology/_plant_view.py +16 -0
  537. skcomplex/models/biology/ecology/_predation.py +290 -0
  538. skcomplex/models/biology/ecology/_predation_interaction.py +71 -0
  539. skcomplex/models/biology/ecology/_predator.py +63 -0
  540. skcomplex/models/biology/ecology/_predator_prey_events.py +120 -0
  541. skcomplex/models/biology/ecology/_predator_view.py +17 -0
  542. skcomplex/models/biology/ecology/_prey.py +52 -0
  543. skcomplex/models/biology/ecology/_prey_view.py +15 -0
  544. skcomplex/models/biology/ecology/_rosenzweig_macarthur.py +91 -0
  545. skcomplex/models/biology/ecology/_seasonal_logistic_growth.py +71 -0
  546. skcomplex/models/biology/ecology/_sequential.py +114 -0
  547. skcomplex/models/biology/ecology/_sheep.py +63 -0
  548. skcomplex/models/biology/ecology/_sheep_view.py +17 -0
  549. skcomplex/models/biology/ecology/_speciation.py +71 -0
  550. skcomplex/models/biology/ecology/_stand.py +47 -0
  551. skcomplex/models/biology/ecology/_stigmergic_predator.py +98 -0
  552. skcomplex/models/biology/ecology/_stigmergic_prey.py +54 -0
  553. skcomplex/models/biology/ecology/_stigmergy.py +413 -0
  554. skcomplex/models/biology/ecology/_succession.py +92 -0
  555. skcomplex/models/biology/ecology/_successional_growth.py +88 -0
  556. skcomplex/models/biology/ecology/_triplet.py +55 -0
  557. skcomplex/models/biology/ecology/_wolf.py +63 -0
  558. skcomplex/models/biology/ecology/_wolf_sheep.py +156 -0
  559. skcomplex/models/biology/ecology/_wolf_view.py +17 -0
  560. skcomplex/models/biology/epidemiology/__init__.py +53 -0
  561. skcomplex/models/biology/epidemiology/_active_host.py +61 -0
  562. skcomplex/models/biology/epidemiology/_adaptive.py +316 -0
  563. skcomplex/models/biology/epidemiology/_agents.py +484 -0
  564. skcomplex/models/biology/epidemiology/_carrier.py +66 -0
  565. skcomplex/models/biology/epidemiology/_degree_class.py +65 -0
  566. skcomplex/models/biology/epidemiology/_factories.py +186 -0
  567. skcomplex/models/biology/epidemiology/_host.py +49 -0
  568. skcomplex/models/biology/epidemiology/_immunity_loss.py +84 -0
  569. skcomplex/models/biology/epidemiology/_infection.py +93 -0
  570. skcomplex/models/biology/epidemiology/_networks.py +170 -0
  571. skcomplex/models/biology/epidemiology/_outbreaks.py +216 -0
  572. skcomplex/models/biology/epidemiology/_person.py +103 -0
  573. skcomplex/models/biology/epidemiology/_person_view.py +23 -0
  574. skcomplex/models/biology/epidemiology/_recovery.py +92 -0
  575. skcomplex/models/biology/epidemiology/_recurrent.py +149 -0
  576. skcomplex/models/biology/epidemiology/_spreading.py +144 -0
  577. skcomplex/models/biology/epidemiology/_subpopulation.py +92 -0
  578. skcomplex/models/biology/epidemiology/_traveller.py +65 -0
  579. skcomplex/models/biology/epidemiology/_traveller_view.py +17 -0
  580. skcomplex/models/biology/epidemiology/_vaccination.py +184 -0
  581. skcomplex/models/biology/epidemiology/_walker.py +66 -0
  582. skcomplex/models/biology/epidemiology/_walker_view.py +17 -0
  583. skcomplex/models/biology/evolution/__init__.py +60 -0
  584. skcomplex/models/biology/evolution/_adaptive_climbing.py +106 -0
  585. skcomplex/models/biology/evolution/_catalysis.py +76 -0
  586. skcomplex/models/biology/evolution/_catalytic_link.py +21 -0
  587. skcomplex/models/biology/evolution/_chemical.py +111 -0
  588. skcomplex/models/biology/evolution/_climber.py +125 -0
  589. skcomplex/models/biology/evolution/_climber_view.py +19 -0
  590. skcomplex/models/biology/evolution/_coevolution.py +148 -0
  591. skcomplex/models/biology/evolution/_cyclic_species.py +44 -0
  592. skcomplex/models/biology/evolution/_dependency_field.py +56 -0
  593. skcomplex/models/biology/evolution/_finite_populations.py +287 -0
  594. skcomplex/models/biology/evolution/_games.py +143 -0
  595. skcomplex/models/biology/evolution/_genotype_class.py +42 -0
  596. skcomplex/models/biology/evolution/_individual.py +54 -0
  597. skcomplex/models/biology/evolution/_individual_view.py +16 -0
  598. skcomplex/models/biology/evolution/_locus.py +47 -0
  599. skcomplex/models/biology/evolution/_master_sequence.py +55 -0
  600. skcomplex/models/biology/evolution/_molecule.py +47 -0
  601. skcomplex/models/biology/evolution/_moran_step.py +83 -0
  602. skcomplex/models/biology/evolution/_networks.py +194 -0
  603. skcomplex/models/biology/evolution/_prebiotic.py +169 -0
  604. skcomplex/models/biology/evolution/_replicator.py +109 -0
  605. skcomplex/models/biology/evolution/_strategy.py +42 -0
  606. skcomplex/models/biology/evolution/_substitution.py +113 -0
  607. skcomplex/models/biology/evolution/_substitutions.py +126 -0
  608. skcomplex/models/biology/evolution/_tangled_nature_life_cycle.py +159 -0
  609. skcomplex/models/biology/evolution/_taxon.py +49 -0
  610. skcomplex/models/biology/neuroscience/__init__.py +63 -0
  611. skcomplex/models/biology/neuroscience/_conductances.py +193 -0
  612. skcomplex/models/biology/neuroscience/_delayed_synapse.py +70 -0
  613. skcomplex/models/biology/neuroscience/_excitable.py +178 -0
  614. skcomplex/models/biology/neuroscience/_fitz_hugh_nagumo_neuron.py +46 -0
  615. skcomplex/models/biology/neuroscience/_global_inhibition.py +71 -0
  616. skcomplex/models/biology/neuroscience/_hodgkin_huxley.py +103 -0
  617. skcomplex/models/biology/neuroscience/_inhibitor.py +62 -0
  618. skcomplex/models/biology/neuroscience/_inhibitor_drive.py +61 -0
  619. skcomplex/models/biology/neuroscience/_izhikevich.py +77 -0
  620. skcomplex/models/biology/neuroscience/_leaky_integrate_and_fire.py +80 -0
  621. skcomplex/models/biology/neuroscience/_mutual_inhibition.py +55 -0
  622. skcomplex/models/biology/neuroscience/_networks.py +235 -0
  623. skcomplex/models/biology/neuroscience/_neural_field_site.py +66 -0
  624. skcomplex/models/biology/neuroscience/_neural_fields.py +94 -0
  625. skcomplex/models/biology/neuroscience/_neurons.py +129 -0
  626. skcomplex/models/biology/neuroscience/_polyhomeostatic_neuron.py +93 -0
  627. skcomplex/models/biology/neuroscience/_populations.py +333 -0
  628. skcomplex/models/biology/neuroscience/_pulse_coupling.py +71 -0
  629. skcomplex/models/biology/neuroscience/_rate_unit.py +67 -0
  630. skcomplex/models/biology/neuroscience/_spike_reset.py +95 -0
  631. skcomplex/models/biology/neuroscience/_spiking_neuron.py +67 -0
  632. skcomplex/models/biology/neuroscience/_synapses.py +226 -0
  633. skcomplex/models/biology/neuroscience/_terman_wang.py +113 -0
  634. skcomplex/models/biology/neuroscience/_theta_neuron.py +66 -0
  635. skcomplex/models/biology/neuroscience/_wilson_cowan.py +122 -0
  636. skcomplex/models/biology/neuroscience/types.py +8 -0
  637. skcomplex/models/biology/oncology/__init__.py +212 -0
  638. skcomplex/models/biology/oncology/_androgen_receptor_prostate.py +240 -0
  639. skcomplex/models/biology/oncology/_androgen_suppression.py +109 -0
  640. skcomplex/models/biology/oncology/_angiogenesis.py +306 -0
  641. skcomplex/models/biology/oncology/_angiogenesis_immunotherapy_tumour.py +247 -0
  642. skcomplex/models/biology/oncology/_angiogenic_tumour.py +110 -0
  643. skcomplex/models/biology/oncology/_antiangiogenic.py +227 -0
  644. skcomplex/models/biology/oncology/_bone_marrow_blood.py +196 -0
  645. skcomplex/models/biology/oncology/_cell_cycle.py +85 -0
  646. skcomplex/models/biology/oncology/_cell_kinetics.py +285 -0
  647. skcomplex/models/biology/oncology/_cell_quota_prostate.py +207 -0
  648. skcomplex/models/biology/oncology/_cell_survival.py +72 -0
  649. skcomplex/models/biology/oncology/_checkpoint_tumour.py +161 -0
  650. skcomplex/models/biology/oncology/_chemoimmunotherapy_tumour.py +251 -0
  651. skcomplex/models/biology/oncology/_chemotherapy.py +565 -0
  652. skcomplex/models/biology/oncology/_chemovirotherapy_tumour.py +139 -0
  653. skcomplex/models/biology/oncology/_clonal_tumour.py +134 -0
  654. skcomplex/models/biology/oncology/_combination_therapy.py +989 -0
  655. skcomplex/models/biology/oncology/_delayed_vaccinated_tumour.py +341 -0
  656. skcomplex/models/biology/oncology/_dormant_cell_cycle.py +95 -0
  657. skcomplex/models/biology/oncology/_erythropoiesis.py +129 -0
  658. skcomplex/models/biology/oncology/_exponential_linear_growth.py +66 -0
  659. skcomplex/models/biology/oncology/_gene_viral_therapy.py +480 -0
  660. skcomplex/models/biology/oncology/_glioma_brain.py +165 -0
  661. skcomplex/models/biology/oncology/_growth.py +378 -0
  662. skcomplex/models/biology/oncology/_her2_tumour.py +156 -0
  663. skcomplex/models/biology/oncology/_hormone_therapy.py +985 -0
  664. skcomplex/models/biology/oncology/_immune_competition.py +241 -0
  665. skcomplex/models/biology/oncology/_immunotherapy.py +1001 -0
  666. skcomplex/models/biology/oncology/_intermittent_suppression.py +130 -0
  667. skcomplex/models/biology/oncology/_irradiated_tumour.py +105 -0
  668. skcomplex/models/biology/oncology/_irradiation.py +97 -0
  669. skcomplex/models/biology/oncology/_kirschner_panetta_tumour.py +132 -0
  670. skcomplex/models/biology/oncology/_leukaemia_stem_cells.py +150 -0
  671. skcomplex/models/biology/oncology/_linear_quadratic_survival.py +112 -0
  672. skcomplex/models/biology/oncology/_log_kill.py +81 -0
  673. skcomplex/models/biology/oncology/_metastasis_chemotherapy.py +211 -0
  674. skcomplex/models/biology/oncology/_multidrug_resistance.py +201 -0
  675. skcomplex/models/biology/oncology/_oncolytic_virus.py +68 -0
  676. skcomplex/models/biology/oncology/_oncolytic_virus_dendritic.py +155 -0
  677. skcomplex/models/biology/oncology/_optimal_chemotherapy.py +157 -0
  678. skcomplex/models/biology/oncology/_optimal_immunotherapy.py +137 -0
  679. skcomplex/models/biology/oncology/_optimal_therapy.py +208 -0
  680. skcomplex/models/biology/oncology/_piecewise_linear_prostate.py +147 -0
  681. skcomplex/models/biology/oncology/_radiation_competition.py +104 -0
  682. skcomplex/models/biology/oncology/_radiotherapy.py +311 -0
  683. skcomplex/models/biology/oncology/_resistance_switching.py +148 -0
  684. skcomplex/models/biology/oncology/_resting_hunting_chemotherapy.py +136 -0
  685. skcomplex/models/biology/oncology/_sirna_tgf_beta.py +189 -0
  686. skcomplex/models/biology/oncology/_sprout.py +65 -0
  687. skcomplex/models/biology/oncology/_sprout_view.py +17 -0
  688. skcomplex/models/biology/oncology/_stem_cell_differentiation.py +262 -0
  689. skcomplex/models/biology/oncology/_stem_cells.py +548 -0
  690. skcomplex/models/biology/oncology/_suppressed_tumour.py +338 -0
  691. skcomplex/models/biology/oncology/_tamoxifen_tumour.py +172 -0
  692. skcomplex/models/biology/oncology/_tcr_gene_therapy.py +98 -0
  693. skcomplex/models/biology/oncology/_therapy_switch.py +86 -0
  694. skcomplex/models/biology/oncology/_tissue.py +71 -0
  695. skcomplex/models/biology/oncology/_tumour_cell.py +85 -0
  696. skcomplex/models/biology/oncology/_tumour_cell_view.py +21 -0
  697. skcomplex/models/biology/oncology/_tumour_immune_chemotherapy.py +169 -0
  698. skcomplex/models/biology/oncology/_vaccinated_tumour.py +180 -0
  699. skcomplex/models/biology/oncology/_vascular_support.py +71 -0
  700. skcomplex/models/biology/oncology/_vascularized_spheroid.py +264 -0
  701. skcomplex/models/biology/oncology/_vasculature.py +42 -0
  702. skcomplex/models/biology/oncology/_vessel.py +49 -0
  703. skcomplex/models/biology/oncology/_vessel_view.py +15 -0
  704. skcomplex/models/biology/physiology/__init__.py +46 -0
  705. skcomplex/models/biology/physiology/_adaptivity.py +277 -0
  706. skcomplex/models/biology/physiology/_cardiac.py +167 -0
  707. skcomplex/models/biology/physiology/_chamber.py +71 -0
  708. skcomplex/models/biology/physiology/_circulation.py +97 -0
  709. skcomplex/models/biology/physiology/_coagulation.py +130 -0
  710. skcomplex/models/biology/physiology/_contour_cell.py +61 -0
  711. skcomplex/models/biology/physiology/_contour_uptake.py +61 -0
  712. skcomplex/models/biology/physiology/_exchange.py +165 -0
  713. skcomplex/models/biology/physiology/_exchanging_cell.py +83 -0
  714. skcomplex/models/biology/physiology/_fitz_hugh_nagumo.py +46 -0
  715. skcomplex/models/biology/physiology/_glucose_control.py +136 -0
  716. skcomplex/models/biology/physiology/_mackey_glass.py +81 -0
  717. skcomplex/models/biology/physiology/_pharmacokinetics.py +104 -0
  718. skcomplex/models/biology/physiology/_physiology.py +118 -0
  719. skcomplex/models/biology/physiology/_regulation.py +251 -0
  720. skcomplex/models/biology/physiology/_resistive_flow.py +67 -0
  721. skcomplex/models/biology/physiology/_toxicity.py +164 -0
  722. skcomplex/models/biology/systems_biology/__init__.py +52 -0
  723. skcomplex/models/biology/systems_biology/_boolean.py +141 -0
  724. skcomplex/models/biology/systems_biology/_boolean_function.py +84 -0
  725. skcomplex/models/biology/systems_biology/_boolean_models.py +206 -0
  726. skcomplex/models/biology/systems_biology/_boolean_node.py +41 -0
  727. skcomplex/models/biology/systems_biology/_cascades.py +178 -0
  728. skcomplex/models/biology/systems_biology/_clocks.py +274 -0
  729. skcomplex/models/biology/systems_biology/_generalized_mass_action.py +123 -0
  730. skcomplex/models/biology/systems_biology/_genes.py +296 -0
  731. skcomplex/models/biology/systems_biology/_min_proteins.py +230 -0
  732. skcomplex/models/biology/systems_biology/_networks.py +359 -0
  733. skcomplex/models/biology/systems_biology/_phosphorylation_loop.py +121 -0
  734. skcomplex/models/biology/systems_biology/_probabilistic.py +75 -0
  735. skcomplex/models/biology/systems_biology/_probabilistic_function.py +127 -0
  736. skcomplex/models/biology/systems_biology/_probabilistic_node.py +47 -0
  737. skcomplex/models/biology/systems_biology/_repression.py +104 -0
  738. skcomplex/models/biology/systems_biology/_s_system.py +88 -0
  739. skcomplex/models/biology/systems_biology/_species.py +44 -0
  740. skcomplex/models/biology/systems_biology/_threshold_function.py +63 -0
  741. skcomplex/models/biology/systems_biology/types.py +9 -0
  742. skcomplex/models/chemistry/__init__.py +1 -0
  743. skcomplex/models/chemistry/common/__init__.py +3 -0
  744. skcomplex/models/chemistry/common/kinetics/__init__.py +9 -0
  745. skcomplex/models/chemistry/common/kinetics/_brusselator.py +61 -0
  746. skcomplex/models/chemistry/common/kinetics/_cubic_autocatalysis.py +80 -0
  747. skcomplex/models/chemistry/kinetics/__init__.py +38 -0
  748. skcomplex/models/chemistry/kinetics/_catalyst_pellet.py +60 -0
  749. skcomplex/models/chemistry/kinetics/_cubic_autocatalysis.py +60 -0
  750. skcomplex/models/chemistry/kinetics/_cyclic.py +130 -0
  751. skcomplex/models/chemistry/kinetics/_hodgepodge.py +157 -0
  752. skcomplex/models/chemistry/kinetics/_nanoparticles.py +103 -0
  753. skcomplex/models/chemistry/kinetics/_oregonator.py +76 -0
  754. skcomplex/models/chemistry/kinetics/_oscillators.py +244 -0
  755. skcomplex/models/chemistry/kinetics/_pulsed_electrode.py +107 -0
  756. skcomplex/models/chemistry/kinetics/_reactions.py +332 -0
  757. skcomplex/models/chemistry/kinetics/_reactors.py +144 -0
  758. skcomplex/models/chemistry/pattern_formation/__init__.py +15 -0
  759. skcomplex/models/chemistry/pattern_formation/_brusselator.py +62 -0
  760. skcomplex/models/chemistry/pattern_formation/_gray_scott.py +68 -0
  761. skcomplex/models/chemistry/pattern_formation/_reaction_diffusion.py +268 -0
  762. skcomplex/models/chemistry/pattern_formation/_schnakenberg.py +67 -0
  763. skcomplex/models/computer_science/__init__.py +1 -0
  764. skcomplex/models/computer_science/automata/__init__.py +56 -0
  765. skcomplex/models/computer_science/automata/_automata.py +229 -0
  766. skcomplex/models/computer_science/automata/_automaton.py +202 -0
  767. skcomplex/models/computer_science/automata/_binary_cell.py +41 -0
  768. skcomplex/models/computer_science/automata/_codes.py +73 -0
  769. skcomplex/models/computer_science/automata/_diffusion_cell.py +47 -0
  770. skcomplex/models/computer_science/automata/_group_automata.py +449 -0
  771. skcomplex/models/computer_science/automata/_groups.py +132 -0
  772. skcomplex/models/computer_science/automata/_linear_automaton.py +128 -0
  773. skcomplex/models/computer_science/automata/_noisy_elementary_cell.py +46 -0
  774. skcomplex/models/computer_science/automata/_pascal_cell.py +41 -0
  775. skcomplex/models/computer_science/automata/_subshift.py +192 -0
  776. skcomplex/models/computer_science/automata/_variants.py +292 -0
  777. skcomplex/models/computer_science/evolutionary_computation/__init__.py +27 -0
  778. skcomplex/models/computer_science/evolutionary_computation/_annealed_candidate.py +39 -0
  779. skcomplex/models/computer_science/evolutionary_computation/_bit_string.py +55 -0
  780. skcomplex/models/computer_science/evolutionary_computation/_bit_string_view.py +13 -0
  781. skcomplex/models/computer_science/evolutionary_computation/_genetic_algorithms.py +92 -0
  782. skcomplex/models/computer_science/evolutionary_computation/_landscapes.py +82 -0
  783. skcomplex/models/computer_science/evolutionary_computation/_optimisers.py +217 -0
  784. skcomplex/models/computer_science/evolutionary_computation/_reproduction.py +129 -0
  785. skcomplex/models/computer_science/evolutionary_computation/_room_cleaning.py +170 -0
  786. skcomplex/models/computer_science/evolutionary_computation/_running_best.py +30 -0
  787. skcomplex/models/computer_science/evolutionary_computation/_running_best_update.py +58 -0
  788. skcomplex/models/computer_science/evolutionary_computation/_search_candidate.py +32 -0
  789. skcomplex/models/computer_science/evolutionary_computation/_strategy.py +54 -0
  790. skcomplex/models/computer_science/evolutionary_computation/_strategy_view.py +14 -0
  791. skcomplex/models/computer_science/neural_networks/__init__.py +34 -0
  792. skcomplex/models/computer_science/neural_networks/_binary_weight.py +32 -0
  793. skcomplex/models/computer_science/neural_networks/_diluted.py +159 -0
  794. skcomplex/models/computer_science/neural_networks/_echo_state.py +173 -0
  795. skcomplex/models/computer_science/neural_networks/_elman.py +160 -0
  796. skcomplex/models/computer_science/neural_networks/_hidden_unit.py +51 -0
  797. skcomplex/models/computer_science/neural_networks/_hopfield.py +134 -0
  798. skcomplex/models/computer_science/neural_networks/_hopfield_update.py +51 -0
  799. skcomplex/models/computer_science/neural_networks/_input_coupling.py +63 -0
  800. skcomplex/models/computer_science/neural_networks/_input_unit.py +39 -0
  801. skcomplex/models/computer_science/neural_networks/_neuron_view.py +14 -0
  802. skcomplex/models/computer_science/neural_networks/_output_unit.py +51 -0
  803. skcomplex/models/computer_science/neural_networks/_perceptron.py +72 -0
  804. skcomplex/models/computer_science/neural_networks/_readout_coupling.py +69 -0
  805. skcomplex/models/computer_science/neural_networks/_recurrence_coupling.py +66 -0
  806. skcomplex/models/economics/__init__.py +1 -0
  807. skcomplex/models/economics/common/__init__.py +3 -0
  808. skcomplex/models/economics/common/forecasting/__init__.py +7 -0
  809. skcomplex/models/economics/common/forecasting/_heuristics.py +51 -0
  810. skcomplex/models/economics/common/resources/__init__.py +7 -0
  811. skcomplex/models/economics/common/resources/_regrowth.py +70 -0
  812. skcomplex/models/economics/econophysics/__init__.py +58 -0
  813. skcomplex/models/economics/econophysics/_crowd_avoidance.py +80 -0
  814. skcomplex/models/economics/econophysics/_debt_exchange.py +74 -0
  815. skcomplex/models/economics/econophysics/_diner.py +59 -0
  816. skcomplex/models/economics/econophysics/_diner_view.py +17 -0
  817. skcomplex/models/economics/econophysics/_el_farol.py +114 -0
  818. skcomplex/models/economics/econophysics/_exchange.py +82 -0
  819. skcomplex/models/economics/econophysics/_game_state_spec.py +26 -0
  820. skcomplex/models/economics/econophysics/_kinetic.py +80 -0
  821. skcomplex/models/economics/econophysics/_kolkata.py +87 -0
  822. skcomplex/models/economics/econophysics/_minority.py +123 -0
  823. skcomplex/models/economics/econophysics/_minority_game.py +161 -0
  824. skcomplex/models/economics/econophysics/_minority_player.py +79 -0
  825. skcomplex/models/economics/econophysics/_minority_player_view.py +22 -0
  826. skcomplex/models/economics/econophysics/_patron.py +105 -0
  827. skcomplex/models/economics/econophysics/_patron_view.py +18 -0
  828. skcomplex/models/economics/econophysics/_predictor_pool.py +181 -0
  829. skcomplex/models/economics/econophysics/_predictor_pool_view.py +14 -0
  830. skcomplex/models/economics/econophysics/_restaurants.py +93 -0
  831. skcomplex/models/economics/econophysics/_saving_exchange.py +73 -0
  832. skcomplex/models/economics/econophysics/_saving_trader.py +47 -0
  833. skcomplex/models/economics/econophysics/_saving_trader_view.py +12 -0
  834. skcomplex/models/economics/econophysics/_wealth_exchange.py +114 -0
  835. skcomplex/models/economics/econophysics/_welfare.py +210 -0
  836. skcomplex/models/economics/econophysics/_welfare_policy.py +99 -0
  837. skcomplex/models/economics/finance/__init__.py +41 -0
  838. skcomplex/models/economics/finance/_arbitrage.py +139 -0
  839. skcomplex/models/economics/finance/_asset.py +42 -0
  840. skcomplex/models/economics/finance/_assets.py +44 -0
  841. skcomplex/models/economics/finance/_book.py +115 -0
  842. skcomplex/models/economics/finance/_contagion.py +116 -0
  843. skcomplex/models/economics/finance/_correlated_assets.py +69 -0
  844. skcomplex/models/economics/finance/_debt_rank_cascade.py +86 -0
  845. skcomplex/models/economics/finance/_geometric_brownian_motion.py +89 -0
  846. skcomplex/models/economics/finance/_gibrat_firm.py +82 -0
  847. skcomplex/models/economics/finance/_gibrat_firm_view.py +18 -0
  848. skcomplex/models/economics/finance/_growth_processes.py +195 -0
  849. skcomplex/models/economics/finance/_interbank.py +76 -0
  850. skcomplex/models/economics/finance/_interbank_view.py +14 -0
  851. skcomplex/models/economics/finance/_kesten_firm.py +88 -0
  852. skcomplex/models/economics/finance/_kesten_firm_view.py +16 -0
  853. skcomplex/models/economics/finance/_order_book.py +164 -0
  854. skcomplex/models/economics/finance/_reflecting_floor.py +66 -0
  855. skcomplex/models/economics/finance/_stock_trader.py +205 -0
  856. skcomplex/models/economics/finance/_stock_trader_view.py +24 -0
  857. skcomplex/models/economics/finance/_wealth.py +143 -0
  858. skcomplex/models/economics/innovation/__init__.py +23 -0
  859. skcomplex/models/economics/innovation/_adoption.py +233 -0
  860. skcomplex/models/economics/innovation/_bass.py +124 -0
  861. skcomplex/models/economics/innovation/_diversity.py +104 -0
  862. skcomplex/models/economics/innovation/_household_view.py +20 -0
  863. skcomplex/models/economics/innovation/_invention.py +140 -0
  864. skcomplex/models/economics/innovation/_part.py +64 -0
  865. skcomplex/models/economics/innovation/_part_view.py +12 -0
  866. skcomplex/models/economics/innovation/_redesign.py +88 -0
  867. skcomplex/models/economics/innovation/_technology.py +203 -0
  868. skcomplex/models/economics/innovation/_technology_view.py +14 -0
  869. skcomplex/models/economics/macroeconomics/__init__.py +70 -0
  870. skcomplex/models/economics/macroeconomics/_banking.py +148 -0
  871. skcomplex/models/economics/macroeconomics/_business.py +221 -0
  872. skcomplex/models/economics/macroeconomics/_business_view.py +24 -0
  873. skcomplex/models/economics/macroeconomics/_capital.py +122 -0
  874. skcomplex/models/economics/macroeconomics/_central_bank.py +80 -0
  875. skcomplex/models/economics/macroeconomics/_central_bank_view.py +13 -0
  876. skcomplex/models/economics/macroeconomics/_circuit.py +93 -0
  877. skcomplex/models/economics/macroeconomics/_commons.py +77 -0
  878. skcomplex/models/economics/macroeconomics/_credit.py +219 -0
  879. skcomplex/models/economics/macroeconomics/_credit_market.py +83 -0
  880. skcomplex/models/economics/macroeconomics/_depositor.py +114 -0
  881. skcomplex/models/economics/macroeconomics/_depositor_view.py +19 -0
  882. skcomplex/models/economics/macroeconomics/_economy.py +42 -0
  883. skcomplex/models/economics/macroeconomics/_estate.py +88 -0
  884. skcomplex/models/economics/macroeconomics/_firm.py +184 -0
  885. skcomplex/models/economics/macroeconomics/_firm_view.py +27 -0
  886. skcomplex/models/economics/macroeconomics/_firms.py +208 -0
  887. skcomplex/models/economics/macroeconomics/_firms_element.py +67 -0
  888. skcomplex/models/economics/macroeconomics/_food_market.py +84 -0
  889. skcomplex/models/economics/macroeconomics/_growth.py +109 -0
  890. skcomplex/models/economics/macroeconomics/_households.py +52 -0
  891. skcomplex/models/economics/macroeconomics/_income.py +59 -0
  892. skcomplex/models/economics/macroeconomics/_investing_firm_view.py +21 -0
  893. skcomplex/models/economics/macroeconomics/_labour_market.py +73 -0
  894. skcomplex/models/economics/macroeconomics/_lender.py +160 -0
  895. skcomplex/models/economics/macroeconomics/_lender_view.py +18 -0
  896. skcomplex/models/economics/macroeconomics/_metaphoria.py +257 -0
  897. skcomplex/models/economics/macroeconomics/_monetary.py +140 -0
  898. skcomplex/models/economics/macroeconomics/_monetary_bank.py +57 -0
  899. skcomplex/models/economics/macroeconomics/_optimal_growth.py +173 -0
  900. skcomplex/models/economics/macroeconomics/_people_spec.py +26 -0
  901. skcomplex/models/economics/macroeconomics/_plot.py +69 -0
  902. skcomplex/models/economics/macroeconomics/_plot_view.py +15 -0
  903. skcomplex/models/economics/macroeconomics/_policy_switch.py +78 -0
  904. skcomplex/models/economics/macroeconomics/_reserve_bank.py +118 -0
  905. skcomplex/models/economics/macroeconomics/_reserve_bank_view.py +14 -0
  906. skcomplex/models/economics/macroeconomics/_settler.py +291 -0
  907. skcomplex/models/economics/macroeconomics/_settler_view.py +56 -0
  908. skcomplex/models/economics/macroeconomics/_solow_growth.py +70 -0
  909. skcomplex/models/economics/macroeconomics/_trade.py +289 -0
  910. skcomplex/models/economics/markets/__init__.py +128 -0
  911. skcomplex/models/economics/markets/_auction_ledger.py +81 -0
  912. skcomplex/models/economics/markets/_barter.py +232 -0
  913. skcomplex/models/economics/markets/_barter_networks.py +169 -0
  914. skcomplex/models/economics/markets/_barter_trader.py +136 -0
  915. skcomplex/models/economics/markets/_barter_trader_view.py +16 -0
  916. skcomplex/models/economics/markets/_bilateral_barter.py +150 -0
  917. skcomplex/models/economics/markets/_brewery.py +67 -0
  918. skcomplex/models/economics/markets/_brock_hommes.py +115 -0
  919. skcomplex/models/economics/markets/_car.py +75 -0
  920. skcomplex/models/economics/markets/_car_view.py +14 -0
  921. skcomplex/models/economics/markets/_car_wash_operation.py +141 -0
  922. skcomplex/models/economics/markets/_cobweb.py +109 -0
  923. skcomplex/models/economics/markets/_commodities.py +286 -0
  924. skcomplex/models/economics/markets/_consumer_view.py +22 -0
  925. skcomplex/models/economics/markets/_cournot_adjustment.py +65 -0
  926. skcomplex/models/economics/markets/_cournot_best_response.py +88 -0
  927. skcomplex/models/economics/markets/_customer.py +147 -0
  928. skcomplex/models/economics/markets/_customer_view.py +16 -0
  929. skcomplex/models/economics/markets/_double_auction.py +141 -0
  930. skcomplex/models/economics/markets/_duopolist.py +54 -0
  931. skcomplex/models/economics/markets/_duopolist_view.py +13 -0
  932. skcomplex/models/economics/markets/_duopoly.py +85 -0
  933. skcomplex/models/economics/markets/_echelon.py +132 -0
  934. skcomplex/models/economics/markets/_employer.py +102 -0
  935. skcomplex/models/economics/markets/_employer_view.py +20 -0
  936. skcomplex/models/economics/markets/_exchange.py +171 -0
  937. skcomplex/models/economics/markets/_exchange_interaction.py +134 -0
  938. skcomplex/models/economics/markets/_factory.py +105 -0
  939. skcomplex/models/economics/markets/_fair_food.py +205 -0
  940. skcomplex/models/economics/markets/_forager.py +64 -0
  941. skcomplex/models/economics/markets/_forager_view.py +14 -0
  942. skcomplex/models/economics/markets/_goods_trader.py +68 -0
  943. skcomplex/models/economics/markets/_goods_traders.py +139 -0
  944. skcomplex/models/economics/markets/_heuristic_pricing.py +122 -0
  945. skcomplex/models/economics/markets/_heuristic_trader.py +108 -0
  946. skcomplex/models/economics/markets/_heuristic_trader_view.py +14 -0
  947. skcomplex/models/economics/markets/_inventory.py +212 -0
  948. skcomplex/models/economics/markets/_jobseeker.py +144 -0
  949. skcomplex/models/economics/markets/_jobseeker_view.py +26 -0
  950. skcomplex/models/economics/markets/_labour.py +188 -0
  951. skcomplex/models/economics/markets/_market.py +39 -0
  952. skcomplex/models/economics/markets/_market_state_spec.py +25 -0
  953. skcomplex/models/economics/markets/_oligopoly.py +167 -0
  954. skcomplex/models/economics/markets/_patch_map_spec.py +22 -0
  955. skcomplex/models/economics/markets/_perishables.py +150 -0
  956. skcomplex/models/economics/markets/_price_point.py +95 -0
  957. skcomplex/models/economics/markets/_prices.py +151 -0
  958. skcomplex/models/economics/markets/_pricing_firm.py +48 -0
  959. skcomplex/models/economics/markets/_pricing_firm_view.py +14 -0
  960. skcomplex/models/economics/markets/_pricing_game_spec.py +81 -0
  961. skcomplex/models/economics/markets/_produce.py +94 -0
  962. skcomplex/models/economics/markets/_product.py +97 -0
  963. skcomplex/models/economics/markets/_product_view.py +13 -0
  964. skcomplex/models/economics/markets/_queues.py +101 -0
  965. skcomplex/models/economics/markets/_resident.py +119 -0
  966. skcomplex/models/economics/markets/_resident_view.py +20 -0
  967. skcomplex/models/economics/markets/_retail_demand.py +52 -0
  968. skcomplex/models/economics/markets/_retailer.py +115 -0
  969. skcomplex/models/economics/markets/_shopper.py +115 -0
  970. skcomplex/models/economics/markets/_shopper_view.py +15 -0
  971. skcomplex/models/economics/markets/_shops.py +199 -0
  972. skcomplex/models/economics/markets/_stall.py +74 -0
  973. skcomplex/models/economics/markets/_stall_view.py +14 -0
  974. skcomplex/models/economics/markets/_store.py +171 -0
  975. skcomplex/models/economics/markets/_store_view.py +27 -0
  976. skcomplex/models/economics/markets/_sugar_patch.py +61 -0
  977. skcomplex/models/economics/markets/_sugar_patch_view.py +14 -0
  978. skcomplex/models/economics/markets/_sugarscape.py +250 -0
  979. skcomplex/models/economics/markets/_supply_chains.py +217 -0
  980. skcomplex/models/economics/markets/_supply_link.py +74 -0
  981. skcomplex/models/economics/markets/_till.py +79 -0
  982. skcomplex/models/economics/markets/_till_view.py +15 -0
  983. skcomplex/models/economics/markets/_washer.py +78 -0
  984. skcomplex/models/economics/markets/_zero_intelligence_buyer.py +99 -0
  985. skcomplex/models/economics/markets/_zero_intelligence_buyer_view.py +20 -0
  986. skcomplex/models/economics/markets/_zero_intelligence_seller.py +100 -0
  987. skcomplex/models/economics/markets/_zero_intelligence_seller_view.py +20 -0
  988. skcomplex/models/economics/resources/__init__.py +50 -0
  989. skcomplex/models/economics/resources/_bid_rent.py +104 -0
  990. skcomplex/models/economics/resources/_commons.py +218 -0
  991. skcomplex/models/economics/resources/_cow.py +69 -0
  992. skcomplex/models/economics/resources/_cow_view.py +13 -0
  993. skcomplex/models/economics/resources/_extraction.py +230 -0
  994. skcomplex/models/economics/resources/_farmer.py +93 -0
  995. skcomplex/models/economics/resources/_farmer_view.py +12 -0
  996. skcomplex/models/economics/resources/_fisheries.py +384 -0
  997. skcomplex/models/economics/resources/_fishery.py +91 -0
  998. skcomplex/models/economics/resources/_food.py +370 -0
  999. skcomplex/models/economics/resources/_grazing.py +148 -0
  1000. skcomplex/models/economics/resources/_harvest.py +69 -0
  1001. skcomplex/models/economics/resources/_harvesting.py +51 -0
  1002. skcomplex/models/economics/resources/_herder.py +78 -0
  1003. skcomplex/models/economics/resources/_herder_view.py +19 -0
  1004. skcomplex/models/economics/resources/_land_cell.py +39 -0
  1005. skcomplex/models/economics/resources/_land_use.py +73 -0
  1006. skcomplex/models/economics/resources/_oil_economy.py +85 -0
  1007. skcomplex/models/economics/resources/_optimal_harvesting.py +180 -0
  1008. skcomplex/models/economics/resources/_pasture.py +98 -0
  1009. skcomplex/models/economics/resources/_pasture_view.py +15 -0
  1010. skcomplex/models/economics/resources/_plantations.py +359 -0
  1011. skcomplex/models/economics/resources/_quota_regulator.py +84 -0
  1012. skcomplex/models/economics/resources/_stock.py +67 -0
  1013. skcomplex/models/engineering/__init__.py +1 -0
  1014. skcomplex/models/engineering/circuits/__init__.py +23 -0
  1015. skcomplex/models/engineering/circuits/_chua_circuit.py +48 -0
  1016. skcomplex/models/engineering/circuits/_circuit.py +47 -0
  1017. skcomplex/models/engineering/circuits/_circuits.py +387 -0
  1018. skcomplex/models/engineering/circuits/_harvesters.py +150 -0
  1019. skcomplex/models/engineering/circuits/_kicked_circuit.py +43 -0
  1020. skcomplex/models/engineering/circuits/_memristor_circuit.py +48 -0
  1021. skcomplex/models/engineering/circuits/_mixed_mode_chua_circuit.py +54 -0
  1022. skcomplex/models/engineering/circuits/_multiscroll_chua_circuit.py +58 -0
  1023. skcomplex/models/engineering/circuits/_tunnel_diode_circuit.py +45 -0
  1024. skcomplex/models/engineering/common/__init__.py +6 -0
  1025. skcomplex/models/engineering/common/mechanics/__init__.py +7 -0
  1026. skcomplex/models/engineering/common/mechanics/_spring_damper.py +121 -0
  1027. skcomplex/models/engineering/control/__init__.py +23 -0
  1028. skcomplex/models/engineering/control/_cart_pendulum.py +119 -0
  1029. skcomplex/models/engineering/control/_control.py +266 -0
  1030. skcomplex/models/engineering/control/_controlled_process.py +72 -0
  1031. skcomplex/models/engineering/control/_driven_oscillator.py +79 -0
  1032. skcomplex/models/engineering/control/_integrator.py +39 -0
  1033. skcomplex/models/engineering/control/_pid.py +106 -0
  1034. skcomplex/models/engineering/control/_regulation.py +170 -0
  1035. skcomplex/models/engineering/control/_room.py +51 -0
  1036. skcomplex/models/engineering/control/_satellite.py +56 -0
  1037. skcomplex/models/engineering/control/_state_feedback.py +82 -0
  1038. skcomplex/models/engineering/control/_swinging_pendulum.py +60 -0
  1039. skcomplex/models/engineering/power_systems/__init__.py +11 -0
  1040. skcomplex/models/engineering/power_systems/_electromechanics.py +224 -0
  1041. skcomplex/models/engineering/power_systems/_faraday_disk.py +93 -0
  1042. skcomplex/models/engineering/power_systems/_grid_node.py +39 -0
  1043. skcomplex/models/engineering/power_systems/_grids.py +89 -0
  1044. skcomplex/models/engineering/power_systems/_rail_segment.py +80 -0
  1045. skcomplex/models/engineering/power_systems/_regenerative_car.py +55 -0
  1046. skcomplex/models/engineering/power_systems/_transmission_line.py +48 -0
  1047. skcomplex/models/engineering/processes/__init__.py +13 -0
  1048. skcomplex/models/engineering/processes/_irrigation_scheme.py +112 -0
  1049. skcomplex/models/engineering/processes/_processes.py +115 -0
  1050. skcomplex/models/engineering/processes/_relief_pipeline.py +79 -0
  1051. skcomplex/models/engineering/processes/_rice_mill.py +112 -0
  1052. skcomplex/models/engineering/processes/_stage.py +34 -0
  1053. skcomplex/models/engineering/processes/_systems.py +316 -0
  1054. skcomplex/models/engineering/processes/_tub.py +42 -0
  1055. skcomplex/models/engineering/processes/_waste_system.py +101 -0
  1056. skcomplex/models/engineering/robotics/__init__.py +12 -0
  1057. skcomplex/models/engineering/robotics/_light_sensitive_robot.py +125 -0
  1058. skcomplex/models/engineering/robotics/_robots.py +177 -0
  1059. skcomplex/models/engineering/robotics/_swarm_robot.py +211 -0
  1060. skcomplex/models/engineering/robotics/_swarm_robot_view.py +23 -0
  1061. skcomplex/models/engineering/traffic/__init__.py +43 -0
  1062. skcomplex/models/engineering/traffic/_arrival.py +117 -0
  1063. skcomplex/models/engineering/traffic/_cab.py +170 -0
  1064. skcomplex/models/engineering/traffic/_cab_view.py +21 -0
  1065. skcomplex/models/engineering/traffic/_car.py +31 -0
  1066. skcomplex/models/engineering/traffic/_car_following.py +245 -0
  1067. skcomplex/models/engineering/traffic/_careless_braking.py +87 -0
  1068. skcomplex/models/engineering/traffic/_continuum.py +429 -0
  1069. skcomplex/models/engineering/traffic/_delayed_following.py +65 -0
  1070. skcomplex/models/engineering/traffic/_driver.py +140 -0
  1071. skcomplex/models/engineering/traffic/_driver_view.py +18 -0
  1072. skcomplex/models/engineering/traffic/_drivers.py +133 -0
  1073. skcomplex/models/engineering/traffic/_gas_kinetic_traffic.py +96 -0
  1074. skcomplex/models/engineering/traffic/_intelligent_driver.py +90 -0
  1075. skcomplex/models/engineering/traffic/_kerner_konhauser.py +42 -0
  1076. skcomplex/models/engineering/traffic/_langevin.py +170 -0
  1077. skcomplex/models/engineering/traffic/_langevin_driving.py +95 -0
  1078. skcomplex/models/engineering/traffic/_lead_car.py +40 -0
  1079. skcomplex/models/engineering/traffic/_lighthill_whitham_richards.py +30 -0
  1080. skcomplex/models/engineering/traffic/_motorist.py +118 -0
  1081. skcomplex/models/engineering/traffic/_motorist_view.py +18 -0
  1082. skcomplex/models/engineering/traffic/_optimal_velocity.py +72 -0
  1083. skcomplex/models/engineering/traffic/_payne.py +38 -0
  1084. skcomplex/models/engineering/traffic/_rider.py +72 -0
  1085. skcomplex/models/engineering/traffic/_rider_view.py +16 -0
  1086. skcomplex/models/engineering/traffic/_ridesharing.py +179 -0
  1087. skcomplex/models/engineering/traffic/_traffic.py +143 -0
  1088. skcomplex/models/engineering/traffic/_traffic_moments.py +57 -0
  1089. skcomplex/models/mathematics/__init__.py +1 -0
  1090. skcomplex/models/mathematics/common/__init__.py +3 -0
  1091. skcomplex/models/mathematics/common/flows/__init__.py +7 -0
  1092. skcomplex/models/mathematics/common/flows/_lorenz.py +90 -0
  1093. skcomplex/models/mathematics/dynamical_systems/__init__.py +90 -0
  1094. skcomplex/models/mathematics/dynamical_systems/_baker_map.py +59 -0
  1095. skcomplex/models/mathematics/dynamical_systems/_blow_up.py +64 -0
  1096. skcomplex/models/mathematics/dynamical_systems/_cat_map.py +44 -0
  1097. skcomplex/models/mathematics/dynamical_systems/_chaotic_ensembles.py +186 -0
  1098. skcomplex/models/mathematics/dynamical_systems/_circle_map.py +49 -0
  1099. skcomplex/models/mathematics/dynamical_systems/_cubic_walk.py +72 -0
  1100. skcomplex/models/mathematics/dynamical_systems/_cusp.py +64 -0
  1101. skcomplex/models/mathematics/dynamical_systems/_doubling_map.py +65 -0
  1102. skcomplex/models/mathematics/dynamical_systems/_driven_flows.py +158 -0
  1103. skcomplex/models/mathematics/dynamical_systems/_flows.py +179 -0
  1104. skcomplex/models/mathematics/dynamical_systems/_henon_map.py +54 -0
  1105. skcomplex/models/mathematics/dynamical_systems/_hopf.py +77 -0
  1106. skcomplex/models/mathematics/dynamical_systems/_intermittency_map.py +44 -0
  1107. skcomplex/models/mathematics/dynamical_systems/_jerk.py +72 -0
  1108. skcomplex/models/mathematics/dynamical_systems/_koopman.py +118 -0
  1109. skcomplex/models/mathematics/dynamical_systems/_logistic_map.py +44 -0
  1110. skcomplex/models/mathematics/dynamical_systems/_maps.py +465 -0
  1111. skcomplex/models/mathematics/dynamical_systems/_newton_map.py +44 -0
  1112. skcomplex/models/mathematics/dynamical_systems/_normal_forms.py +154 -0
  1113. skcomplex/models/mathematics/dynamical_systems/_rossler.py +83 -0
  1114. skcomplex/models/mathematics/dynamical_systems/_saddle_node.py +59 -0
  1115. skcomplex/models/mathematics/dynamical_systems/_skew_tent_map.py +63 -0
  1116. skcomplex/models/mathematics/dynamical_systems/_standard_map.py +52 -0
  1117. skcomplex/models/mathematics/dynamical_systems/_subcritical_forms.py +160 -0
  1118. skcomplex/models/mathematics/dynamical_systems/_takens_bogdanov.py +74 -0
  1119. skcomplex/models/mathematics/dynamical_systems/_tent_map.py +44 -0
  1120. skcomplex/models/mathematics/dynamical_systems/_towel_map.py +59 -0
  1121. skcomplex/models/mathematics/fractals/__init__.py +61 -0
  1122. skcomplex/models/mathematics/fractals/_affine_spec.py +100 -0
  1123. skcomplex/models/mathematics/fractals/_cantor_element.py +92 -0
  1124. skcomplex/models/mathematics/fractals/_chaos_game.py +140 -0
  1125. skcomplex/models/mathematics/fractals/_geometry_spec.py +84 -0
  1126. skcomplex/models/mathematics/fractals/_geometry_visual.py +190 -0
  1127. skcomplex/models/mathematics/fractals/_group_spec.py +24 -0
  1128. skcomplex/models/mathematics/fractals/_koch_element.py +43 -0
  1129. skcomplex/models/mathematics/fractals/_module_spec.py +47 -0
  1130. skcomplex/models/mathematics/fractals/_patch_element.py +89 -0
  1131. skcomplex/models/mathematics/fractals/_patch_kernel.py +200 -0
  1132. skcomplex/models/mathematics/fractals/_patch_structure_spec.py +108 -0
  1133. skcomplex/models/mathematics/fractals/_production_law.py +105 -0
  1134. skcomplex/models/mathematics/fractals/_prototile_spec.py +53 -0
  1135. skcomplex/models/mathematics/fractals/_quadratic.py +191 -0
  1136. skcomplex/models/mathematics/fractals/_random_affine_map.py +100 -0
  1137. skcomplex/models/mathematics/fractals/_rewriting_compiler.py +300 -0
  1138. skcomplex/models/mathematics/fractals/_rewriting_error.py +10 -0
  1139. skcomplex/models/mathematics/fractals/_rewriting_loops.py +180 -0
  1140. skcomplex/models/mathematics/fractals/_rewriting_problem_spec.py +30 -0
  1141. skcomplex/models/mathematics/fractals/_rewriting_solver.py +125 -0
  1142. skcomplex/models/mathematics/fractals/_sierpinski_element.py +110 -0
  1143. skcomplex/models/mathematics/fractals/_substitution.py +130 -0
  1144. skcomplex/models/mathematics/fractals/_substitution_law.py +76 -0
  1145. skcomplex/models/mathematics/fractals/_successor_spec.py +23 -0
  1146. skcomplex/models/mathematics/fractals/_word_element.py +94 -0
  1147. skcomplex/models/mathematics/fractals/_word_kernel.py +526 -0
  1148. skcomplex/models/mathematics/fractals/_word_structure_spec.py +110 -0
  1149. skcomplex/models/mathematics/fractals/_words.py +38 -0
  1150. skcomplex/models/mathematics/fractals/types.py +12 -0
  1151. skcomplex/models/mathematics/fractional_dynamics/__init__.py +29 -0
  1152. skcomplex/models/mathematics/fractional_dynamics/_fractional.py +338 -0
  1153. skcomplex/models/mathematics/fractional_dynamics/_oscillator.py +71 -0
  1154. skcomplex/models/mathematics/fractional_dynamics/_relaxation.py +59 -0
  1155. skcomplex/models/mathematics/fractional_dynamics/_van_der_pol.py +66 -0
  1156. skcomplex/models/mathematics/networks/__init__.py +61 -0
  1157. skcomplex/models/mathematics/networks/_copying_vertex.py +50 -0
  1158. skcomplex/models/mathematics/networks/_ensemble_node.py +48 -0
  1159. skcomplex/models/mathematics/networks/_ensembles.py +195 -0
  1160. skcomplex/models/mathematics/networks/_failing.py +58 -0
  1161. skcomplex/models/mathematics/networks/_giant_component.py +52 -0
  1162. skcomplex/models/mathematics/networks/_growth.py +223 -0
  1163. skcomplex/models/mathematics/networks/_hypergraphs.py +131 -0
  1164. skcomplex/models/mathematics/networks/_link.py +21 -0
  1165. skcomplex/models/mathematics/networks/_network_measures.py +59 -0
  1166. skcomplex/models/mathematics/networks/_network_node.py +86 -0
  1167. skcomplex/models/mathematics/networks/_network_walker.py +49 -0
  1168. skcomplex/models/mathematics/networks/_network_walker_view.py +12 -0
  1169. skcomplex/models/mathematics/networks/_node_content.py +47 -0
  1170. skcomplex/models/mathematics/networks/_node_rank.py +57 -0
  1171. skcomplex/models/mathematics/networks/_processes.py +148 -0
  1172. skcomplex/models/mathematics/networks/_regulated_link.py +47 -0
  1173. skcomplex/models/mathematics/networks/_regulated_node.py +43 -0
  1174. skcomplex/models/mathematics/networks/_simplex.py +46 -0
  1175. skcomplex/models/mathematics/networks/_simplex_ageing.py +46 -0
  1176. skcomplex/models/mathematics/networks/_size_biased_move.py +44 -0
  1177. skcomplex/models/mathematics/networks/_structure.py +170 -0
  1178. skcomplex/models/mathematics/networks/_triad_vertex.py +64 -0
  1179. skcomplex/models/mathematics/networks/_triadic.py +114 -0
  1180. skcomplex/models/mathematics/networks/_triadic_regulation.py +65 -0
  1181. skcomplex/models/mathematics/networks/_vertex.py +52 -0
  1182. skcomplex/models/mathematics/networks/_walker_density.py +51 -0
  1183. skcomplex/models/mathematics/stochastic_processes/__init__.py +62 -0
  1184. skcomplex/models/mathematics/stochastic_processes/_ageing_walker.py +68 -0
  1185. skcomplex/models/mathematics/stochastic_processes/_ageing_walker_view.py +15 -0
  1186. skcomplex/models/mathematics/stochastic_processes/_bernoulli_trial.py +61 -0
  1187. skcomplex/models/mathematics/stochastic_processes/_bernoulli_trial_view.py +14 -0
  1188. skcomplex/models/mathematics/stochastic_processes/_branching.py +103 -0
  1189. skcomplex/models/mathematics/stochastic_processes/_counting.py +88 -0
  1190. skcomplex/models/mathematics/stochastic_processes/_fragment.py +91 -0
  1191. skcomplex/models/mathematics/stochastic_processes/_fragment_view.py +13 -0
  1192. skcomplex/models/mathematics/stochastic_processes/_hidden_markov_source.py +46 -0
  1193. skcomplex/models/mathematics/stochastic_processes/_individual_view.py +13 -0
  1194. skcomplex/models/mathematics/stochastic_processes/_intermittency.py +115 -0
  1195. skcomplex/models/mathematics/stochastic_processes/_markov_source.py +41 -0
  1196. skcomplex/models/mathematics/stochastic_processes/_memory_walker.py +57 -0
  1197. skcomplex/models/mathematics/stochastic_processes/_persistent_walker.py +52 -0
  1198. skcomplex/models/mathematics/stochastic_processes/_poisson_counter.py +47 -0
  1199. skcomplex/models/mathematics/stochastic_processes/_queues.py +117 -0
  1200. skcomplex/models/mathematics/stochastic_processes/_random_walker.py +52 -0
  1201. skcomplex/models/mathematics/stochastic_processes/_reducing.py +104 -0
  1202. skcomplex/models/mathematics/stochastic_processes/_reducing_ball.py +63 -0
  1203. skcomplex/models/mathematics/stochastic_processes/_reducing_ball_view.py +14 -0
  1204. skcomplex/models/mathematics/stochastic_processes/_reducing_jump.py +44 -0
  1205. skcomplex/models/mathematics/stochastic_processes/_sources.py +90 -0
  1206. skcomplex/models/mathematics/stochastic_processes/_urns.py +112 -0
  1207. skcomplex/models/mathematics/stochastic_processes/_walks.py +280 -0
  1208. skcomplex/models/mathematics/stochastic_processes/_weakening_particle.py +57 -0
  1209. skcomplex/models/mathematics/stochastic_processes/types.py +8 -0
  1210. skcomplex/models/physics/__init__.py +1 -0
  1211. skcomplex/models/physics/active_matter/__init__.py +95 -0
  1212. skcomplex/models/physics/active_matter/_active_particle.py +88 -0
  1213. skcomplex/models/physics/active_matter/_alignment.py +192 -0
  1214. skcomplex/models/physics/active_matter/_angular_alignment.py +98 -0
  1215. skcomplex/models/physics/active_matter/_angular_diffusion.py +67 -0
  1216. skcomplex/models/physics/active_matter/_binary_collisions.py +126 -0
  1217. skcomplex/models/physics/active_matter/_chemotaxis.py +173 -0
  1218. skcomplex/models/physics/active_matter/_cohesive_particle.py +132 -0
  1219. skcomplex/models/physics/active_matter/_collective.py +327 -0
  1220. skcomplex/models/physics/active_matter/_collisions.py +127 -0
  1221. skcomplex/models/physics/active_matter/_contractile_gel_site.py +81 -0
  1222. skcomplex/models/physics/active_matter/_cucker_smale_alignment.py +89 -0
  1223. skcomplex/models/physics/active_matter/_depot_particle.py +103 -0
  1224. skcomplex/models/physics/active_matter/_flocker.py +46 -0
  1225. skcomplex/models/physics/active_matter/_flocker_view.py +20 -0
  1226. skcomplex/models/physics/active_matter/_flocks.py +258 -0
  1227. skcomplex/models/physics/active_matter/_gels.py +141 -0
  1228. skcomplex/models/physics/active_matter/_heading_alignment.py +73 -0
  1229. skcomplex/models/physics/active_matter/_kinetic_flocks.py +111 -0
  1230. skcomplex/models/physics/active_matter/_landau_de_gennes_energy.py +107 -0
  1231. skcomplex/models/physics/active_matter/_model_b.py +170 -0
  1232. skcomplex/models/physics/active_matter/_nematic_density_site.py +78 -0
  1233. skcomplex/models/physics/active_matter/_nematic_gel_site.py +115 -0
  1234. skcomplex/models/physics/active_matter/_nematic_particle.py +61 -0
  1235. skcomplex/models/physics/active_matter/_nematics.py +323 -0
  1236. skcomplex/models/physics/active_matter/_nonreciprocal.py +214 -0
  1237. skcomplex/models/physics/active_matter/_ornstein_uhlenbeck_particle.py +87 -0
  1238. skcomplex/models/physics/active_matter/_particles.py +323 -0
  1239. skcomplex/models/physics/active_matter/_phoretic_attraction.py +80 -0
  1240. skcomplex/models/physics/active_matter/_polar_fluid.py +119 -0
  1241. skcomplex/models/physics/active_matter/_polar_gel_site.py +120 -0
  1242. skcomplex/models/physics/active_matter/_propulsion_step.py +64 -0
  1243. skcomplex/models/physics/active_matter/_self_propulsion.py +73 -0
  1244. skcomplex/models/physics/active_matter/_tumbler.py +100 -0
  1245. skcomplex/models/physics/active_matter/_tumbler_view.py +23 -0
  1246. skcomplex/models/physics/active_matter/_vicsek_particle.py +61 -0
  1247. skcomplex/models/physics/celestial_mechanics/__init__.py +19 -0
  1248. skcomplex/models/physics/celestial_mechanics/_dipoles.py +160 -0
  1249. skcomplex/models/physics/celestial_mechanics/_kepler_body.py +76 -0
  1250. skcomplex/models/physics/celestial_mechanics/_orbits.py +332 -0
  1251. skcomplex/models/physics/celestial_mechanics/_rotating_frame_body.py +72 -0
  1252. skcomplex/models/physics/celestial_mechanics/_sitnikov_body.py +54 -0
  1253. skcomplex/models/physics/celestial_mechanics/types.py +6 -0
  1254. skcomplex/models/physics/climate/__init__.py +60 -0
  1255. skcomplex/models/physics/climate/_carbon_cycle.py +169 -0
  1256. skcomplex/models/physics/climate/_climate_anomaly.py +55 -0
  1257. skcomplex/models/physics/climate/_daisyworld.py +158 -0
  1258. skcomplex/models/physics/climate/_delayed_oscillator.py +68 -0
  1259. skcomplex/models/physics/climate/_early_warning.py +102 -0
  1260. skcomplex/models/physics/climate/_energy_balance.py +207 -0
  1261. skcomplex/models/physics/climate/_geodynamo.py +86 -0
  1262. skcomplex/models/physics/climate/_ice_ages.py +179 -0
  1263. skcomplex/models/physics/climate/_ice_albedo_climate.py +100 -0
  1264. skcomplex/models/physics/climate/_latitude_band.py +156 -0
  1265. skcomplex/models/physics/climate/_lorenz84.py +91 -0
  1266. skcomplex/models/physics/climate/_lorenz96.py +67 -0
  1267. skcomplex/models/physics/climate/_low_order.py +162 -0
  1268. skcomplex/models/physics/climate/_net_energy.py +210 -0
  1269. skcomplex/models/physics/climate/_ramped_fold.py +92 -0
  1270. skcomplex/models/physics/climate/_saltzman_maasch.py +123 -0
  1271. skcomplex/models/physics/climate/_soil.py +116 -0
  1272. skcomplex/models/physics/climate/_stochastic_energy_balance.py +124 -0
  1273. skcomplex/models/physics/climate/_tipping.py +141 -0
  1274. skcomplex/models/physics/climate/_tipping_types.py +159 -0
  1275. skcomplex/models/physics/climate/_van_der_pol_ice_ages.py +101 -0
  1276. skcomplex/models/physics/climate/_variability.py +103 -0
  1277. skcomplex/models/physics/common/__init__.py +6 -0
  1278. skcomplex/models/physics/common/fields/__init__.py +14 -0
  1279. skcomplex/models/physics/common/fields/_landau_energy.py +76 -0
  1280. skcomplex/models/physics/common/fields/_phase_field.py +43 -0
  1281. skcomplex/models/physics/common/fields/_swift_hohenberg_energy.py +74 -0
  1282. skcomplex/models/physics/common/fields/_transports.py +119 -0
  1283. skcomplex/models/physics/common/mechanics/__init__.py +5 -0
  1284. skcomplex/models/physics/common/mechanics/_reflection.py +139 -0
  1285. skcomplex/models/physics/common/oscillators/__init__.py +13 -0
  1286. skcomplex/models/physics/common/oscillators/_kuramoto_coupling.py +140 -0
  1287. skcomplex/models/physics/common/oscillators/_phase_oscillator.py +68 -0
  1288. skcomplex/models/physics/common/oscillators/_sited_oscillator.py +55 -0
  1289. skcomplex/models/physics/common/oscillators/_stuart_landau.py +106 -0
  1290. skcomplex/models/physics/common/particles/__init__.py +28 -0
  1291. skcomplex/models/physics/common/particles/_constant_force.py +65 -0
  1292. skcomplex/models/physics/common/particles/_damping.py +72 -0
  1293. skcomplex/models/physics/common/particles/_gravity.py +74 -0
  1294. skcomplex/models/physics/common/particles/_harmonic_potential.py +77 -0
  1295. skcomplex/models/physics/common/particles/_lammps.py +47 -0
  1296. skcomplex/models/physics/common/particles/_langevin_thermostat.py +103 -0
  1297. skcomplex/models/physics/common/particles/_lennard_jones.py +87 -0
  1298. skcomplex/models/physics/common/particles/_mass_point.py +57 -0
  1299. skcomplex/models/physics/common/particles/_potential_energy.py +56 -0
  1300. skcomplex/models/physics/common/particles/_soft_sphere.py +82 -0
  1301. skcomplex/models/physics/common/particles/_spring.py +78 -0
  1302. skcomplex/models/physics/common/particles/_utils.py +25 -0
  1303. skcomplex/models/physics/common/quantum/__init__.py +18 -0
  1304. skcomplex/models/physics/common/quantum/_mode.py +46 -0
  1305. skcomplex/models/physics/common/quantum/_quantum.py +127 -0
  1306. skcomplex/models/physics/common/quantum/_qubit.py +61 -0
  1307. skcomplex/models/physics/common/quantum/_site.py +49 -0
  1308. skcomplex/models/physics/common/quantum/_spin.py +92 -0
  1309. skcomplex/models/physics/common/spins/__init__.py +15 -0
  1310. skcomplex/models/physics/common/spins/_ising_sampling.py +75 -0
  1311. skcomplex/models/physics/common/spins/_potts_sampling.py +73 -0
  1312. skcomplex/models/physics/common/spins/_spin_sampling.py +100 -0
  1313. skcomplex/models/physics/common/spins/_thermal_sampling.py +105 -0
  1314. skcomplex/models/physics/common/spins/_xy_sampling.py +67 -0
  1315. skcomplex/models/physics/cosmology/__init__.py +8 -0
  1316. skcomplex/models/physics/cosmology/_expansion.py +148 -0
  1317. skcomplex/models/physics/criticality/__init__.py +29 -0
  1318. skcomplex/models/physics/criticality/_absorbing.py +210 -0
  1319. skcomplex/models/physics/criticality/_avalanche.py +69 -0
  1320. skcomplex/models/physics/criticality/_crackling_noise.py +129 -0
  1321. skcomplex/models/physics/criticality/_criticality.py +235 -0
  1322. skcomplex/models/physics/criticality/_evolutionary_learning.py +231 -0
  1323. skcomplex/models/physics/criticality/_fire.py +70 -0
  1324. skcomplex/models/physics/criticality/_forest.py +55 -0
  1325. skcomplex/models/physics/criticality/_learning.py +175 -0
  1326. skcomplex/models/physics/criticality/_sandpile_cell.py +47 -0
  1327. skcomplex/models/physics/fluids/__init__.py +49 -0
  1328. skcomplex/models/physics/fluids/_bhatnagar_gross_krook.py +54 -0
  1329. skcomplex/models/physics/fluids/_boussinesq.py +62 -0
  1330. skcomplex/models/physics/fluids/_burgers.py +39 -0
  1331. skcomplex/models/physics/fluids/_carleman_gas.py +61 -0
  1332. skcomplex/models/physics/fluids/_flows.py +436 -0
  1333. skcomplex/models/physics/fluids/_kinetic_equations.py +327 -0
  1334. skcomplex/models/physics/fluids/_kinetics.py +147 -0
  1335. skcomplex/models/physics/fluids/_kuramoto_sivashinsky.py +41 -0
  1336. skcomplex/models/physics/fluids/_lattice_gases.py +217 -0
  1337. skcomplex/models/physics/fluids/_marangoni.py +136 -0
  1338. skcomplex/models/physics/fluids/_shallow_water.py +55 -0
  1339. skcomplex/models/physics/fluids/_vorticity.py +56 -0
  1340. skcomplex/models/physics/fluids/_wave_number.py +50 -0
  1341. skcomplex/models/physics/heat/__init__.py +13 -0
  1342. skcomplex/models/physics/heat/_cooling.py +96 -0
  1343. skcomplex/models/physics/heat/_heat.py +182 -0
  1344. skcomplex/models/physics/mechanics/__init__.py +93 -0
  1345. skcomplex/models/physics/mechanics/_ballistic_pendulum.py +80 -0
  1346. skcomplex/models/physics/mechanics/_bouncing_ball.py +51 -0
  1347. skcomplex/models/physics/mechanics/_cart_pendulum.py +92 -0
  1348. skcomplex/models/physics/mechanics/_cart_pendulum_interaction.py +57 -0
  1349. skcomplex/models/physics/mechanics/_clock_pendulum.py +94 -0
  1350. skcomplex/models/physics/mechanics/_clock_pendulum_interaction.py +60 -0
  1351. skcomplex/models/physics/mechanics/_disc_billiard.py +90 -0
  1352. skcomplex/models/physics/mechanics/_double_pendulum.py +95 -0
  1353. skcomplex/models/physics/mechanics/_double_pendulum_interaction.py +53 -0
  1354. skcomplex/models/physics/mechanics/_elastic_collision.py +78 -0
  1355. skcomplex/models/physics/mechanics/_gyroscope.py +105 -0
  1356. skcomplex/models/physics/mechanics/_gyroscope_interaction.py +57 -0
  1357. skcomplex/models/physics/mechanics/_hanging_ball.py +65 -0
  1358. skcomplex/models/physics/mechanics/_magnet.py +70 -0
  1359. skcomplex/models/physics/mechanics/_mechanics.py +426 -0
  1360. skcomplex/models/physics/mechanics/_parametric_pendulum.py +75 -0
  1361. skcomplex/models/physics/mechanics/_parametric_pendulum_interaction.py +56 -0
  1362. skcomplex/models/physics/mechanics/_pendulum.py +73 -0
  1363. skcomplex/models/physics/mechanics/_pendulum_interaction.py +52 -0
  1364. skcomplex/models/physics/mechanics/_pendulum_spring.py +68 -0
  1365. skcomplex/models/physics/mechanics/_pendulums.py +547 -0
  1366. skcomplex/models/physics/mechanics/_rotating_ball.py +66 -0
  1367. skcomplex/models/physics/mechanics/_rotating_swing.py +100 -0
  1368. skcomplex/models/physics/mechanics/_rotating_swing_interaction.py +70 -0
  1369. skcomplex/models/physics/mechanics/_rotations.py +244 -0
  1370. skcomplex/models/physics/mechanics/_springs.py +176 -0
  1371. skcomplex/models/physics/mechanics/_support_spring.py +65 -0
  1372. skcomplex/models/physics/mechanics/_wells.py +102 -0
  1373. skcomplex/models/physics/nonlinear_oscillators/__init__.py +26 -0
  1374. skcomplex/models/physics/nonlinear_oscillators/_adler_phase.py +73 -0
  1375. skcomplex/models/physics/nonlinear_oscillators/_billiards.py +137 -0
  1376. skcomplex/models/physics/nonlinear_oscillators/_duffing.py +78 -0
  1377. skcomplex/models/physics/nonlinear_oscillators/_henon_heiles.py +57 -0
  1378. skcomplex/models/physics/nonlinear_oscillators/_mushroom_billiard.py +96 -0
  1379. skcomplex/models/physics/nonlinear_oscillators/_oscillators.py +313 -0
  1380. skcomplex/models/physics/nonlinear_oscillators/_sinai_billiard.py +101 -0
  1381. skcomplex/models/physics/nonlinear_oscillators/_van_der_pol.py +92 -0
  1382. skcomplex/models/physics/oceanography/__init__.py +12 -0
  1383. skcomplex/models/physics/oceanography/_gyres.py +145 -0
  1384. skcomplex/models/physics/oceanography/_quasi_geostrophic_site.py +66 -0
  1385. skcomplex/models/physics/oceanography/_thermohaline.py +133 -0
  1386. skcomplex/models/physics/pattern_formation/__init__.py +18 -0
  1387. skcomplex/models/physics/pattern_formation/_conserved.py +168 -0
  1388. skcomplex/models/physics/pattern_formation/_ginzburg_landau.py +83 -0
  1389. skcomplex/models/physics/pattern_formation/_ordering.py +183 -0
  1390. skcomplex/models/physics/pattern_formation/_pattern_field.py +37 -0
  1391. skcomplex/models/physics/pattern_formation/_patterns.py +135 -0
  1392. skcomplex/models/physics/seismology/__init__.py +11 -0
  1393. skcomplex/models/physics/seismology/_faults.py +118 -0
  1394. skcomplex/models/physics/seismology/_spring_blocks.py +175 -0
  1395. skcomplex/models/physics/soft_matter/__init__.py +76 -0
  1396. skcomplex/models/physics/soft_matter/_anomalous.py +331 -0
  1397. skcomplex/models/physics/soft_matter/_brownian.py +137 -0
  1398. skcomplex/models/physics/soft_matter/_brownian_particle.py +58 -0
  1399. skcomplex/models/physics/soft_matter/_colored_noise.py +137 -0
  1400. skcomplex/models/physics/soft_matter/_continuous_time_walker.py +62 -0
  1401. skcomplex/models/physics/soft_matter/_diffusion.py +418 -0
  1402. skcomplex/models/physics/soft_matter/_double_well.py +57 -0
  1403. skcomplex/models/physics/soft_matter/_flashing_sawtooth.py +82 -0
  1404. skcomplex/models/physics/soft_matter/_fractional_walker.py +54 -0
  1405. skcomplex/models/physics/soft_matter/_friction.py +214 -0
  1406. skcomplex/models/physics/soft_matter/_levy_flier.py +54 -0
  1407. skcomplex/models/physics/soft_matter/_levy_walker.py +67 -0
  1408. skcomplex/models/physics/soft_matter/_modulated_particle.py +76 -0
  1409. skcomplex/models/physics/soft_matter/_optical_trap.py +93 -0
  1410. skcomplex/models/physics/soft_matter/_ratchets.py +163 -0
  1411. skcomplex/models/physics/soft_matter/_scaled_walker.py +57 -0
  1412. skcomplex/models/physics/soft_matter/_speckle_field.py +81 -0
  1413. skcomplex/models/physics/soft_matter/_thermal_noise.py +52 -0
  1414. skcomplex/models/physics/soft_matter/_tilted_washboard.py +70 -0
  1415. skcomplex/models/physics/soft_matter/_transient_walker.py +61 -0
  1416. skcomplex/models/physics/soft_matter/_traps.py +166 -0
  1417. skcomplex/models/physics/soft_matter/_wall_particle.py +72 -0
  1418. skcomplex/models/physics/statistical_mechanics/__init__.py +114 -0
  1419. skcomplex/models/physics/statistical_mechanics/_absorbing_processes.py +156 -0
  1420. skcomplex/models/physics/statistical_mechanics/_boltzmann_average.py +44 -0
  1421. skcomplex/models/physics/statistical_mechanics/_boltzmann_sum.py +83 -0
  1422. skcomplex/models/physics/statistical_mechanics/_bond_sampling.py +46 -0
  1423. skcomplex/models/physics/statistical_mechanics/_bond_spin.py +76 -0
  1424. skcomplex/models/physics/statistical_mechanics/_contact_site.py +85 -0
  1425. skcomplex/models/physics/statistical_mechanics/_dephasing.py +59 -0
  1426. skcomplex/models/physics/statistical_mechanics/_disk.py +36 -0
  1427. skcomplex/models/physics/statistical_mechanics/_driven_particles.py +250 -0
  1428. skcomplex/models/physics/statistical_mechanics/_energy_level.py +30 -0
  1429. skcomplex/models/physics/statistical_mechanics/_exclusion_hops.py +76 -0
  1430. skcomplex/models/physics/statistical_mechanics/_exclusion_site.py +61 -0
  1431. skcomplex/models/physics/statistical_mechanics/_fully_connected_spins.py +232 -0
  1432. skcomplex/models/physics/statistical_mechanics/_gases.py +156 -0
  1433. skcomplex/models/physics/statistical_mechanics/_graph_spins.py +93 -0
  1434. skcomplex/models/physics/statistical_mechanics/_ising_spin.py +63 -0
  1435. skcomplex/models/physics/statistical_mechanics/_kinetic_temperature.py +66 -0
  1436. skcomplex/models/physics/statistical_mechanics/_master_equations.py +171 -0
  1437. skcomplex/models/physics/statistical_mechanics/_mattis_spin.py +79 -0
  1438. skcomplex/models/physics/statistical_mechanics/_maxwell_boltzmann.py +96 -0
  1439. skcomplex/models/physics/statistical_mechanics/_microstate.py +102 -0
  1440. skcomplex/models/physics/statistical_mechanics/_order_parameter.py +90 -0
  1441. skcomplex/models/physics/statistical_mechanics/_particle_site.py +41 -0
  1442. skcomplex/models/physics/statistical_mechanics/_percolation.py +60 -0
  1443. skcomplex/models/physics/statistical_mechanics/_percolation_site.py +73 -0
  1444. skcomplex/models/physics/statistical_mechanics/_potts_spin.py +58 -0
  1445. skcomplex/models/physics/statistical_mechanics/_processes.py +355 -0
  1446. skcomplex/models/physics/statistical_mechanics/_q2r_spin.py +51 -0
  1447. skcomplex/models/physics/statistical_mechanics/_quantum_spins.py +153 -0
  1448. skcomplex/models/physics/statistical_mechanics/_random_energy.py +68 -0
  1449. skcomplex/models/physics/statistical_mechanics/_reservoir.py +81 -0
  1450. skcomplex/models/physics/statistical_mechanics/_spin_glasses.py +203 -0
  1451. skcomplex/models/physics/statistical_mechanics/_spins.py +200 -0
  1452. skcomplex/models/physics/statistical_mechanics/_susceptibility.py +112 -0
  1453. skcomplex/models/physics/statistical_mechanics/_traps.py +135 -0
  1454. skcomplex/models/physics/statistical_mechanics/_tree_node.py +48 -0
  1455. skcomplex/models/physics/statistical_mechanics/_urns.py +107 -0
  1456. skcomplex/models/physics/statistical_mechanics/_walker.py +81 -0
  1457. skcomplex/models/physics/statistical_mechanics/_walker_view.py +20 -0
  1458. skcomplex/models/physics/statistical_mechanics/_xxz_exchange.py +67 -0
  1459. skcomplex/models/physics/statistical_mechanics/_xy_spin.py +58 -0
  1460. skcomplex/models/physics/statistical_mechanics/_zeeman_field.py +56 -0
  1461. skcomplex/models/physics/statistical_mechanics/_zero_range_hop.py +86 -0
  1462. skcomplex/models/physics/statistical_mechanics/_zero_range_hops.py +81 -0
  1463. skcomplex/models/physics/statistical_mechanics/_zone.py +78 -0
  1464. skcomplex/models/physics/synchronization/__init__.py +64 -0
  1465. skcomplex/models/physics/synchronization/_aggregate_averaging.py +63 -0
  1466. skcomplex/models/physics/synchronization/_amplitude_death.py +278 -0
  1467. skcomplex/models/physics/synchronization/_chaos.py +152 -0
  1468. skcomplex/models/physics/synchronization/_diffusive_coupling.py +69 -0
  1469. skcomplex/models/physics/synchronization/_edge_coupling.py +50 -0
  1470. skcomplex/models/physics/synchronization/_hypergraphs.py +166 -0
  1471. skcomplex/models/physics/synchronization/_integrate_and_fire_oscillator.py +80 -0
  1472. skcomplex/models/physics/synchronization/_kuramoto.py +423 -0
  1473. skcomplex/models/physics/synchronization/_link.py +46 -0
  1474. skcomplex/models/physics/synchronization/_logistic_coupling.py +78 -0
  1475. skcomplex/models/physics/synchronization/_logistic_node.py +59 -0
  1476. skcomplex/models/physics/synchronization/_logistic_unit.py +43 -0
  1477. skcomplex/models/physics/synchronization/_networks.py +184 -0
  1478. skcomplex/models/physics/synchronization/_pulses.py +138 -0
  1479. skcomplex/models/physics/synchronization/_rossler_oscillator.py +95 -0
  1480. skcomplex/models/physics/synchronization/_swarmalator.py +48 -0
  1481. skcomplex/models/physics/synchronization/_swarmalators.py +182 -0
  1482. skcomplex/models/physics/synchronization/_utils.py +29 -0
  1483. skcomplex/models/physics/synchronization/_winfree_mean_field.py +62 -0
  1484. skcomplex/models/physics/waves/__init__.py +23 -0
  1485. skcomplex/models/physics/waves/_charged.py +203 -0
  1486. skcomplex/models/physics/waves/_driven_anchor.py +63 -0
  1487. skcomplex/models/physics/waves/_lattice_hamiltonian.py +60 -0
  1488. skcomplex/models/physics/waves/_position_dephasing.py +64 -0
  1489. skcomplex/models/physics/waves/_quantum.py +125 -0
  1490. skcomplex/models/physics/waves/_strings.py +169 -0
  1491. skcomplex/models/physics/waves/_wave_function.py +79 -0
  1492. skcomplex/models/physics/waves/_wave_string.py +52 -0
  1493. skcomplex/models/social/__init__.py +1 -0
  1494. skcomplex/models/social/cooperation/__init__.py +34 -0
  1495. skcomplex/models/social/cooperation/_contributor.py +62 -0
  1496. skcomplex/models/social/cooperation/_dilemma.py +56 -0
  1497. skcomplex/models/social/cooperation/_hyperedge_goods.py +54 -0
  1498. skcomplex/models/social/cooperation/_hypergraph_games.py +249 -0
  1499. skcomplex/models/social/cooperation/_prisoner.py +56 -0
  1500. skcomplex/models/social/cooperation/_prisoners_dilemma.py +126 -0
  1501. skcomplex/models/social/cooperation/_public_goods.py +54 -0
  1502. skcomplex/models/social/cooperation/_simplicial_dilemma.py +119 -0
  1503. skcomplex/models/social/cooperation/_spatial_games.py +159 -0
  1504. skcomplex/models/social/cooperation/_strategist.py +57 -0
  1505. skcomplex/models/social/cooperation/_strategist_view.py +14 -0
  1506. skcomplex/models/social/cooperation/_tournament.py +126 -0
  1507. skcomplex/models/social/cooperation/_tournaments.py +87 -0
  1508. skcomplex/models/social/crowds/__init__.py +46 -0
  1509. skcomplex/models/social/crowds/_criminal_contagion.py +108 -0
  1510. skcomplex/models/social/crowds/_criminality.py +223 -0
  1511. skcomplex/models/social/crowds/_crowding.py +115 -0
  1512. skcomplex/models/social/crowds/_deterrence.py +101 -0
  1513. skcomplex/models/social/crowds/_evacuation.py +196 -0
  1514. skcomplex/models/social/crowds/_guidance.py +69 -0
  1515. skcomplex/models/social/crowds/_motivation.py +67 -0
  1516. skcomplex/models/social/crowds/_pedestrians.py +85 -0
  1517. skcomplex/models/social/crowds/_recruitment.py +90 -0
  1518. skcomplex/models/social/crowds/_security_agents.py +48 -0
  1519. skcomplex/models/social/crowds/_social_repulsion.py +86 -0
  1520. skcomplex/models/social/crowds/_walking.py +186 -0
  1521. skcomplex/models/social/crowds/_walls.py +69 -0
  1522. skcomplex/models/social/language/__init__.py +13 -0
  1523. skcomplex/models/social/language/_language.py +30 -0
  1524. skcomplex/models/social/language/_least_effort.py +69 -0
  1525. skcomplex/models/social/language/_word.py +39 -0
  1526. skcomplex/models/social/language/_word_frequencies.py +48 -0
  1527. skcomplex/models/social/opinion_dynamics/__init__.py +142 -0
  1528. skcomplex/models/social/opinion_dynamics/_adopter.py +61 -0
  1529. skcomplex/models/social/opinion_dynamics/_adopter_view.py +14 -0
  1530. skcomplex/models/social/opinion_dynamics/_adoption.py +83 -0
  1531. skcomplex/models/social/opinion_dynamics/_axelrod.py +160 -0
  1532. skcomplex/models/social/opinion_dynamics/_believer.py +71 -0
  1533. skcomplex/models/social/opinion_dynamics/_believer_view.py +16 -0
  1534. skcomplex/models/social/opinion_dynamics/_bounded_confidence.py +126 -0
  1535. skcomplex/models/social/opinion_dynamics/_citizen.py +49 -0
  1536. skcomplex/models/social/opinion_dynamics/_citizen_view.py +12 -0
  1537. skcomplex/models/social/opinion_dynamics/_club_member.py +78 -0
  1538. skcomplex/models/social/opinion_dynamics/_coevolution.py +187 -0
  1539. skcomplex/models/social/opinion_dynamics/_coevolving_voter.py +63 -0
  1540. skcomplex/models/social/opinion_dynamics/_cognition.py +73 -0
  1541. skcomplex/models/social/opinion_dynamics/_complex_agent.py +58 -0
  1542. skcomplex/models/social/opinion_dynamics/_complex_agent_view.py +13 -0
  1543. skcomplex/models/social/opinion_dynamics/_confidence_coupling.py +76 -0
  1544. skcomplex/models/social/opinion_dynamics/_confident.py +50 -0
  1545. skcomplex/models/social/opinion_dynamics/_conventions.py +44 -0
  1546. skcomplex/models/social/opinion_dynamics/_conversations.py +116 -0
  1547. skcomplex/models/social/opinion_dynamics/_cultural_influence.py +93 -0
  1548. skcomplex/models/social/opinion_dynamics/_diffusion.py +205 -0
  1549. skcomplex/models/social/opinion_dynamics/_discussant.py +60 -0
  1550. skcomplex/models/social/opinion_dynamics/_discussant_view.py +14 -0
  1551. skcomplex/models/social/opinion_dynamics/_discussions.py +51 -0
  1552. skcomplex/models/social/opinion_dynamics/_encounters.py +48 -0
  1553. skcomplex/models/social/opinion_dynamics/_hypergraph_consensus.py +106 -0
  1554. skcomplex/models/social/opinion_dynamics/_influencee.py +70 -0
  1555. skcomplex/models/social/opinion_dynamics/_influencee_view.py +16 -0
  1556. skcomplex/models/social/opinion_dynamics/_kinetic_opinion.py +287 -0
  1557. skcomplex/models/social/opinion_dynamics/_majority_voter.py +43 -0
  1558. skcomplex/models/social/opinion_dynamics/_namer.py +53 -0
  1559. skcomplex/models/social/opinion_dynamics/_namer_view.py +13 -0
  1560. skcomplex/models/social/opinion_dynamics/_naming_games.py +68 -0
  1561. skcomplex/models/social/opinion_dynamics/_opinion.py +39 -0
  1562. skcomplex/models/social/opinion_dynamics/_persuader.py +52 -0
  1563. skcomplex/models/social/opinion_dynamics/_persuader_view.py +12 -0
  1564. skcomplex/models/social/opinion_dynamics/_persuasion.py +247 -0
  1565. skcomplex/models/social/opinion_dynamics/_random_pairs.py +53 -0
  1566. skcomplex/models/social/opinion_dynamics/_schedule.py +39 -0
  1567. skcomplex/models/social/opinion_dynamics/_separation.py +71 -0
  1568. skcomplex/models/social/opinion_dynamics/_social_impact.py +60 -0
  1569. skcomplex/models/social/opinion_dynamics/_standardization.py +212 -0
  1570. skcomplex/models/social/opinion_dynamics/_thinker.py +61 -0
  1571. skcomplex/models/social/opinion_dynamics/_thinker_view.py +15 -0
  1572. skcomplex/models/social/opinion_dynamics/_three_body_consensus.py +71 -0
  1573. skcomplex/models/social/opinion_dynamics/_tie.py +21 -0
  1574. skcomplex/models/social/opinion_dynamics/_variant_voter.py +67 -0
  1575. skcomplex/models/social/opinion_dynamics/_variant_voter_view.py +14 -0
  1576. skcomplex/models/social/opinion_dynamics/_variant_voting.py +63 -0
  1577. skcomplex/models/social/opinion_dynamics/_village.py +61 -0
  1578. skcomplex/models/social/opinion_dynamics/_village_view.py +14 -0
  1579. skcomplex/models/social/opinion_dynamics/_voter.py +49 -0
  1580. skcomplex/models/social/opinion_dynamics/_voter_imitation.py +48 -0
  1581. skcomplex/models/social/opinion_dynamics/_voter_view.py +12 -0
  1582. skcomplex/models/social/opinion_dynamics/_voters.py +197 -0
  1583. skcomplex/models/social/organizations/__init__.py +68 -0
  1584. skcomplex/models/social/organizations/_arms_race.py +34 -0
  1585. skcomplex/models/social/organizations/_burden.py +38 -0
  1586. skcomplex/models/social/organizations/_city_resident.py +41 -0
  1587. skcomplex/models/social/organizations/_contender_view.py +14 -0
  1588. skcomplex/models/social/organizations/_contest.py +32 -0
  1589. skcomplex/models/social/organizations/_daily_movements.py +144 -0
  1590. skcomplex/models/social/organizations/_eater.py +282 -0
  1591. skcomplex/models/social/organizations/_eater_view.py +24 -0
  1592. skcomplex/models/social/organizations/_employee.py +173 -0
  1593. skcomplex/models/social/organizations/_employee_view.py +35 -0
  1594. skcomplex/models/social/organizations/_employment.py +127 -0
  1595. skcomplex/models/social/organizations/_execution.py +79 -0
  1596. skcomplex/models/social/organizations/_gravity_contact.py +69 -0
  1597. skcomplex/models/social/organizations/_hierarchies.py +174 -0
  1598. skcomplex/models/social/organizations/_obesity.py +131 -0
  1599. skcomplex/models/social/organizations/_premises.py +75 -0
  1600. skcomplex/models/social/organizations/_premises_view.py +16 -0
  1601. skcomplex/models/social/organizations/_queues.py +52 -0
  1602. skcomplex/models/social/organizations/_restaurant.py +59 -0
  1603. skcomplex/models/social/organizations/_restaurant_view.py +14 -0
  1604. skcomplex/models/social/organizations/_sabotage.py +183 -0
  1605. skcomplex/models/social/organizations/_supervisor.py +25 -0
  1606. skcomplex/models/social/organizations/_task.py +65 -0
  1607. skcomplex/models/social/organizations/_task_view.py +15 -0
  1608. skcomplex/models/social/organizations/_trafficking.py +184 -0
  1609. skcomplex/models/social/organizations/_traps.py +322 -0
  1610. skcomplex/models/social/organizations/_traveller.py +55 -0
  1611. skcomplex/models/social/organizations/_traveller_view.py +13 -0
  1612. skcomplex/models/social/organizations/_urban_scaling.py +72 -0
  1613. skcomplex/models/social/segregation/__init__.py +21 -0
  1614. skcomplex/models/social/segregation/_block_moves.py +127 -0
  1615. skcomplex/models/social/segregation/_blocks.py +111 -0
  1616. skcomplex/models/social/segregation/_dweller.py +70 -0
  1617. skcomplex/models/social/segregation/_dweller_view.py +16 -0
  1618. skcomplex/models/social/segregation/_relocation.py +60 -0
  1619. skcomplex/models/social/segregation/_resident.py +55 -0
  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 +1,365 @@
1
+ """Define the base class of visuals, which log one element or agent group to a Rerun recording."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+
7
+ from typing import Self
8
+
9
+ import networkx as nx
10
+ import numpy as np
11
+ import numpy.typing as npt
12
+ import rerun as rr
13
+ import rerun.blueprint as rrb
14
+
15
+ from ...base import BaseConfig
16
+ from ...core.spaces import BaseSpace, NetworkSpace
17
+ from ...core.specs import CompiledAgentsSpec, CompiledElementSpec
18
+ from ...errors import ValidationError
19
+ from ...specs import AgentSnapshotSpec
20
+ from ..problems import BaseProblemSpec, FrameSpec
21
+
22
+ _UPWARD = np.array([1.0, -1.0])
23
+ _LAYOUT_SEED = 0
24
+ _NODE_SPACING = 40.0
25
+ _POINT_SHARE = 0.02
26
+ _CROWD_SIZE = 10
27
+ _CROWD_EXPONENT = 0.25
28
+ _GRID_RADIUS = 0.4
29
+ _MODULUS = 'modulus'
30
+ _PHASE = 'phase'
31
+ PARTS = ('real', 'imag')
32
+ _SERIES_COLORS = (
33
+ (230, 159, 0),
34
+ (86, 180, 233),
35
+ (0, 158, 115),
36
+ (240, 228, 66),
37
+ (0, 114, 178),
38
+ (213, 94, 0),
39
+ (204, 121, 167),
40
+ (170, 170, 170),
41
+ )
42
+ _POINT_FLOOR = 0.25
43
+ _COLOR_SCALE = np.array(
44
+ [[68, 1, 84], [59, 82, 139], [33, 145, 140], [94, 201, 98], [253, 231, 37]],
45
+ dtype=float,
46
+ )
47
+ _PALETTE = (
48
+ np.stack(
49
+ [
50
+ np.interp(np.linspace(0.0, 1.0, 256), np.linspace(0.0, 1.0, len(_COLOR_SCALE)), _COLOR_SCALE[:, channel])
51
+ for channel in range(3)
52
+ ],
53
+ axis=-1,
54
+ )
55
+ .round()
56
+ .astype(np.uint8)
57
+ )
58
+ _PHASE_SCALE = np.array(
59
+ [[230, 90, 80], [225, 190, 70], [90, 190, 110], [70, 160, 210], [150, 100, 200], [230, 90, 80]],
60
+ dtype=float,
61
+ )
62
+ _PHASE_PALETTE = (
63
+ np.stack(
64
+ [
65
+ np.interp(np.linspace(0.0, 1.0, 256), np.linspace(0.0, 1.0, len(_PHASE_SCALE)), _PHASE_SCALE[:, channel])
66
+ for channel in range(3)
67
+ ],
68
+ axis=-1,
69
+ )
70
+ .round()
71
+ .astype(np.uint8)
72
+ )
73
+
74
+
75
+ class BaseVisual(BaseConfig[BaseProblemSpec, FrameSpec]):
76
+ """Base class of visuals, which log the state of one element or agent group to a Rerun recording.
77
+
78
+ A visual follows the common API of the engine. `prepare(problem)` finds the element or agent group of the problem
79
+ at the entity path `path`, forgets what earlier frames left, and sets the Rerun views that show what the visual
80
+ logs. `run(frame)` logs the element at one frame to the recording `recording`: a compiled element through the hook
81
+ `_log`, and agents through the hook `_log_agents` with the snapshot of the frame. Subclasses implement `_log`,
82
+ `_log_agents`, or both, declare their views with `_views`, and are named by the kind of a `VisualSpec`.
83
+ `RerunObserver` builds the visual of every element and agent group with their path and its recording.
84
+
85
+ Args:
86
+ path:
87
+ The entity path of the element or agent group to draw, which also names it in the problem.
88
+
89
+ recording:
90
+ The Rerun recording to log to, or `None` for the active recording of the thread.
91
+
92
+ Attributes:
93
+ element_:
94
+ The compiled element or agents the visual logs.
95
+
96
+ recording_:
97
+ The Rerun recording the visual logs to, or `None` while no recording is active.
98
+
99
+ space_:
100
+ The space the agents of the problem live in, or `None`.
101
+
102
+ layouts_:
103
+ The positions of the nodes of every network drawn so far, by the id of its graph.
104
+
105
+ views_:
106
+ The Rerun views that show what the visual logs, each with an entity path of the element as origin.
107
+
108
+ Examples:
109
+ >>> from skcomplex.engine.compile import compile_system
110
+ >>> from skcomplex.engine.viz import ScalarsVisual
111
+ >>> from skcomplex.models import create
112
+ >>> problem = compile_system(create('lotka_volterra'))
113
+ >>> visual = ScalarsVisual(path='prey').check().prepare(problem)
114
+ >>> visual.element_.path, str(visual.views_[0].origin)
115
+ ('prey', 'prey')
116
+ """
117
+
118
+ def __init__(self, *, path: str | None = None, recording: rr.RecordingStream | None = None) -> None:
119
+ self.path = path
120
+ self.recording = recording
121
+
122
+ def _check(self) -> None:
123
+ """Raise an error unless the path is a string."""
124
+ if not isinstance(self.path, str):
125
+ error_msg = f'path = {self.path!r} must be the entity path of the element or agent group to draw.'
126
+ raise ValidationError(error_msg)
127
+
128
+ def _prepare(self, context: BaseProblemSpec | None) -> None:
129
+ """Find the element at the path, keep the recording and the space of the agents, and set the views.
130
+
131
+ Args:
132
+ context:
133
+ The compiled problem.
134
+
135
+ Raises:
136
+ ValidationError:
137
+ No problem is passed, or no element or agent group of the problem has the path of the visual.
138
+ """
139
+ if context is None:
140
+ error_msg = 'A visual prepares on a compiled problem. Pass the problem to `prepare`.'
141
+ raise ValidationError(error_msg)
142
+ problem = context
143
+ elements = {item.path: item for item in (*problem.elements, *problem.agents)}
144
+ if self.path not in elements:
145
+ error_msg = (
146
+ f'No element or agent group of the problem has the path {self.path!r}. The paths are: '
147
+ f'{", ".join(elements)}.'
148
+ )
149
+ raise ValidationError(error_msg)
150
+ self.element_ = elements[self.path]
151
+ self.recording_ = self.recording if self.recording is not None else rr.get_data_recording()
152
+ self.space_: BaseSpace | None = problem.agent_space
153
+ self.layouts_: dict[int, dict[str, npt.NDArray[np.float64]]] = {}
154
+ self.views_ = self._views(self.element_, problem)
155
+
156
+ def _run(self, inputs: FrameSpec | None) -> None:
157
+ """Log the element at a frame, or the agents of the frame when the element is an agent group.
158
+
159
+ Args:
160
+ inputs:
161
+ The frame.
162
+
163
+ Raises:
164
+ ValidationError:
165
+ No frame is passed, or no Rerun recording is active.
166
+ """
167
+ if inputs is None:
168
+ error_msg = 'A visual runs on a frame. Pass the frame to `run`.'
169
+ raise ValidationError(error_msg)
170
+ if self.recording_ is None:
171
+ error_msg = 'No Rerun recording is active. Pass `recording` or start one with `rerun.init`.'
172
+ raise ValidationError(error_msg)
173
+ if isinstance(self.element_, CompiledAgentsSpec):
174
+ snapshot = inputs.agents.get(self.element_.path)
175
+ if snapshot is not None:
176
+ self._log_agents(self.recording_, self.element_.path, snapshot, self.space_)
177
+ return
178
+ self._log(self.recording_, self.element_, inputs)
179
+
180
+ def prepare(self, problem: BaseProblemSpec | None = None) -> Self:
181
+ """Prepare the checked visual for the element at its path in a compiled problem.
182
+
183
+ Args:
184
+ problem:
185
+ The compiled problem.
186
+
187
+ Returns:
188
+ self:
189
+ The prepared visual, with its views `views_`.
190
+
191
+ Raises:
192
+ ValidationError:
193
+ No element or agent group of the problem has the path of the visual.
194
+ """
195
+ return super().prepare(problem)
196
+
197
+ def run(self, frame: FrameSpec | None = None, final: bool = False) -> Self:
198
+ """Log the element or the agents of the visual at a frame.
199
+
200
+ Args:
201
+ frame:
202
+ The frame.
203
+
204
+ final:
205
+ Whether this is the last call of the run.
206
+
207
+ Returns:
208
+ self:
209
+ The visual.
210
+ """
211
+ super().run(frame, final)
212
+ return self
213
+
214
+ def _views(self, element: CompiledElementSpec | CompiledAgentsSpec, problem: BaseProblemSpec) -> list[rrb.View]:
215
+ """Return the Rerun views that show what the visual logs for an element, none by default."""
216
+ return []
217
+
218
+ def _log(self, recording: rr.RecordingStream, element: CompiledElementSpec, frame: FrameSpec) -> None:
219
+ """Log the state of a compiled element at one frame; a subclass that logs elements implements it."""
220
+ raise NotImplementedError
221
+
222
+ def _log_agents(
223
+ self,
224
+ recording: rr.RecordingStream,
225
+ path: str,
226
+ snapshot: AgentSnapshotSpec,
227
+ space: BaseSpace | None,
228
+ ) -> None:
229
+ """Log the agents of a group at one frame; log nothing by default."""
230
+
231
+ def _colors(
232
+ self,
233
+ values: npt.NDArray[np.float64],
234
+ low: float | None,
235
+ high: float | None,
236
+ ) -> npt.NDArray[np.uint8]:
237
+ """Return the colors of values over the given range, or over the extremes of the values for a missing end."""
238
+ low = float(values.min()) if low is None else float(low)
239
+ high = float(values.max()) if high is None else float(high)
240
+ return self._palette_colors(values, low, high)
241
+
242
+ def _layout(self, space: NetworkSpace) -> dict[str, npt.NDArray[np.float64]]:
243
+ """Return the positions of the nodes of a network, computed once per network."""
244
+ if id(space.graph) not in self.layouts_:
245
+ self.layouts_[id(space.graph)] = self._network_layout(space.graph)
246
+ return self.layouts_[id(space.graph)]
247
+
248
+ @staticmethod
249
+ def _phase_colors(phases: npt.NDArray[np.float64]) -> npt.NDArray[np.uint8]:
250
+ """Return the colors of phases in `(-pi, pi]` from a cyclic palette, so `-pi` and `pi` share one color."""
251
+ levels = np.mod(phases + np.pi, 2 * np.pi) * (255.0 / (2 * np.pi))
252
+ return _PHASE_PALETTE[np.clip(levels, 0.0, 255.0).astype(np.uint8)]
253
+
254
+ @staticmethod
255
+ def _widened(span: tuple[float, float] | None, values: npt.NDArray[np.float64]) -> tuple[float, float]:
256
+ """Return a color range widened to cover values, starting from their extremes when there is no range yet."""
257
+ low, high = float(np.min(values)), float(np.max(values))
258
+ return (low, high) if span is None else (min(span[0], low), max(span[1], high))
259
+
260
+ @staticmethod
261
+ def _colors_of(values: npt.NDArray[np.float64], low: float, high: float) -> npt.NDArray[np.uint8]:
262
+ """Return one color per value on a scale from blue at `low` to yellow at `high`, bright enough to see on black.
263
+
264
+ Args:
265
+ values:
266
+ The values.
267
+
268
+ low:
269
+ The value of the darkest color.
270
+
271
+ high:
272
+ The value of the brightest color.
273
+
274
+ Returns:
275
+ colors:
276
+ One RGB color per value.
277
+
278
+ Examples:
279
+ >>> import numpy as np
280
+ >>> from skcomplex.engine.viz import BaseVisual
281
+ >>> BaseVisual._colors_of(np.array([0.0, 1.0]), 0.0, 1.0).shape
282
+ (2, 3)
283
+ """
284
+ fractions = np.clip((values - low) / (high - low), 0.0, 1.0) if high > low else np.zeros_like(values)
285
+ fractions = _POINT_FLOOR + (1.0 - _POINT_FLOOR) * fractions
286
+ anchors = np.linspace(0.0, 1.0, len(_COLOR_SCALE))
287
+ channels = [np.interp(fractions, anchors, _COLOR_SCALE[:, channel]) for channel in range(3)]
288
+ return np.stack(channels, axis=-1).round().astype(np.uint8)
289
+
290
+ @staticmethod
291
+ def _palette_colors(values: npt.NDArray[np.float64], low: float, high: float) -> npt.NDArray[np.uint8]:
292
+ """Return the colors of an array of values from a palette of 256 levels, fast enough for large images.
293
+
294
+ Args:
295
+ values:
296
+ The values.
297
+
298
+ low:
299
+ The value of the darkest color.
300
+
301
+ high:
302
+ The value of the brightest color.
303
+
304
+ Returns:
305
+ colors:
306
+ One RGB color per value, the darkest one for every value when the range is empty.
307
+
308
+ Examples:
309
+ >>> import numpy as np
310
+ >>> from skcomplex.engine.viz import BaseVisual
311
+ >>> BaseVisual._palette_colors(np.array([0.0, 1.0]), 0.0, 1.0).shape
312
+ (2, 3)
313
+ """
314
+ if high <= low:
315
+ return np.broadcast_to(_PALETTE[0], (*values.shape, 3))
316
+ levels = np.clip((values - low) * (255.0 / (high - low)), 0.0, 255.0).astype(np.uint8)
317
+ return _PALETTE[levels]
318
+
319
+ @staticmethod
320
+ def _network_layout(graph: nx.Graph) -> dict[str, npt.NDArray[np.float64]]:
321
+ """Return fixed positions of the nodes of a network, with neighbours about a spacing apart.
322
+
323
+ The positions are the `pos` attributes of the nodes when every node has one, and a seeded spring layout
324
+ otherwise.
325
+ """
326
+ scale = _NODE_SPACING * float(np.sqrt(max(graph.number_of_nodes(), 1))) / 2
327
+ given = nx.get_node_attributes(graph, 'pos')
328
+ if given and len(given) == graph.number_of_nodes():
329
+ layout = nx.rescale_layout_dict(
330
+ {node: np.asarray(position, dtype=float) for node, position in given.items()},
331
+ )
332
+ else:
333
+ layout = nx.spring_layout(graph, seed=_LAYOUT_SEED)
334
+ return {str(node): np.asarray(position, dtype=float) * scale for node, position in layout.items()}
335
+
336
+ @staticmethod
337
+ def _radius_of(extent: float, count: int) -> float:
338
+ """Return a point radius that is a share of the extent of a view, smaller for crowds so they do not overlap."""
339
+ return _POINT_SHARE * (extent if extent > 0 else 1.0) / max(count / _CROWD_SIZE, 1.0) ** _CROWD_EXPONENT
340
+
341
+ @staticmethod
342
+ def _log_scalars(recording: rr.RecordingStream, path: str, value: object) -> None:
343
+ """Log the components of a value as scalar series, the real and imaginary parts of a complex value apart.
344
+
345
+ Args:
346
+ recording:
347
+ The Rerun recording.
348
+
349
+ path:
350
+ The entity path of the series.
351
+
352
+ value:
353
+ A number or an array of numbers, real or complex.
354
+
355
+ Examples:
356
+ >>> import rerun as rr
357
+ >>> from skcomplex.engine.viz import BaseVisual
358
+ >>> BaseVisual._log_scalars(rr.RecordingStream('example'), 'value', 1.0 + 2.0j)
359
+ """
360
+ values = np.ravel(np.asarray(value))
361
+ if not np.iscomplexobj(values):
362
+ recording.log(path, rr.Scalars(values))
363
+ return
364
+ for part, components in zip(PARTS, (values.real, values.imag), strict=True):
365
+ recording.log(f'{path}/{part}', rr.Scalars(components))
@@ -0,0 +1,334 @@
1
+ """Draw bodies, the rods that join them, their fading trails, and static outlines from the states of an element."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ from collections import deque
7
+ from collections.abc import Callable, Sequence
8
+
9
+ import numpy as np
10
+ import numpy.typing as npt
11
+ import rerun as rr
12
+ import rerun.blueprint as rrb
13
+
14
+ from ...core.specs import CompiledAgentsSpec, CompiledElementSpec
15
+ from ...errors import ValidationError
16
+ from ..problems import BaseProblemSpec, FrameSpec
17
+ from ..types import Colors, Marks, Outline, Positions
18
+ from ._base import _UPWARD, BaseVisual
19
+ from ._points import _TRAIL_LENGTH
20
+
21
+ _BODY_COLOR = (250, 180, 60)
22
+ _ROD_COLOR = (220, 220, 220)
23
+ _TRAIL_COLOR = (90, 170, 230)
24
+ _OUTLINE_COLOR = (200, 200, 200)
25
+ _MARK_COLOR = (150, 150, 150)
26
+ _FAINTEST = 20
27
+ _ROD_SHARE = 0.25
28
+ _TRAIL_SHARE = 0.1
29
+ MARGIN = 0.1
30
+ PAIR = 2
31
+ _SPACE = 3
32
+
33
+
34
+ class BodiesVisual(BaseVisual):
35
+ """Visual that draws bodies at positions computed from the states of an element, with rods, trails, and outlines.
36
+
37
+ The bodies are logged as points under `<path>/bodies`, the rods from the pivot through the bodies in order as one
38
+ line strip under `<path>/rods`, the trails of the traced bodies as segments under `<path>/trail` that grow more
39
+ transparent with age, the outlines once as static line strips under `<path>/outline`, and the marks once as static
40
+ points under `<path>/marks`. Every state is also logged as a time series under `<path>/<state>`. Bodies with three
41
+ coordinates are drawn in a 3D view. Bodies with two are drawn in a 2D view with the second coordinate negated,
42
+ since Rerun's 2D views point their vertical axis down, so the views draw it upward.
43
+
44
+ Args:
45
+ positions:
46
+ A function of the parameters and states of the element by keyword that returns one row `(x, y)` per body,
47
+ or the names of the two states that hold the position of a single body.
48
+
49
+ pivot:
50
+ The fixed point the rods start from, or `None` to start them at the first body.
51
+
52
+ rods:
53
+ Whether to draw rods through the bodies.
54
+
55
+ traced:
56
+ The indices of the bodies whose trails are drawn, or `None` for every body.
57
+
58
+ trail:
59
+ The number of recent positions in a trail, 0 for no trail, or `None` for the whole path.
60
+
61
+ outline:
62
+ Static polylines, each an array of rows `(x, y)`, such as the walls of a table, or a function of the
63
+ parameters and states by keyword that returns them from the first frame.
64
+
65
+ marks:
66
+ Static points, such as fixed attracting centres, or a function of the parameters and states by keyword that
67
+ returns them from the first frame.
68
+
69
+ radius:
70
+ The radius of the bodies, or `None` for a share of the extent of the view.
71
+
72
+ path:
73
+ The entity path of the element or agent group to draw, which also names it in the problem.
74
+
75
+ recording:
76
+ The Rerun recording to log to, or `None` for the active recording of the thread.
77
+
78
+ Attributes:
79
+ history_:
80
+ The recent positions of the traced bodies, the oldest first.
81
+
82
+ drawn_:
83
+ The entity paths whose outline and marks are logged.
84
+
85
+ Examples:
86
+ >>> from skcomplex.engine.viz import BodiesVisual
87
+ >>> BodiesVisual(('x', 'y'), trail=None).trail is None
88
+ True
89
+ """
90
+
91
+ def __init__(
92
+ self,
93
+ positions: Positions,
94
+ *,
95
+ pivot: Sequence[float] | None = None,
96
+ rods: bool = False,
97
+ traced: Sequence[int] | None = None,
98
+ trail: int | None = _TRAIL_LENGTH,
99
+ outline: Outline = (),
100
+ marks: Marks = (),
101
+ radius: float | None = None,
102
+ path: str | None = None,
103
+ recording: rr.RecordingStream | None = None,
104
+ ) -> None:
105
+ self.positions = positions
106
+ self.pivot = pivot
107
+ self.rods = rods
108
+ self.traced = traced
109
+ self.trail = trail
110
+ self.outline = outline
111
+ self.marks = marks
112
+ self.radius = radius
113
+ self.path = path
114
+ self.recording = recording
115
+
116
+ def _prepare(self, context: BaseProblemSpec | None) -> None:
117
+ """Keep the element, forget the trail and the static drawings of earlier runs, and set the views."""
118
+ self.history_: deque[npt.NDArray[np.float64]] = deque(maxlen=self.trail if self.trail else None)
119
+ self.drawn_: set[str] = set()
120
+ super()._prepare(context)
121
+
122
+ def _bodies(self, values: dict[str, object]) -> npt.NDArray[np.float64]:
123
+ """Return the positions of the bodies as rows `(x, y)` or `(x, y, z)`."""
124
+ if callable(self.positions):
125
+ points = np.asarray(self.positions(**values), dtype=float)
126
+ else:
127
+ points = np.array([[float(np.ravel(np.asarray(values[name]))[0]) for name in self.positions]])
128
+ points = np.atleast_2d(points)
129
+ if points.ndim != PAIR or points.shape[1] not in {PAIR, _SPACE}:
130
+ error_msg = (
131
+ f'The positions of the bodies visual have shape {points.shape}, but they must be pairs of coordinates, '
132
+ 'one row (x, y) per body, or triples, one row (x, y, z) per body.'
133
+ )
134
+ raise ValidationError(error_msg)
135
+ return points
136
+
137
+ def _static(
138
+ self,
139
+ values: dict[str, object],
140
+ dimension: int,
141
+ ) -> tuple[list[npt.NDArray[np.float64]], npt.NDArray[np.float64]]:
142
+ """Return the outline polylines and the marks, evaluated from the values when they are functions."""
143
+ outline = self.outline(**values) if callable(self.outline) else self.outline
144
+ marks = self.marks(**values) if callable(self.marks) else self.marks
145
+ strips = [np.atleast_2d(np.asarray(item, dtype=float)) for item in outline]
146
+ points = np.asarray(marks, dtype=float).reshape(-1, dimension)
147
+ return strips, points
148
+
149
+ def _chain(self, bodies: npt.NDArray[np.float64]) -> npt.NDArray[np.float64]:
150
+ """Return the points the rods join, from the pivot when there is one."""
151
+ return bodies if self.pivot is None else np.vstack([np.asarray(self.pivot, dtype=float), bodies])
152
+
153
+ def _scale(self, bodies: npt.NDArray[np.float64], values: dict[str, object]) -> float:
154
+ """Return the extent of the drawing: the outline, the marks, the pivot, and the rods at full length."""
155
+ chain = self._chain(bodies)
156
+ strips, marks = self._static(values, bodies.shape[1])
157
+ points = np.vstack([chain, *strips, marks])
158
+ extent = float(np.ptp(points, axis=0).max())
159
+ if self.rods and len(chain) > 1:
160
+ extent = max(extent, 2 * float(np.linalg.norm(np.diff(chain, axis=0), axis=1).sum()))
161
+ return extent
162
+
163
+ def _log_static(
164
+ self,
165
+ recording: rr.RecordingStream,
166
+ path: str,
167
+ values: dict[str, object],
168
+ sizes: tuple[int, float],
169
+ ) -> None:
170
+ """Log the outline and the marks once, for bodies of a dimension and a radius."""
171
+ if path in self.drawn_:
172
+ return
173
+ self.drawn_.add(path)
174
+ dimension, radius = sizes
175
+ strips, marks = self._static(values, dimension)
176
+ if strips:
177
+ recording.log(f'{path}/outline', self._strips(strips, None, _OUTLINE_COLOR), static=True)
178
+ if len(marks):
179
+ recording.log(f'{path}/marks', self._points(marks, radius, _MARK_COLOR), static=True)
180
+
181
+ def _log_trail(
182
+ self,
183
+ recording: rr.RecordingStream,
184
+ path: str,
185
+ bodies: npt.NDArray[np.float64],
186
+ width: float,
187
+ ) -> None:
188
+ """Log the fading trails of the traced bodies."""
189
+ if self.trail == 0:
190
+ return
191
+ traced = list(range(len(bodies))) if self.traced is None else list(self.traced)
192
+ self.history_.append(bodies[traced])
193
+ if len(self.history_) < PAIR:
194
+ return
195
+ history = np.stack(self.history_)
196
+ segments, colors = self._fading_segments([history[:, column] for column in range(len(traced))])
197
+ recording.log(f'{path}/trail', self._strips(segments, width, colors))
198
+
199
+ def _log(self, recording: rr.RecordingStream, element: CompiledElementSpec, frame: FrameSpec) -> None:
200
+ """Log the bodies, the rods, the trails, the outline, and the states of an element at one frame.
201
+
202
+ Args:
203
+ recording:
204
+ The Rerun recording.
205
+
206
+ element:
207
+ The compiled element, with its path and the dotted names of its variables.
208
+
209
+ frame:
210
+ The frame.
211
+
212
+ Raises:
213
+ ValidationError:
214
+ The positions are not pairs of coordinates.
215
+ """
216
+ path = element.path
217
+ values = self._values_of(element, frame.value)
218
+ bodies = self._bodies(values)
219
+ share = BaseVisual._radius_of(self._scale(bodies, values), len(bodies))
220
+ radius = share if self.radius is None else float(self.radius)
221
+ self._log_static(recording, path, values, (bodies.shape[1], radius))
222
+ recording.log(f'{path}/bodies', self._points(bodies, radius, _BODY_COLOR))
223
+ if self.rods:
224
+ recording.log(
225
+ f'{path}/rods',
226
+ self._strips([self._chain(bodies)], share * _ROD_SHARE, _ROD_COLOR),
227
+ )
228
+ self._log_trail(recording, path, bodies, share * _TRAIL_SHARE)
229
+ for state, name in element.states.items():
230
+ BaseVisual._log_scalars(recording, f'{path}/{state}', frame.value(name))
231
+
232
+ def _views(self, element: CompiledElementSpec | CompiledAgentsSpec, problem: BaseProblemSpec) -> list[rrb.View]:
233
+ """Return a 2D view of the bodies that covers the drawing, and a time series view of the states.
234
+
235
+ Args:
236
+ element:
237
+ The compiled element, with its path and the dotted names of its variables.
238
+
239
+ problem:
240
+ The compiled problem the element belongs to.
241
+
242
+ Returns:
243
+ views:
244
+ A 2D spatial view with the element path as origin, bounded by the rods at full length around the
245
+ pivot or by the outline, and prepared to the drawing otherwise, and a time series view of the states.
246
+ """
247
+ if not isinstance(element, CompiledElementSpec):
248
+ return []
249
+
250
+ def read(name: str) -> object:
251
+ layout, vector = (
252
+ (problem.states, problem.initial_state)
253
+ if problem.states.has(name)
254
+ else (problem.parameters, problem.initial_parameters)
255
+ )
256
+ return layout.read(vector, name)
257
+
258
+ values = self._values_of(element, read)
259
+ bodies = self._bodies(values)
260
+ path = element.path
261
+ contents = [f'+ {path}/{state}/**' for state in element.states]
262
+ series = rrb.TimeSeriesView(origin=path, contents=contents, name=f'{path} states')
263
+ if bodies.shape[1] == _SPACE:
264
+ return [rrb.Spatial3DView(origin=path, name=path), series]
265
+ chain = self._chain(bodies)
266
+ strips, marks = self._static(values, PAIR)
267
+ bounds = None
268
+ if self.rods and self.pivot is not None:
269
+ half = self._scale(bodies, values) / 2
270
+ bounds = self._bounds_of(np.vstack([chain[0] - half, chain[0] + half]))
271
+ elif strips:
272
+ bounds = self._bounds_of(np.vstack([chain, *strips, marks]))
273
+ return [rrb.Spatial2DView(origin=path, name=path, visual_bounds=bounds), series]
274
+
275
+ @staticmethod
276
+ def _strips(
277
+ strips: Sequence[npt.NDArray[np.float64]],
278
+ radius: float | None,
279
+ colors: Colors,
280
+ ) -> rr.LineStrips2D | rr.LineStrips3D:
281
+ """Return the line strips archetype of the dimension of some polylines."""
282
+ if strips and strips[0].shape[-1] == _SPACE:
283
+ return rr.LineStrips3D(list(strips), radii=radius, colors=colors)
284
+ return rr.LineStrips2D([BodiesVisual._shown(strip) for strip in strips], radii=radius, colors=colors)
285
+
286
+ @staticmethod
287
+ def _values_of(element: CompiledElementSpec, read: Callable[[str], object]) -> dict[str, object]:
288
+ """Return the parameters and states of an element by their short names, read by dotted name."""
289
+ names = {**element.parameters, **element.states}
290
+ return {name: read(dotted) for name, dotted in names.items()}
291
+
292
+ @staticmethod
293
+ def _fading_segments(
294
+ paths: Sequence[npt.NDArray[np.float64]],
295
+ ) -> tuple[list[npt.NDArray[np.float64]], list[tuple[int, int, int, int]]]:
296
+ """Return the segments of paths and their colors, more transparent for older segments."""
297
+ segments: list[npt.NDArray[np.float64]] = []
298
+ colors: list[tuple[int, int, int, int]] = []
299
+ for path in paths:
300
+ count = len(path) - 1
301
+ for index in range(count):
302
+ segments.append(path[index : index + 2])
303
+ alpha = round(_FAINTEST + (255 - _FAINTEST) * (index + 1) / count)
304
+ colors.append((*_TRAIL_COLOR, alpha))
305
+ return segments, colors
306
+
307
+ @staticmethod
308
+ def _bounds_of(points: npt.NDArray[np.float64]) -> rrb.VisualBounds2D | None:
309
+ """Return 2D view bounds around points with a margin, in logged coordinates, or `None` for one point."""
310
+ low, high = points.min(axis=0), points.max(axis=0)
311
+ extent = float((high - low).max())
312
+ if extent <= 0:
313
+ return None
314
+ center, half = (low + high) / 2, (1 + MARGIN) * extent / 2
315
+ return rrb.VisualBounds2D(
316
+ x_range=(center[0] - half, center[0] + half),
317
+ y_range=(-(center[1] + half), -(center[1] - half)),
318
+ )
319
+
320
+ @staticmethod
321
+ def _shown(points: npt.NDArray[np.float64]) -> npt.NDArray[np.float64]:
322
+ """Return points as logged: with the vertical axis up in two dimensions, unchanged in three."""
323
+ return points * _UPWARD if points.shape[-1] == PAIR else points
324
+
325
+ @staticmethod
326
+ def _points(
327
+ points: npt.NDArray[np.float64],
328
+ radius: float,
329
+ colors: Colors,
330
+ ) -> rr.Points2D | rr.Points3D:
331
+ """Return the points archetype of the dimension of some points."""
332
+ if points.shape[-1] == PAIR:
333
+ return rr.Points2D(BodiesVisual._shown(points), radii=radius, colors=colors)
334
+ return rr.Points3D(points, radii=radius, colors=colors)