scikit-complexity 0.2.0__py3-none-any.whl

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  1. scikit_complexity-0.2.0.dist-info/METADATA +317 -0
  2. scikit_complexity-0.2.0.dist-info/RECORD +1748 -0
  3. scikit_complexity-0.2.0.dist-info/WHEEL +4 -0
  4. scikit_complexity-0.2.0.dist-info/entry_points.txt +4 -0
  5. scikit_complexity-0.2.0.dist-info/licenses/LICENSE +21 -0
  6. skcomplex/__init__.py +1 -0
  7. skcomplex/analysis/__init__.py +101 -0
  8. skcomplex/analysis/_alignment.py +263 -0
  9. skcomplex/analysis/_automata.py +658 -0
  10. skcomplex/analysis/_base.py +841 -0
  11. skcomplex/analysis/_clusters.py +298 -0
  12. skcomplex/analysis/_coarse_grain.py +183 -0
  13. skcomplex/analysis/_collapse.py +318 -0
  14. skcomplex/analysis/_complexity.py +129 -0
  15. skcomplex/analysis/_computational_mechanics.py +220 -0
  16. skcomplex/analysis/_correlation.py +364 -0
  17. skcomplex/analysis/_defects.py +111 -0
  18. skcomplex/analysis/_discovery.py +101 -0
  19. skcomplex/analysis/_displacement.py +135 -0
  20. skcomplex/analysis/_distribution.py +327 -0
  21. skcomplex/analysis/_domains.py +220 -0
  22. skcomplex/analysis/_embedding.py +235 -0
  23. skcomplex/analysis/_emergence.py +503 -0
  24. skcomplex/analysis/_entropy.py +425 -0
  25. skcomplex/analysis/_ergodicity.py +228 -0
  26. skcomplex/analysis/_events.py +301 -0
  27. skcomplex/analysis/_fit.py +368 -0
  28. skcomplex/analysis/_groups.py +205 -0
  29. skcomplex/analysis/_information.py +488 -0
  30. skcomplex/analysis/_invariants.py +409 -0
  31. skcomplex/analysis/_irreversibility.py +421 -0
  32. skcomplex/analysis/_kramers_moyal.py +104 -0
  33. skcomplex/analysis/_large_deviations.py +378 -0
  34. skcomplex/analysis/_linearization.py +231 -0
  35. skcomplex/analysis/_local_information.py +166 -0
  36. skcomplex/analysis/_loops.py +394 -0
  37. skcomplex/analysis/_lyapunov.py +342 -0
  38. skcomplex/analysis/_markov.py +303 -0
  39. skcomplex/analysis/_mode_decomposition.py +209 -0
  40. skcomplex/analysis/_motifs.py +239 -0
  41. skcomplex/analysis/_neighbors.py +303 -0
  42. skcomplex/analysis/_networks.py +286 -0
  43. skcomplex/analysis/_operator.py +312 -0
  44. skcomplex/analysis/_partial_information.py +118 -0
  45. skcomplex/analysis/_passage.py +244 -0
  46. skcomplex/analysis/_recurrence.py +202 -0
  47. skcomplex/analysis/_reservoirs.py +387 -0
  48. skcomplex/analysis/_rolling.py +168 -0
  49. skcomplex/analysis/_scaling.py +370 -0
  50. skcomplex/analysis/_sections.py +225 -0
  51. skcomplex/analysis/_signatures.py +250 -0
  52. skcomplex/analysis/_sparse_identification.py +398 -0
  53. skcomplex/analysis/_spectrum.py +164 -0
  54. skcomplex/analysis/_stability.py +547 -0
  55. skcomplex/analysis/_surrogates.py +127 -0
  56. skcomplex/analysis/_symbolic.py +639 -0
  57. skcomplex/analysis/types.py +43 -0
  58. skcomplex/base.py +159 -0
  59. skcomplex/core/__init__.py +1 -0
  60. skcomplex/core/base.py +150 -0
  61. skcomplex/core/elements/__init__.py +21 -0
  62. skcomplex/core/elements/_base.py +84 -0
  63. skcomplex/core/elements/_compartment.py +52 -0
  64. skcomplex/core/elements/_density.py +52 -0
  65. skcomplex/core/elements/_element.py +80 -0
  66. skcomplex/core/elements/_field.py +192 -0
  67. skcomplex/core/elements/_group.py +241 -0
  68. skcomplex/core/elements/_lattice.py +115 -0
  69. skcomplex/core/elements/_point.py +66 -0
  70. skcomplex/core/interactions/__init__.py +89 -0
  71. skcomplex/core/interactions/_advection.py +134 -0
  72. skcomplex/core/interactions/_base.py +361 -0
  73. skcomplex/core/interactions/_cascade.py +195 -0
  74. skcomplex/core/interactions/_choice.py +320 -0
  75. skcomplex/core/interactions/_conservation.py +164 -0
  76. skcomplex/core/interactions/_coupling.py +741 -0
  77. skcomplex/core/interactions/_crossing.py +136 -0
  78. skcomplex/core/interactions/_diffusion.py +99 -0
  79. skcomplex/core/interactions/_encounter.py +201 -0
  80. skcomplex/core/interactions/_euler_lagrange.py +183 -0
  81. skcomplex/core/interactions/_evolution.py +520 -0
  82. skcomplex/core/interactions/_feedback.py +79 -0
  83. skcomplex/core/interactions/_gradient.py +293 -0
  84. skcomplex/core/interactions/_grouping.py +399 -0
  85. skcomplex/core/interactions/_hamiltonian.py +191 -0
  86. skcomplex/core/interactions/_hyperedge.py +96 -0
  87. skcomplex/core/interactions/_imitation.py +357 -0
  88. skcomplex/core/interactions/_impulse.py +133 -0
  89. skcomplex/core/interactions/_interaction.py +58 -0
  90. skcomplex/core/interactions/_jump.py +201 -0
  91. skcomplex/core/interactions/_life_cycle.py +424 -0
  92. skcomplex/core/interactions/_local_rule.py +134 -0
  93. skcomplex/core/interactions/_map.py +239 -0
  94. skcomplex/core/interactions/_matching.py +701 -0
  95. skcomplex/core/interactions/_movement.py +377 -0
  96. skcomplex/core/interactions/_neighbor.py +88 -0
  97. skcomplex/core/interactions/_optimization.py +206 -0
  98. skcomplex/core/interactions/_pair.py +82 -0
  99. skcomplex/core/interactions/_pair_coupling.py +169 -0
  100. skcomplex/core/interactions/_rate.py +240 -0
  101. skcomplex/core/interactions/_reaction.py +466 -0
  102. skcomplex/core/interactions/_reinforcement.py +226 -0
  103. skcomplex/core/interactions/_relaxation.py +103 -0
  104. skcomplex/core/interactions/_sampling.py +177 -0
  105. skcomplex/core/interactions/_satisfiability.py +145 -0
  106. skcomplex/core/interactions/_sign_adjustment.py +222 -0
  107. skcomplex/core/interactions/_topology.py +215 -0
  108. skcomplex/core/interactions/_training.py +184 -0
  109. skcomplex/core/interactions/_transfer.py +669 -0
  110. skcomplex/core/interactions/_transition.py +427 -0
  111. skcomplex/core/laws/__init__.py +60 -0
  112. skcomplex/core/laws/_base.py +194 -0
  113. skcomplex/core/laws/_bilinear.py +91 -0
  114. skcomplex/core/laws/_boundary.py +59 -0
  115. skcomplex/core/laws/_cascade.py +79 -0
  116. skcomplex/core/laws/_crossing.py +87 -0
  117. skcomplex/core/laws/_dissipator.py +79 -0
  118. skcomplex/core/laws/_drive.py +56 -0
  119. skcomplex/core/laws/_emission.py +81 -0
  120. skcomplex/core/laws/_encounter.py +96 -0
  121. skcomplex/core/laws/_equation.py +105 -0
  122. skcomplex/core/laws/_extremal.py +94 -0
  123. skcomplex/core/laws/_flux.py +108 -0
  124. skcomplex/core/laws/_fractional_noise.py +65 -0
  125. skcomplex/core/laws/_generator.py +66 -0
  126. skcomplex/core/laws/_gradient_step.py +89 -0
  127. skcomplex/core/laws/_jump.py +137 -0
  128. skcomplex/core/laws/_local_rule.py +92 -0
  129. skcomplex/core/laws/_match.py +321 -0
  130. skcomplex/core/laws/_noise.py +125 -0
  131. skcomplex/core/laws/_rate.py +82 -0
  132. skcomplex/core/laws/_rule.py +82 -0
  133. skcomplex/core/laws/_sample.py +65 -0
  134. skcomplex/core/laws/_transfer.py +165 -0
  135. skcomplex/core/laws/_transition.py +77 -0
  136. skcomplex/core/laws/_update.py +121 -0
  137. skcomplex/core/laws/utils/__init__.py +142 -0
  138. skcomplex/core/laws/utils/_agents.py +127 -0
  139. skcomplex/core/laws/utils/_components.py +63 -0
  140. skcomplex/core/laws/utils/_conditions.py +198 -0
  141. skcomplex/core/laws/utils/_contractions.py +74 -0
  142. skcomplex/core/laws/utils/_delays.py +170 -0
  143. skcomplex/core/laws/utils/_history.py +167 -0
  144. skcomplex/core/laws/utils/_local_operators.py +68 -0
  145. skcomplex/core/laws/utils/_lookups.py +40 -0
  146. skcomplex/core/laws/utils/_moments.py +122 -0
  147. skcomplex/core/laws/utils/_operators.py +237 -0
  148. skcomplex/core/laws/utils/_phase.py +126 -0
  149. skcomplex/core/laws/utils/_pointwise.py +160 -0
  150. skcomplex/core/laws/utils/_reductions.py +942 -0
  151. skcomplex/core/laws/utils/_signals.py +214 -0
  152. skcomplex/core/laws/utils/_tables.py +4 -0
  153. skcomplex/core/laws/utils/_tensors.py +235 -0
  154. skcomplex/core/spaces/__init__.py +52 -0
  155. skcomplex/core/spaces/_adjacency.py +34 -0
  156. skcomplex/core/spaces/_base.py +218 -0
  157. skcomplex/core/spaces/_box.py +41 -0
  158. skcomplex/core/spaces/_cayley.py +352 -0
  159. skcomplex/core/spaces/_cone.py +65 -0
  160. skcomplex/core/spaces/_continuous.py +93 -0
  161. skcomplex/core/spaces/_continuous_time.py +27 -0
  162. skcomplex/core/spaces/_discrete_time.py +53 -0
  163. skcomplex/core/spaces/_generator.py +51 -0
  164. skcomplex/core/spaces/_lattice.py +194 -0
  165. skcomplex/core/spaces/_lattice_neighborhood.py +50 -0
  166. skcomplex/core/spaces/_memory.py +45 -0
  167. skcomplex/core/spaces/_mesh.py +71 -0
  168. skcomplex/core/spaces/_moore.py +49 -0
  169. skcomplex/core/spaces/_nearest.py +41 -0
  170. skcomplex/core/spaces/_network.py +256 -0
  171. skcomplex/core/spaces/_phase.py +136 -0
  172. skcomplex/core/spaces/_radius.py +40 -0
  173. skcomplex/core/spaces/_static_time.py +34 -0
  174. skcomplex/core/spaces/_triangular.py +37 -0
  175. skcomplex/core/spaces/_von_neumann.py +51 -0
  176. skcomplex/core/specs/__init__.py +25 -0
  177. skcomplex/core/specs/_census_record_spec.py +72 -0
  178. skcomplex/core/specs/_census_spec.py +40 -0
  179. skcomplex/core/specs/_compiled_agents_spec.py +62 -0
  180. skcomplex/core/specs/_compiled_element_spec.py +59 -0
  181. skcomplex/core/specs/_compiled_interaction_spec.py +33 -0
  182. skcomplex/core/specs/_lattice_context_spec.py +40 -0
  183. skcomplex/core/specs/_lattice_state_spec.py +49 -0
  184. skcomplex/core/specs/_node_spec.py +64 -0
  185. skcomplex/core/specs/_operator_view_spec.py +135 -0
  186. skcomplex/core/specs/_scenario_spec.py +45 -0
  187. skcomplex/core/specs/_subsystem_spec.py +24 -0
  188. skcomplex/core/system.py +140 -0
  189. skcomplex/core/types.py +249 -0
  190. skcomplex/engine/__init__.py +5 -0
  191. skcomplex/engine/_utils.py +278 -0
  192. skcomplex/engine/backends/__init__.py +13 -0
  193. skcomplex/engine/backends/_base.py +329 -0
  194. skcomplex/engine/backends/_jax.py +285 -0
  195. skcomplex/engine/backends/_numba.py +601 -0
  196. skcomplex/engine/backends/_numba_components.py +67 -0
  197. skcomplex/engine/backends/_numba_loops.py +163 -0
  198. skcomplex/engine/backends/_numba_neighbours.py +435 -0
  199. skcomplex/engine/backends/_numba_printer.py +1023 -0
  200. skcomplex/engine/backends/_numba_stencils.py +66 -0
  201. skcomplex/engine/backends/_numpy.py +215 -0
  202. skcomplex/engine/compile/__init__.py +27 -0
  203. skcomplex/engine/compile/_base.py +582 -0
  204. skcomplex/engine/compile/_bound_renewal_spec.py +47 -0
  205. skcomplex/engine/compile/_compilation.py +351 -0
  206. skcomplex/engine/compile/_compile.py +100 -0
  207. skcomplex/engine/compile/_complex.py +216 -0
  208. skcomplex/engine/compile/_draw_lowering.py +373 -0
  209. skcomplex/engine/compile/_field_lowering.py +1668 -0
  210. skcomplex/engine/compile/_flows.py +691 -0
  211. skcomplex/engine/compile/_forms.py +48 -0
  212. skcomplex/engine/compile/_laws.py +42 -0
  213. skcomplex/engine/compile/_learning_compiler.py +481 -0
  214. skcomplex/engine/compile/_member_reductions.py +206 -0
  215. skcomplex/engine/compile/_members.py +244 -0
  216. skcomplex/engine/compile/_observables.py +940 -0
  217. skcomplex/engine/compile/_observer.py +185 -0
  218. skcomplex/engine/compile/_pass_compiler.py +1534 -0
  219. skcomplex/engine/compile/_probe.py +78 -0
  220. skcomplex/engine/compile/_renewal_law.py +70 -0
  221. skcomplex/engine/compile/passes/__init__.py +34 -0
  222. skcomplex/engine/compile/passes/_agents.py +111 -0
  223. skcomplex/engine/compile/passes/_agents_problem.py +143 -0
  224. skcomplex/engine/compile/passes/_census.py +808 -0
  225. skcomplex/engine/compile/passes/_check_fractional_noise.py +107 -0
  226. skcomplex/engine/compile/passes/_collect.py +31 -0
  227. skcomplex/engine/compile/passes/_compile_encounters.py +301 -0
  228. skcomplex/engine/compile/passes/_complex.py +198 -0
  229. skcomplex/engine/compile/passes/_conserved_noise.py +224 -0
  230. skcomplex/engine/compile/passes/_core.py +116 -0
  231. skcomplex/engine/compile/passes/_declare_renewals.py +84 -0
  232. skcomplex/engine/compile/passes/_draws.py +29 -0
  233. skcomplex/engine/compile/passes/_encounter_functions.py +60 -0
  234. skcomplex/engine/compile/passes/_encounter_jacobian.py +25 -0
  235. skcomplex/engine/compile/passes/_encounter_problem.py +32 -0
  236. skcomplex/engine/compile/passes/_events.py +204 -0
  237. skcomplex/engine/compile/passes/_expand_flows.py +32 -0
  238. skcomplex/engine/compile/passes/_field_functions.py +647 -0
  239. skcomplex/engine/compile/passes/_field_jacobian.py +38 -0
  240. skcomplex/engine/compile/passes/_field_problem.py +106 -0
  241. skcomplex/engine/compile/passes/_flatten.py +339 -0
  242. skcomplex/engine/compile/passes/_flows_problem.py +29 -0
  243. skcomplex/engine/compile/passes/_form.py +82 -0
  244. skcomplex/engine/compile/passes/_fractional_form.py +172 -0
  245. skcomplex/engine/compile/passes/_fractional_problem.py +91 -0
  246. skcomplex/engine/compile/passes/_functions.py +485 -0
  247. skcomplex/engine/compile/passes/_hilbert_space_error.py +10 -0
  248. skcomplex/engine/compile/passes/_hyperedges.py +598 -0
  249. skcomplex/engine/compile/passes/_jacobian.py +38 -0
  250. skcomplex/engine/compile/passes/_kernels.py +407 -0
  251. skcomplex/engine/compile/passes/_lattices.py +818 -0
  252. skcomplex/engine/compile/passes/_layout.py +667 -0
  253. skcomplex/engine/compile/passes/_lower_fields.py +225 -0
  254. skcomplex/engine/compile/passes/_lower_flows.py +28 -0
  255. skcomplex/engine/compile/passes/_markov.py +329 -0
  256. skcomplex/engine/compile/passes/_mask_requests.py +121 -0
  257. skcomplex/engine/compile/passes/_members.py +30 -0
  258. skcomplex/engine/compile/passes/_noise.py +196 -0
  259. skcomplex/engine/compile/passes/_operator_compiler.py +843 -0
  260. skcomplex/engine/compile/passes/_orders.py +409 -0
  261. skcomplex/engine/compile/passes/_owners.py +90 -0
  262. skcomplex/engine/compile/passes/_particles.py +69 -0
  263. skcomplex/engine/compile/passes/_plan.py +130 -0
  264. skcomplex/engine/compile/passes/_problem.py +802 -0
  265. skcomplex/engine/compile/passes/_reduction_lowering.py +1193 -0
  266. skcomplex/engine/compile/passes/_reductions.py +84 -0
  267. skcomplex/engine/compile/passes/_renewal_problem.py +357 -0
  268. skcomplex/engine/compile/passes/_request_jumps.py +51 -0
  269. skcomplex/engine/compile/passes/_residences.py +140 -0
  270. skcomplex/engine/compile/passes/_rows.py +162 -0
  271. skcomplex/engine/compile/passes/_set_renewals_apart.py +29 -0
  272. skcomplex/engine/compile/passes/_set_rules_apart.py +28 -0
  273. skcomplex/engine/compile/passes/_specs.py +1317 -0
  274. skcomplex/engine/compile/passes/_split_requests.py +44 -0
  275. skcomplex/engine/compile/passes/_topology_functions.py +265 -0
  276. skcomplex/engine/compile/passes/_topology_problem.py +27 -0
  277. skcomplex/engine/compile/passes/_towards.py +66 -0
  278. skcomplex/engine/compile/passes/_unpack_matches.py +29 -0
  279. skcomplex/engine/compile/passes/_unpack_renewals.py +41 -0
  280. skcomplex/engine/problems/__init__.py +61 -0
  281. skcomplex/engine/problems/_base.py +150 -0
  282. skcomplex/engine/problems/_base_problem_spec.py +153 -0
  283. skcomplex/engine/problems/_block_spec.py +48 -0
  284. skcomplex/engine/problems/_born_spec.py +24 -0
  285. skcomplex/engine/problems/_cascade_kernel.py +134 -0
  286. skcomplex/engine/problems/_collision_kernel.py +147 -0
  287. skcomplex/engine/problems/_compiled_delay_spec.py +21 -0
  288. skcomplex/engine/problems/_compiled_request_spec.py +46 -0
  289. skcomplex/engine/problems/_control_problem_spec.py +90 -0
  290. skcomplex/engine/problems/_declarations_spec.py +126 -0
  291. skcomplex/engine/problems/_delayed_state_spec.py +50 -0
  292. skcomplex/engine/problems/_diffusive_limit_spec.py +50 -0
  293. skcomplex/engine/problems/_draw_kernel.py +128 -0
  294. skcomplex/engine/problems/_drive_kernel.py +65 -0
  295. skcomplex/engine/problems/_dynamics_spec.py +28 -0
  296. skcomplex/engine/problems/_edge_row_search.py +78 -0
  297. skcomplex/engine/problems/_edge_search.py +64 -0
  298. skcomplex/engine/problems/_encounter_kernel.py +200 -0
  299. skcomplex/engine/problems/_event_kernel.py +70 -0
  300. skcomplex/engine/problems/_expression_printer.py +410 -0
  301. skcomplex/engine/problems/_extremal_kernel.py +125 -0
  302. skcomplex/engine/problems/_field_operator_kernel.py +105 -0
  303. skcomplex/engine/problems/_finite_volume_kernel.py +423 -0
  304. skcomplex/engine/problems/_flow_term_spec.py +45 -0
  305. skcomplex/engine/problems/_frame_spec.py +105 -0
  306. skcomplex/engine/problems/_jacobian_kernel.py +575 -0
  307. skcomplex/engine/problems/_kernel_spec.py +130 -0
  308. skcomplex/engine/problems/_kinetic_problem_spec.py +23 -0
  309. skcomplex/engine/problems/_law_kernel.py +604 -0
  310. skcomplex/engine/problems/_learning_problem_spec.py +67 -0
  311. skcomplex/engine/problems/_linear_term_spec.py +50 -0
  312. skcomplex/engine/problems/_loop_term_spec.py +44 -0
  313. skcomplex/engine/problems/_lowered_kernels_spec.py +59 -0
  314. skcomplex/engine/problems/_markov_kernel.py +68 -0
  315. skcomplex/engine/problems/_metric_search.py +155 -0
  316. skcomplex/engine/problems/_monte_carlo_kernel.py +213 -0
  317. skcomplex/engine/problems/_neighborhood_kernel.py +594 -0
  318. skcomplex/engine/problems/_noise_term_spec.py +26 -0
  319. skcomplex/engine/problems/_observed_spec.py +22 -0
  320. skcomplex/engine/problems/_operator_kernel.py +102 -0
  321. skcomplex/engine/problems/_operator_lowering.py +323 -0
  322. skcomplex/engine/problems/_operator_problem_spec.py +138 -0
  323. skcomplex/engine/problems/_output_spec.py +78 -0
  324. skcomplex/engine/problems/_pair_search.py +86 -0
  325. skcomplex/engine/problems/_partials_spec.py +27 -0
  326. skcomplex/engine/problems/_partition_spec.py +39 -0
  327. skcomplex/engine/problems/_printed_spec.py +24 -0
  328. skcomplex/engine/problems/_problem_functions_spec.py +102 -0
  329. skcomplex/engine/problems/_problem_spec.py +365 -0
  330. skcomplex/engine/problems/_random_stream.py +49 -0
  331. skcomplex/engine/problems/_record_spec.py +22 -0
  332. skcomplex/engine/problems/_recorded_spec.py +21 -0
  333. skcomplex/engine/problems/_reduction_kernel.py +254 -0
  334. skcomplex/engine/problems/_reduction_schedule_spec.py +97 -0
  335. skcomplex/engine/problems/_reference_spec.py +114 -0
  336. skcomplex/engine/problems/_relation_spec.py +29 -0
  337. skcomplex/engine/problems/_renewal_kernel.py +250 -0
  338. skcomplex/engine/problems/_request_spec.py +27 -0
  339. skcomplex/engine/problems/_rule_kernel.py +227 -0
  340. skcomplex/engine/problems/_set_symbol_spec.py +28 -0
  341. skcomplex/engine/problems/_source_loader.py +113 -0
  342. skcomplex/engine/problems/_static_search.py +42 -0
  343. skcomplex/engine/problems/_steps.py +39 -0
  344. skcomplex/engine/problems/_sweep_spec.py +26 -0
  345. skcomplex/engine/problems/_symmetry_spec.py +29 -0
  346. skcomplex/engine/problems/_too_dense.py +8 -0
  347. skcomplex/engine/problems/_topology_kernel.py +589 -0
  348. skcomplex/engine/problems/_transfer_network.py +4 -0
  349. skcomplex/engine/problems/_transfer_network_spec.py +50 -0
  350. skcomplex/engine/problems/_transfer_state_spec.py +68 -0
  351. skcomplex/engine/runtime/__init__.py +22 -0
  352. skcomplex/engine/runtime/_as_fast_as_possible.py +17 -0
  353. skcomplex/engine/runtime/_base.py +137 -0
  354. skcomplex/engine/runtime/_conservation.py +125 -0
  355. skcomplex/engine/runtime/_invariants.py +100 -0
  356. skcomplex/engine/runtime/_real_time.py +55 -0
  357. skcomplex/engine/runtime/_recorder.py +84 -0
  358. skcomplex/engine/runtime/_simulations.py +665 -0
  359. skcomplex/engine/runtime/_trajectories.py +314 -0
  360. skcomplex/engine/solvers/__init__.py +95 -0
  361. skcomplex/engine/solvers/_base.py +372 -0
  362. skcomplex/engine/solvers/_caputo.py +194 -0
  363. skcomplex/engine/solvers/_collocation.py +334 -0
  364. skcomplex/engine/solvers/_convolution.py +155 -0
  365. skcomplex/engine/solvers/_cosimulation.py +400 -0
  366. skcomplex/engine/solvers/_crank_nicolson.py +32 -0
  367. skcomplex/engine/solvers/_defaults.py +34 -0
  368. skcomplex/engine/solvers/_etdrk4.py +86 -0
  369. skcomplex/engine/solvers/_euler_maruyama.py +161 -0
  370. skcomplex/engine/solvers/_event_locator.py +249 -0
  371. skcomplex/engine/solvers/_external.py +94 -0
  372. skcomplex/engine/solvers/_fractional_abm.py +126 -0
  373. skcomplex/engine/solvers/_fractional_euler_maruyama.py +322 -0
  374. skcomplex/engine/solvers/_gillespie.py +135 -0
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  1620. skcomplex/models/social/segregation/_resident_view.py +13 -0
  1621. skcomplex/models/social/segregation/_schelling.py +75 -0
  1622. skcomplex/models/social/spreading/__init__.py +37 -0
  1623. skcomplex/models/social/spreading/_cascades.py +118 -0
  1624. skcomplex/models/social/spreading/_exposure.py +166 -0
  1625. skcomplex/models/social/spreading/_growing_word.py +55 -0
  1626. skcomplex/models/social/spreading/_growing_word_view.py +13 -0
  1627. skcomplex/models/social/spreading/_growth.py +52 -0
  1628. skcomplex/models/social/spreading/_infective.py +55 -0
  1629. skcomplex/models/social/spreading/_listeners.py +41 -0
  1630. skcomplex/models/social/spreading/_participant.py +50 -0
  1631. skcomplex/models/social/spreading/_rumour_contacts.py +81 -0
  1632. skcomplex/models/social/spreading/_rumours.py +57 -0
  1633. skcomplex/models/social/spreading/_simplicial.py +120 -0
  1634. skcomplex/models/social/spreading/_simplicial_infection.py +64 -0
  1635. skcomplex/models/social/spreading/_threshold_activation.py +50 -0
  1636. skcomplex/models/social/spreading/_threshold_node_view.py +13 -0
  1637. skcomplex/models/social/spreading/_writing.py +86 -0
  1638. skcomplex/models/types.py +10 -0
  1639. skcomplex/specs/__init__.py +198 -0
  1640. skcomplex/specs/_accelerated_spec.py +46 -0
  1641. skcomplex/specs/_agent_snapshot_spec.py +34 -0
  1642. skcomplex/specs/_agent_state_spec.py +26 -0
  1643. skcomplex/specs/_arguments_spec.py +60 -0
  1644. skcomplex/specs/_axis_spec.py +59 -0
  1645. skcomplex/specs/_base_record_spec.py +16 -0
  1646. skcomplex/specs/_base_spec.py +73 -0
  1647. skcomplex/specs/_base_structure_spec.py +173 -0
  1648. skcomplex/specs/_batch_matching_spec.py +23 -0
  1649. skcomplex/specs/_breakpoints_spec.py +58 -0
  1650. skcomplex/specs/_call_spec.py +64 -0
  1651. skcomplex/specs/_capacity_rows_spec.py +120 -0
  1652. skcomplex/specs/_cardinality_spec.py +58 -0
  1653. skcomplex/specs/_cascade_record_spec.py +36 -0
  1654. skcomplex/specs/_clamp_spec.py +54 -0
  1655. skcomplex/specs/_clause_spec.py +42 -0
  1656. skcomplex/specs/_compiled_flow_spec.py +20 -0
  1657. skcomplex/specs/_composed_rule_spec.py +33 -0
  1658. skcomplex/specs/_continuous_matching_spec.py +48 -0
  1659. skcomplex/specs/_control_solution_spec.py +54 -0
  1660. skcomplex/specs/_control_spec.py +21 -0
  1661. skcomplex/specs/_covariance_adaptation_spec.py +25 -0
  1662. skcomplex/specs/_dataset_spec.py +85 -0
  1663. skcomplex/specs/_delay_spec.py +27 -0
  1664. skcomplex/specs/_dialect_spec.py +207 -0
  1665. skcomplex/specs/_differential_evolution_spec.py +33 -0
  1666. skcomplex/specs/_direction_spec.py +44 -0
  1667. skcomplex/specs/_draw_spec.py +273 -0
  1668. skcomplex/specs/_entry_spec.py +403 -0
  1669. skcomplex/specs/_event_record_spec.py +37 -0
  1670. skcomplex/specs/_evolution_strategy_spec.py +25 -0
  1671. skcomplex/specs/_extremal_record_spec.py +32 -0
  1672. skcomplex/specs/_fractional_rows_spec.py +33 -0
  1673. skcomplex/specs/_fractional_state_spec.py +30 -0
  1674. skcomplex/specs/_held_reduction_spec.py +29 -0
  1675. skcomplex/specs/_hilbert_spec.py +75 -0
  1676. skcomplex/specs/_hyperedge_reduction_spec.py +38 -0
  1677. skcomplex/specs/_issue_spec.py +52 -0
  1678. skcomplex/specs/_iterative_matching_spec.py +39 -0
  1679. skcomplex/specs/_jump_channels_spec.py +40 -0
  1680. skcomplex/specs/_jump_path_spec.py +29 -0
  1681. skcomplex/specs/_layer_spec.py +47 -0
  1682. skcomplex/specs/_layout_spec.py +158 -0
  1683. skcomplex/specs/_local_operator_spec.py +72 -0
  1684. skcomplex/specs/_lookup_spec.py +33 -0
  1685. skcomplex/specs/_loop_spec.py +17 -0
  1686. skcomplex/specs/_lowered_functions_spec.py +71 -0
  1687. skcomplex/specs/_match_spec.py +37 -0
  1688. skcomplex/specs/_matrix_law_spec.py +31 -0
  1689. skcomplex/specs/_move_spec.py +69 -0
  1690. skcomplex/specs/_neighbor_read_spec.py +83 -0
  1691. skcomplex/specs/_neighbor_reduction_spec.py +39 -0
  1692. skcomplex/specs/_network_rows_spec.py +124 -0
  1693. skcomplex/specs/_network_snapshot_spec.py +61 -0
  1694. skcomplex/specs/_noise_process_spec.py +41 -0
  1695. skcomplex/specs/_objective_spec.py +39 -0
  1696. skcomplex/specs/_observable_spec.py +79 -0
  1697. skcomplex/specs/_operator_spec.py +170 -0
  1698. skcomplex/specs/_orders_spec.py +16 -0
  1699. skcomplex/specs/_outer_totalistic_spec.py +38 -0
  1700. skcomplex/specs/_owners_spec.py +28 -0
  1701. skcomplex/specs/_pair_read_spec.py +38 -0
  1702. skcomplex/specs/_parameter_spec.py +81 -0
  1703. skcomplex/specs/_parameters_spec.py +26 -0
  1704. skcomplex/specs/_particle_swarm_spec.py +33 -0
  1705. skcomplex/specs/_partner_spec.py +98 -0
  1706. skcomplex/specs/_partner_switch_spec.py +39 -0
  1707. skcomplex/specs/_phase_spec.py +61 -0
  1708. skcomplex/specs/_phases_schedule_spec.py +59 -0
  1709. skcomplex/specs/_plan_spec.py +18 -0
  1710. skcomplex/specs/_planned_partition_spec.py +30 -0
  1711. skcomplex/specs/_queue_spec.py +46 -0
  1712. skcomplex/specs/_radius_spec.py +66 -0
  1713. skcomplex/specs/_random_search_spec.py +51 -0
  1714. skcomplex/specs/_read_spec.py +45 -0
  1715. skcomplex/specs/_reduction_spec.py +48 -0
  1716. skcomplex/specs/_renewal_record_spec.py +49 -0
  1717. skcomplex/specs/_requirement_spec.py +32 -0
  1718. skcomplex/specs/_role_spec.py +54 -0
  1719. skcomplex/specs/_run_result_spec.py +52 -0
  1720. skcomplex/specs/_run_state_spec.py +41 -0
  1721. skcomplex/specs/_sampled_draw_spec.py +32 -0
  1722. skcomplex/specs/_sampler_spec.py +57 -0
  1723. skcomplex/specs/_samples_spec.py +29 -0
  1724. skcomplex/specs/_schedule_spec.py +17 -0
  1725. skcomplex/specs/_sector_spec.py +31 -0
  1726. skcomplex/specs/_segment_spec.py +21 -0
  1727. skcomplex/specs/_series_spec.py +29 -0
  1728. skcomplex/specs/_signature_spec.py +55 -0
  1729. skcomplex/specs/_snapshots_spec.py +56 -0
  1730. skcomplex/specs/_stable_matching_spec.py +58 -0
  1731. skcomplex/specs/_state_spec.py +138 -0
  1732. skcomplex/specs/_step_spec.py +39 -0
  1733. skcomplex/specs/_structure_state_spec.py +30 -0
  1734. skcomplex/specs/_support_spec.py +76 -0
  1735. skcomplex/specs/_symmetry_spec.py +59 -0
  1736. skcomplex/specs/_table_spec.py +42 -0
  1737. skcomplex/specs/_table_values_spec.py +36 -0
  1738. skcomplex/specs/_tensor_spec.py +197 -0
  1739. skcomplex/specs/_topology_request_spec.py +97 -0
  1740. skcomplex/specs/_totalistic_spec.py +37 -0
  1741. skcomplex/specs/_unknown_spec.py +22 -0
  1742. skcomplex/specs/_validation_report_spec.py +62 -0
  1743. skcomplex/specs/_variable_spec.py +124 -0
  1744. skcomplex/specs/_visual_spec.py +30 -0
  1745. skcomplex/specs/_weight_spec.py +16 -0
  1746. skcomplex/specs/_wiener_block_spec.py +31 -0
  1747. skcomplex/specs/_wiener_process_spec.py +54 -0
  1748. skcomplex/types.py +140 -0
@@ -0,0 +1,1023 @@
1
+ """Print the kernels and reductions of a problem as the source of fused Numba functions, with its layout slots."""
2
+
3
+ # Author: Georgios Douzas <gdouzas@icloud.com>
4
+ # License: MIT
5
+
6
+ import hashlib
7
+ import re
8
+ from collections.abc import Callable, Mapping, Sequence
9
+
10
+ import numpy as np
11
+ import scipy.sparse
12
+ from sage.all__sagemath_symbolics import Expression
13
+
14
+ from ...core.spaces import ConeNeighborhood, NearestNeighborhood
15
+ from ...errors import ValidationError
16
+ from ...specs import EntrySpec, ReadSpec
17
+ from .._utils import symbols_of
18
+ from ..problems import BasePrinter, ExpressionPrinter, OutputSpec, ReductionScheduleSpec, ReferenceSpec
19
+ from ..problems._edge_row_search import EdgeRowSearch
20
+ from ..problems._edge_search import EdgeSearch
21
+ from ..problems._law_kernel import LawKernel
22
+ from ..problems._metric_search import MetricSearch
23
+ from ..problems._neighborhood_kernel import NeighborhoodKernel
24
+ from ..problems._pair_search import PairSearch
25
+ from ..problems._reduction_kernel import ReductionKernel
26
+ from ..problems._static_search import StaticSearch
27
+ from ..types import ReadKind
28
+ from ._base import _AUTO_MEMBERS
29
+ from ._numba_components import GIANT, LABEL, LARGEST, SIZE
30
+
31
+ INDENT = ' '
32
+ COMPONENT_KINDS = {
33
+ 'component-label': LABEL,
34
+ 'component-size': SIZE,
35
+ 'component-largest': LARGEST,
36
+ 'component-giant': GIANT,
37
+ }
38
+
39
+
40
+ class NumbaPrinter(BasePrinter[ReductionScheduleSpec, Sequence[tuple[str, str, list[LawKernel], bool]]]):
41
+ """Printer of the kernels and reductions of a problem as the source of fused Numba functions.
42
+
43
+ `prepare(reductions)` starts an empty source and prints the function that fuses the reductions, or none for
44
+ `None`, and `run(parts)` prints the kernels of every law kind into the source lines of `code_`. A part is the label
45
+ of the entry function, its mode, `'add'`, `'assign'`, or `'concatenate'`, the kernels, and whether they read the
46
+ reductions. After a run, `functions_` holds the compiled functions the source calls by name, and `layout(entries)`
47
+ returns the array of the starts and rows of the entries it reads.
48
+
49
+ Args:
50
+ parallel:
51
+ Whether member and pair loops over groups of at least 1000 members, and the fused reductions, run in
52
+ parallel threads.
53
+
54
+ Attributes:
55
+ code_:
56
+ The printed source lines.
57
+
58
+ slots_:
59
+ The layout slot of every entry and data array by name.
60
+
61
+ functions_:
62
+ The compiled functions the source calls, by global name.
63
+
64
+ data_:
65
+ The integer data appended to the layout, by name.
66
+
67
+ orders_:
68
+ The orders drawn at every step that gather tables read through, by the name of their data.
69
+ """
70
+
71
+ code_: list[str]
72
+
73
+ def __init__(self, parallel: bool = False) -> None:
74
+ self.parallel = parallel
75
+
76
+ def _prepare(self, context: ReductionScheduleSpec | None) -> None:
77
+ """Start an empty source and print the function that fuses the reductions, unless there are none."""
78
+ self.code_ = []
79
+ self.slots_: dict[str, int] = {}
80
+ self.functions_: dict[str, object] = {}
81
+ self.data_: dict[str, np.ndarray] = {}
82
+ self.orders_: dict[str, np.ndarray] = {}
83
+ if context is not None and context.steps:
84
+ self._reduce_function(context, self.parallel)
85
+
86
+ def _run(self, inputs: Sequence[tuple[str, str, list[LawKernel], bool]] | None) -> None:
87
+ """Print the kernels of every part, each part with its entry function, into the source lines.
88
+
89
+ Args:
90
+ inputs:
91
+ The parts: the label of the entry function, its mode, the kernels, and whether they read reductions.
92
+
93
+ Raises:
94
+ ValidationError:
95
+ No parts are passed.
96
+ """
97
+ if inputs is None:
98
+ error_msg = 'The Numba printer runs on the parts of a problem. Pass them to `run`.'
99
+ raise ValidationError(error_msg)
100
+ for label, mode, kernels, reduced in inputs:
101
+ names = []
102
+ for index, kernel in enumerate(kernels):
103
+ name = f'_{label}{index}_'
104
+ if isinstance(kernel.pairs, EdgeSearch):
105
+ self._edge_kernel(kernel, name, mode)
106
+ elif kernel.pairs is not None:
107
+ self._pair_kernel(kernel, name, self._is_parallel(kernel))
108
+ else:
109
+ self._member_kernel(kernel, name, mode, self._is_parallel(kernel))
110
+ names.append(name)
111
+ size = ' + '.join(self._output_count(kernel) for kernel in kernels) or '0'
112
+ self._entry_function(label, names, mode, size, reduced=reduced)
113
+
114
+ def _is_parallel(self, kernel: LawKernel) -> bool:
115
+ """Check whether a kernel runs in parallel threads: over groups of at least 1000 members."""
116
+ if not self.parallel:
117
+ return False
118
+ rows = [
119
+ reference.entry.rows
120
+ for reference in kernel.references.values()
121
+ if reference.source in {ReadKind.MEMBER, ReadKind.FIRST, ReadKind.SECOND}
122
+ ]
123
+ return max(rows, default=0) >= _AUTO_MEMBERS
124
+
125
+ def _slot(self, entry: EntrySpec) -> int:
126
+ """Return the layout slot of an entry, whose start is `L[2 * slot]` and rows `L[2 * slot + 1]`.
127
+
128
+ Args:
129
+ entry:
130
+ The entry.
131
+
132
+ Returns:
133
+ slot:
134
+ The slot.
135
+ """
136
+ return self.slots_.setdefault(entry.name, len(self.slots_))
137
+
138
+ def _data_slot(self, name: str, values: np.ndarray) -> int:
139
+ """Return the layout slot of integer data appended to the layout, whose offset is `L[2 * slot]`.
140
+
141
+ Args:
142
+ name:
143
+ The name of the data, unique in the source.
144
+
145
+ values:
146
+ The integers.
147
+
148
+ Returns:
149
+ slot:
150
+ The slot.
151
+ """
152
+ self.data_[name] = np.asarray(values, dtype=np.int64)
153
+ return self.slots_.setdefault(name, len(self.slots_))
154
+
155
+ def layout(self, entries: Mapping[str, EntrySpec]) -> np.ndarray:
156
+ """Return the layout array of starts and rows of every slot, followed by the data of the data slots.
157
+
158
+ Args:
159
+ entries:
160
+ Every entry by name.
161
+
162
+ Returns:
163
+ layout:
164
+ The layout array.
165
+ """
166
+ layout = np.zeros(2 * len(self.slots_), dtype=np.int64)
167
+ offset = layout.size
168
+ for name, slot in self.slots_.items():
169
+ if name in self.data_:
170
+ layout[2 * slot], layout[2 * slot + 1] = offset, self.data_[name].size
171
+ offset += self.data_[name].size
172
+ else:
173
+ layout[2 * slot], layout[2 * slot + 1] = entries[name].start, entries[name].rows
174
+ return np.concatenate([layout, *(self.data_[name] for name in self.slots_ if name in self.data_)])
175
+
176
+ def _function_name(self, function: object) -> str:
177
+ """Return the global name of a compiled function called from the generated source.
178
+
179
+ Args:
180
+ function:
181
+ The Numba-compiled function.
182
+
183
+ Returns:
184
+ name:
185
+ The global name.
186
+ """
187
+ for name, known in self.functions_.items():
188
+ if known is function:
189
+ return name
190
+ name = f'_function{len(self.functions_)}_'
191
+ self.functions_[name] = function
192
+ return name
193
+
194
+ @staticmethod
195
+ def _vector(reference: ReferenceSpec) -> str:
196
+ """Return the name of the vector that holds a reference."""
197
+ return 'x' if reference.is_state else 'p'
198
+
199
+ @staticmethod
200
+ def _is_shared(reference: ReferenceSpec) -> bool:
201
+ """Check whether a reference holds one value for every evaluation index, a single element or a reduction."""
202
+ return reference.source is ReadKind.SINGLE or (
203
+ reference.source is ReadKind.REDUCED and reference.entry.members is None
204
+ )
205
+
206
+ @staticmethod
207
+ def _hoist_layout(lines: list[str]) -> list[str]:
208
+ """Return function lines with every layout lookup `_L<k>_` read once after the signature."""
209
+ used = sorted({int(index) for line in lines for index in re.findall(r'_L(\d+)_', line)})
210
+ reads = [f'{INDENT}_L{index}_ = L[{index}]' for index in used]
211
+ return [*lines[:2], *reads, *lines[2:]]
212
+
213
+ def _index(self, reference: ReferenceSpec, member: str | None) -> str:
214
+ """Return the flat index of a reference for a member variable, or for a single element."""
215
+ start = f'_L{2 * self._slot(reference.entry)}_'
216
+ if member is None:
217
+ return f'{start} + {reference.column}'
218
+ return f'{start} + {member} * {reference.entry.columns} + {reference.column}'
219
+
220
+ @staticmethod
221
+ def _printed(printer: ExpressionPrinter, expressions: list[Expression]) -> tuple[list[tuple[str, str]], list[str]]:
222
+ """Return the assignments of the repeated subexpressions and the codes of expressions printed by a printer.
223
+
224
+ Args:
225
+ printer:
226
+ The prepared printer of code, not of a compiled function.
227
+
228
+ expressions:
229
+ The expressions.
230
+
231
+ Returns:
232
+ printed:
233
+ The assignments and the code of every expression.
234
+
235
+ Raises:
236
+ TypeError:
237
+ The printer keeps a compiled function instead of code.
238
+ """
239
+ printed = printer.run(expressions).code_
240
+ if not isinstance(printed, tuple):
241
+ error_msg = f'The printer keeps assignments and codes, not a {type(printed).__name__}.'
242
+ raise TypeError(error_msg)
243
+ assignments, codes = printed
244
+ return assignments, codes
245
+
246
+ @staticmethod
247
+ def _target_of(output: OutputSpec) -> ReferenceSpec:
248
+ """Return the target of an output a kernel writes.
249
+
250
+ Args:
251
+ output:
252
+ The output.
253
+
254
+ Returns:
255
+ target:
256
+ The target reference.
257
+
258
+ Raises:
259
+ ValidationError:
260
+ The output has no target.
261
+ """
262
+ if output.target is None:
263
+ error_msg = 'A kernel output that the Numba printer writes needs a target.'
264
+ raise ValidationError(error_msg)
265
+ return output.target
266
+
267
+ @staticmethod
268
+ def _pair_search_of(kernel: LawKernel) -> PairSearch:
269
+ """Return the pair search of a pair kernel.
270
+
271
+ Args:
272
+ kernel:
273
+ The pair kernel.
274
+
275
+ Returns:
276
+ search:
277
+ The pair search.
278
+
279
+ Raises:
280
+ TypeError:
281
+ The kernel holds no pair search.
282
+ """
283
+ if not isinstance(kernel.pairs, PairSearch):
284
+ error_msg = f'A pair kernel holds a pair search, not a {type(kernel.pairs).__name__}.'
285
+ raise TypeError(error_msg)
286
+ return kernel.pairs
287
+
288
+ @staticmethod
289
+ def _by_end(
290
+ outputs: Sequence[tuple[int, OutputSpec]],
291
+ ) -> tuple[list[tuple[int, OutputSpec]], list[tuple[int, OutputSpec]]]:
292
+ """Return the outputs that target the first members of pairs and those that target the second members.
293
+
294
+ Args:
295
+ outputs:
296
+ The outputs, with their indices.
297
+
298
+ Returns:
299
+ ends:
300
+ The outputs of the first members and of the second members.
301
+ """
302
+ firsts = [item for item in outputs if NumbaPrinter._target_of(item[1]).source is ReadKind.FIRST]
303
+ seconds = [item for item in outputs if NumbaPrinter._target_of(item[1]).source is ReadKind.SECOND]
304
+ return firsts, seconds
305
+
306
+ def _emit_values(
307
+ self,
308
+ outputs: Sequence[OutputSpec],
309
+ read: Callable[[Expression], str],
310
+ depth: int,
311
+ ) -> tuple[list[str], list[str]]:
312
+ """Return the lines that read symbols and compute outputs, and the code of every output value."""
313
+ pad = INDENT * depth
314
+ expressions = [output.expression for output in outputs if output.expression is not None]
315
+ arguments = [argument for output in outputs if output.expression is None for argument in output.arguments or ()]
316
+ symbols = sorted(symbols_of(expressions + arguments), key=str)
317
+ reads = [(str(item), read(item)) for item in symbols if str(item) != 't']
318
+ lines = [f'{pad}{name} = {code}' for name, code in reads if name != code]
319
+ assignments, codes = self._printed(ExpressionPrinter('scalar').check().prepare(), [*expressions, *arguments])
320
+ lines += [f'{pad}{name} = {code}' for name, code in assignments]
321
+ expression_codes, argument_codes = iter(codes[: len(expressions)]), iter(codes[len(expressions) :])
322
+ values: list[str] = []
323
+ calls: dict[tuple[int, tuple[str, ...]], str] = {}
324
+ for output in outputs:
325
+ if output.expression is not None:
326
+ values.append(next(expression_codes))
327
+ continue
328
+ printed = [next(argument_codes) for _ in output.arguments or ()]
329
+ key = (id(output.function), tuple(printed))
330
+ if key not in calls:
331
+ calls[key] = f'_call{len(calls)}_'
332
+ call_arguments = ', '.join(['t', *printed])
333
+ lines.append(f'{pad}{calls[key]} = {self._function_name(output.function)}({call_arguments})')
334
+ values.append(calls[key] if output.components == 1 else f'{calls[key]}[{output.component}]')
335
+ return lines, values
336
+
337
+ def _single_reads(self, kernel: LawKernel, outputs: Sequence[OutputSpec]) -> list[str]:
338
+ """Return the lines that read every single-element symbol of outputs once, before the member loops."""
339
+ expressions = [output.expression for output in outputs if output.expression is not None]
340
+ arguments = [argument for output in outputs for argument in output.arguments or ()]
341
+ symbols = sorted(symbols_of(expressions + arguments), key=str)
342
+ return [
343
+ f'{INDENT}{item} = {NumbaPrinter._vector(reference)}[{self._index(reference, None)}]'
344
+ for item in symbols
345
+ if (reference := kernel.references.get(item)) is not None and NumbaPrinter._is_shared(reference)
346
+ ]
347
+
348
+ def _edge_rows(self, search: EdgeSearch) -> tuple[str, list[str]]:
349
+ """Return the code of the number of edges and the lines that read the ends `_a_` and `_b_` of the edge `_m_`."""
350
+ pad = INDENT * 2
351
+ if search.source is not None and search.target is not None:
352
+ first, second = self._slot(search.source), self._slot(search.target)
353
+ return f'_L{2 * first + 1}_', [
354
+ f'{pad}_a_ = int(p[_L{2 * first}_ + _m_])',
355
+ f'{pad}_b_ = int(p[_L{2 * second}_ + _m_])',
356
+ ]
357
+ digest = hashlib.sha256(search.sources.tobytes() + search.targets.tobytes()).hexdigest()[:16]
358
+ first = self._data_slot(f'__edge_sources_{digest}', search.sources)
359
+ second = self._data_slot(f'__edge_targets_{digest}', search.targets)
360
+ return f'_L{2 * first + 1}_', [f'{pad}_a_ = L[_L{2 * first}_ + _m_]', f'{pad}_b_ = L[_L{2 * second}_ + _m_]']
361
+
362
+ @staticmethod
363
+ def _is_gathered(reference: ReferenceSpec) -> bool:
364
+ """Check whether a reference reads a group through a gather table of members, with no value outside it."""
365
+ return (
366
+ reference.source is ReadKind.NEIGHBOR
367
+ and reference.shifted.sizes is None
368
+ and reference.shifted.ghost is None
369
+ )
370
+
371
+ def _gathered_member(self, reference: ReferenceSpec) -> str:
372
+ """Return the code of the member a gathered reference reads at the row `_m_`, from its table in the layout.
373
+
374
+ A table whose members change during a run holds positions in a parameter entry, which holds the members, and a
375
+ table of the positions in an order drawn at every step reads the member at its position in the order, whose data
376
+ the layout holds after the tables.
377
+ """
378
+ read = reference.shifted
379
+ digest = hashlib.sha256(np.asarray(read.table, dtype=np.int64).tobytes()).hexdigest()[:16]
380
+ slot = self._data_slot(f'__gather_{digest}', read.table)
381
+ row = f'L[_L{2 * slot}_ + _m_]'
382
+ if read.entry is not None:
383
+ row = f'int(p[_L{2 * self._slot(read.entry)}_ + {row}])'
384
+ if read.order is None:
385
+ return row
386
+ name = f'__order_{id(read.order)}'
387
+ self.orders_[name] = read.order
388
+ order = self._data_slot(name, read.order)
389
+ return f'L[_L{2 * order}_ + {row}]'
390
+
391
+ def _output_count(self, kernel: LawKernel) -> str:
392
+ """Return the code of the number of values a member kernel writes, its outputs times its rows."""
393
+ if isinstance(kernel.pairs, EdgeSearch):
394
+ rows, _ = self._edge_rows(kernel.pairs)
395
+ return f'{len(kernel.outputs)} * L[{rows[2:-1]}]'
396
+ if any(NumbaPrinter._is_gathered(reference) for reference in kernel.references.values()):
397
+ return f'{len(kernel.outputs)} * {kernel.rows}'
398
+ entry = next((item.entry for item in kernel.references.values() if item.source is ReadKind.MEMBER), None)
399
+ if entry is None:
400
+ return str(len(kernel.outputs))
401
+ return f'{len(kernel.outputs)} * L[{2 * self._slot(entry) + 1}]'
402
+
403
+ def _pair_block(
404
+ self,
405
+ kernel: LawKernel,
406
+ selected: list[tuple[int, OutputSpec]],
407
+ *,
408
+ first: str,
409
+ second: str,
410
+ second_positions: str,
411
+ depth: int,
412
+ ) -> list[str]:
413
+ """Return the lines that add the outputs of one pair orientation to their accumulators within the cutoff."""
414
+ pairs = self._pair_search_of(kernel)
415
+ pad = INDENT * depth
416
+ lines = []
417
+ for column in range(pairs.first.columns):
418
+ lines.append(f'{pad}_d{column}_ = positions_a[{first}, {column}] - {second_positions}[{second}, {column}]')
419
+ if pairs.period is not None:
420
+ lines.append(f'{pad}_d{column}_ -= PERIOD * np.rint(_d{column}_ / PERIOD)')
421
+ distance = ' + '.join(f'_d{column}_ * _d{column}_' for column in range(pairs.first.columns))
422
+ lines.append(f'{pad}if {distance} <= _cutoff_ * _cutoff_:')
423
+
424
+ def read(item: Expression) -> str:
425
+ reference = kernel.references[item]
426
+ if NumbaPrinter._is_shared(reference):
427
+ return str(item)
428
+ if reference.source is ReadKind.SECOND and reference.is_state and reference.entry == pairs.second:
429
+ return f'positions_a[{first}, {reference.column}] - _d{reference.column}_'
430
+ member = first if reference.source is ReadKind.FIRST else second
431
+ return f'{NumbaPrinter._vector(reference)}[{self._index(reference, member)}]'
432
+
433
+ body, values = self._emit_values([output for _, output in selected], read, depth + 1)
434
+ lines += body
435
+ lines += [
436
+ f'{INDENT * (depth + 1)}_acc{index}_ += {value}' for (index, _), value in zip(selected, values, strict=True)
437
+ ]
438
+ return lines
439
+
440
+ def _pair_loop(self, kernel: LawKernel, outputs: list[tuple[int, OutputSpec]], loop: str, same: bool) -> list[str]:
441
+ """Return the lines of one loop over members and their neighbours that accumulates pair outputs.
442
+
443
+ The loop over `_a_` runs over the first members and computes the outputs of first members with `first=_a_` and
444
+ `second=_n_`. The outputs of second members are computed with `first=_n_` and `second` the loop member, either
445
+ in the same loop for pairs inside one group or in a loop over `_b_` for two groups.
446
+ """
447
+ cells = 'a' if same or loop == '_b_' else 'b'
448
+ own = 'a' if loop == '_a_' else 'b'
449
+ second_positions = 'positions_a' if same else 'positions_b'
450
+ pairs = self._pair_search_of(kernel)
451
+ n_dim = pairs.first.columns
452
+ lines = [f'{INDENT}for _i_ in prange(rows_{loop}):', f'{INDENT * 2}{loop} = order_{own}[_i_]']
453
+ lines += [f'{INDENT * 2}_acc{index}_ = 0.0' for index, _ in outputs]
454
+ for dimension in range(n_dim):
455
+ value = f'positions_{own}[{loop}, {dimension}]'
456
+ lines.append(f'{INDENT * 2}_c{dimension}_ = _cell_coordinate({value}, {dimension}, shape_{cells}, _box_)')
457
+ depth = 2
458
+ for dimension in range(n_dim):
459
+ pad = INDENT * depth
460
+ counts = f'shape_{cells}[0][{dimension}]'
461
+ lines.append(f'{pad}for _o{dimension}_ in range(-1, 2):')
462
+ if pairs.period is not None:
463
+ lines += [
464
+ (
465
+ f'{pad}{INDENT}if (_o{dimension}_ == -1 and {counts} < 3) or '
466
+ f'(_o{dimension}_ == 1 and {counts} < 2):'
467
+ ),
468
+ f'{pad}{INDENT * 2}continue',
469
+ f'{pad}{INDENT}_g{dimension}_ = (_c{dimension}_ + _o{dimension}_) % {counts}',
470
+ ]
471
+ else:
472
+ lines += [
473
+ f'{pad}{INDENT}_g{dimension}_ = _c{dimension}_ + _o{dimension}_',
474
+ f'{pad}{INDENT}if _g{dimension}_ < 0 or _g{dimension}_ >= {counts}:',
475
+ f'{pad}{INDENT * 2}continue',
476
+ ]
477
+ depth += 1
478
+ pad = INDENT * depth
479
+ flat = ' + '.join(f'_g{dimension}_ * strides_{cells}[{dimension}]' for dimension in range(n_dim))
480
+ lines += [
481
+ f'{pad}_cell_ = {flat}',
482
+ f'{pad}for _k_ in range(starts_{cells}[_cell_], starts_{cells}[_cell_ + 1]):',
483
+ f'{pad}{INDENT}_n_ = order_{cells}[_k_]',
484
+ ]
485
+ base = depth + 1
486
+ if same:
487
+ lines += [f'{INDENT * base}if _n_ == _a_:', f'{INDENT * (base + 1)}continue']
488
+ firsts, seconds = self._by_end(outputs)
489
+ for selected, first, second, condition in ((firsts, '_a_', '_n_', '>'), (seconds, '_n_', loop, '<')):
490
+ if not selected:
491
+ continue
492
+ depth = base
493
+ if same:
494
+ lines.append(f'{INDENT * base}if _n_ {condition} _a_:')
495
+ depth = base + 1
496
+ lines += self._pair_block(
497
+ kernel,
498
+ selected,
499
+ first=first,
500
+ second=second,
501
+ second_positions=second_positions,
502
+ depth=depth,
503
+ )
504
+ lines += [
505
+ f'{INDENT * 2}out[{self._index(self._target_of(output), loop)}] += _acc{index}_'
506
+ for index, output in outputs
507
+ ]
508
+ return lines
509
+
510
+ @staticmethod
511
+ def _written(output: OutputSpec, index: str, value: str, mode: str) -> str:
512
+ """Return the line that adds or assigns the value of an output, or adds the change of a combined output."""
513
+ if mode == 'add':
514
+ return f'{INDENT * 2}out[{index}] += {value}'
515
+ if output.combined:
516
+ return f'{INDENT * 2}out[{index}] += ({value}) - x[{index}]'
517
+ return f'{INDENT * 2}out[{index}] = {value}'
518
+
519
+ def _reduced(self, output: OutputSpec, index: str, value: str) -> str:
520
+ """Return the line that adds the share of the row `_m_` of an output that reduces over rows to its member."""
521
+ counts = np.asarray(output.counts, dtype=np.int64)
522
+ digest = hashlib.sha256(counts.tobytes()).hexdigest()[:16]
523
+ count = f'L[_L{2 * self._data_slot(f"__counts_{digest}", counts)}_ + _m_]'
524
+ if output.reduce == 'sum':
525
+ return f'{INDENT * 2}out[{index}] += ({value}) - x[{index}] / {count}'
526
+ return f'{INDENT * 2}out[{index}] += (({value}) - x[{index}]) / {count}'
527
+
528
+ def _member_written(self, output: OutputSpec, value: str, mode: str) -> str:
529
+ """Return the line that writes the value of an output of a member kernel for the row `_m_`."""
530
+ target = self._target_of(output)
531
+ member = '_m_' if target.source is ReadKind.MEMBER else None
532
+ member = self._gathered_member(target) if NumbaPrinter._is_gathered(target) else member
533
+ if output.reduce is not None:
534
+ return self._reduced(output, self._index(target, member), value)
535
+ return NumbaPrinter._written(output, self._index(target, member), value, mode)
536
+
537
+ def _member_kernel(self, kernel: LawKernel, name: str, mode: str, parallel: bool) -> None:
538
+ """Add the source of a kernel evaluated once per member, for adding, assigning, or concatenating outputs."""
539
+ member_entry = next(
540
+ (reference.entry for reference in kernel.references.values() if reference.source is ReadKind.MEMBER),
541
+ None,
542
+ )
543
+ gathered = any(NumbaPrinter._is_gathered(reference) for reference in kernel.references.values())
544
+ rows = f'_L{2 * self._slot(member_entry) + 1}_' if member_entry is not None else '1'
545
+ rows = str(kernel.rows) if gathered and member_entry is None else rows
546
+ lines = [
547
+ f'@njit(cache=CACHE, parallel={parallel and not gathered})',
548
+ f'def {name}(t, x, p, L, out, offset):',
549
+ f'{INDENT}rows = {rows}',
550
+ ]
551
+
552
+ lines += self._single_reads(kernel, kernel.outputs)
553
+
554
+ def read_single(item: Expression) -> str:
555
+ reference = kernel.references[item]
556
+ if NumbaPrinter._is_shared(reference):
557
+ return str(item)
558
+ if NumbaPrinter._is_gathered(reference):
559
+ return f'{NumbaPrinter._vector(reference)}[{self._index(reference, self._gathered_member(reference))}]'
560
+ if reference.source is ReadKind.NEIGHBOR:
561
+ read = reference.shifted
562
+ if read.sizes is None or read.steps is None:
563
+ error_msg = f'The neighbour read of {reference.entry.name} is not on a lattice.'
564
+ raise ValidationError(error_msg)
565
+ return (
566
+ f'_neighbor_value({NumbaPrinter._vector(reference)}, _m_, (_L{2 * self._slot(reference.entry)}_, '
567
+ f'{reference.entry.columns}, {reference.column}), ({tuple(read.sizes)}, {tuple(read.steps)}), '
568
+ f'({read.mode}, {float(read.ghost or 0.0)}))'
569
+ )
570
+ return f'{NumbaPrinter._vector(reference)}[{self._index(reference, '_m_')}]'
571
+
572
+ sums = [
573
+ index
574
+ for index, output in enumerate(kernel.outputs)
575
+ if output.target is not None and output.target.source is ReadKind.SINGLE and mode == 'add'
576
+ ]
577
+ lines += [f'{INDENT}_sum{index}_ = 0.0' for index in sums]
578
+ lines.append(f'{INDENT}for _m_ in prange(rows):')
579
+ body, values = self._emit_values(kernel.outputs, read_single, 2)
580
+ lines += body
581
+ for index, (output, value) in enumerate(zip(kernel.outputs, values, strict=True)):
582
+ if mode == 'concatenate':
583
+ lines.append(f'{INDENT * 2}out[offset + {index} * rows + _m_] = {value}')
584
+ elif index in sums:
585
+ lines.append(f'{INDENT * 2}_sum{index}_ += {value}')
586
+ else:
587
+ lines.append(self._member_written(output, value, mode))
588
+ for index in sums:
589
+ target = self._target_of(kernel.outputs[index])
590
+ lines.append(f'{INDENT}out[{self._index(target, None)}] += _sum{index}_')
591
+ lines.append(f'{INDENT}return offset + {len(kernel.outputs)} * rows')
592
+ self.code_ += ['', '', *NumbaPrinter._hoist_layout(lines)]
593
+
594
+ def _pair_kernel(self, kernel: LawKernel, name: str, parallel: bool) -> None:
595
+ """Add the source of a pair kernel that sums pair outputs over neighbours found in the bounded cell grids."""
596
+ pairs = self._pair_search_of(kernel)
597
+ same = pairs.first == pairs.second
598
+ columns = pairs.first.columns
599
+ cutoff = ReferenceSpec(pairs.cutoff, is_state=False, column=0)
600
+ lines = [
601
+ f'@njit(cache=CACHE, parallel={parallel})',
602
+ f'def {name}(t, x, p, L, out, offset):',
603
+ f'{INDENT}_cutoff_ = p[{self._index(cutoff, None)}]',
604
+ f'{INDENT}_box_ = (np.full({columns}, PERIOD), PERIODIC)',
605
+ ]
606
+ for label, entry in (('a', pairs.first), ('b', pairs.second)) if not same else (('a', pairs.first),):
607
+ start, rows = f'_L{2 * self._slot(entry)}_', f'_L{2 * self._slot(entry) + 1}_'
608
+ cells = ', '.join(f'{part}_{label}' for part in ('shape', 'strides', 'starts', 'order'))
609
+ positions = f'x[{start} : {start} + rows__{label}_ * {columns}].reshape((rows__{label}_, {columns}))'
610
+ lines += [
611
+ f'{INDENT}rows__{label}_ = {rows}',
612
+ f'{INDENT}positions_{label} = {positions}',
613
+ f'{INDENT}{cells} = _build_grid(positions_{label}, _cutoff_, _box_)',
614
+ ]
615
+ lines += self._single_reads(kernel, kernel.outputs)
616
+ outputs = list(enumerate(kernel.outputs))
617
+ if same:
618
+ lines += self._pair_loop(kernel, outputs, '_a_', same=True)
619
+ else:
620
+ firsts, seconds = self._by_end(outputs)
621
+ if firsts:
622
+ lines += self._pair_loop(kernel, firsts, '_a_', same=False)
623
+ if seconds:
624
+ lines += self._pair_loop(kernel, seconds, '_b_', same=False)
625
+ lines.append(f'{INDENT}return offset')
626
+ period = pairs.period if pairs.period is not None else 1.0
627
+ text = '\n'.join(NumbaPrinter._hoist_layout(lines)).replace('PERIODIC', str(pairs.period is not None))
628
+ text = text.replace('PERIOD', repr(float(period)))
629
+ self.code_ += ['', '', text]
630
+
631
+ def _edge_kernel(self, kernel: LawKernel, name: str, mode: str) -> None:
632
+ """Add the source of a kernel evaluated once per edge, whose laws read the ends and the edge member."""
633
+ search = kernel.pairs
634
+ assert isinstance(search, EdgeSearch)
635
+ rows, ends = self._edge_rows(search)
636
+ lines = ['@njit(cache=CACHE)', f'def {name}(t, x, p, L, out, offset):', f'{INDENT}rows = {rows}']
637
+ lines += self._single_reads(kernel, kernel.outputs)
638
+ members = {ReadKind.MEMBER: '_m_', ReadKind.FIRST: '_a_', ReadKind.SECOND: '_b_'}
639
+
640
+ def read(item: Expression) -> str:
641
+ reference = kernel.references[item]
642
+ if NumbaPrinter._is_shared(reference):
643
+ return str(item)
644
+ return f'{NumbaPrinter._vector(reference)}[{self._index(reference, members[reference.source])}]'
645
+
646
+ sums = [
647
+ index
648
+ for index, output in enumerate(kernel.outputs)
649
+ if output.target is not None and output.target.source is ReadKind.SINGLE and mode == 'add'
650
+ ]
651
+ lines += [f'{INDENT}_sum{index}_ = 0.0' for index in sums]
652
+ lines += [f'{INDENT}for _m_ in range(rows):', *ends]
653
+ body, values = self._emit_values(kernel.outputs, read, 2)
654
+ lines += body
655
+ for index, (output, value) in enumerate(zip(kernel.outputs, values, strict=True)):
656
+ if mode == 'concatenate':
657
+ lines.append(f'{INDENT * 2}out[offset + {index} * rows + _m_] = {value}')
658
+ elif index in sums:
659
+ lines.append(f'{INDENT * 2}_sum{index}_ += {value}')
660
+ else:
661
+ target = output.target
662
+ assert target is not None
663
+ lines.append(NumbaPrinter._written(output, self._index(target, members[target.source]), value, mode))
664
+ for index in sums:
665
+ target = self._target_of(kernel.outputs[index])
666
+ lines.append(f'{INDENT}out[{self._index(target, None)}] += _sum{index}_')
667
+ lines.append(f'{INDENT}return offset + {len(kernel.outputs)} * rows')
668
+ self.code_ += ['', '', *NumbaPrinter._hoist_layout(lines)]
669
+
670
+ def _entry_function(
671
+ self,
672
+ name: str,
673
+ kernels: list[str],
674
+ mode: str,
675
+ size_expression: str,
676
+ *,
677
+ reduced: bool,
678
+ ) -> None:
679
+ """Add a top-level function that evaluates the reductions and runs kernels into a new output vector."""
680
+ start = {'add': 'np.zeros(x.size)', 'assign': 'x.copy()', 'concatenate': f'np.empty({size_expression})'}[mode]
681
+ lines = [
682
+ '@njit(cache=CACHE)',
683
+ f'def {name}(t, x, p, L):',
684
+ *([f'{INDENT}p = _reduce(t, x, p, L)'] if reduced else []),
685
+ f'{INDENT}out = {start}',
686
+ f'{INDENT}offset = 0',
687
+ ]
688
+ lines += [f'{INDENT}offset = {kernel}(t, x, p, L, out, offset)' for kernel in kernels]
689
+ lines.append(f'{INDENT}return out')
690
+ self.code_ += ['', '', *lines]
691
+
692
+ def _reduction_read(self, name: str, read: ReadSpec, index: int) -> str:
693
+ """Return the line that reads one symbol of a reduction, for the member `_m_` or once for a shared value."""
694
+ vector = 'x' if read.is_state else 'p'
695
+ if read.entry is None:
696
+ array = f'_set{index}_{name}_'
697
+ self.functions_[array] = np.asarray(read.index, dtype=np.int64)
698
+ return f'{name} = {vector}[{array}[_m_]]'
699
+ start = f'_L{2 * self._slot(read.entry)}_'
700
+ if read.per_member:
701
+ return f'{name} = {vector}[{start} + _m_ * {read.stride} + {read.column}]'
702
+ return f'{name} = {vector}[{start} + {read.column}]'
703
+
704
+ def _reduction_rows(self, reduction: ReductionKernel) -> str:
705
+ """Return the code of the number of members a reduction reduces over."""
706
+ if reduction.members is not None:
707
+ return f'_L{2 * self._slot(reduction.members) + 1}_'
708
+ return str(reduction.size)
709
+
710
+ def _reduction_loop(
711
+ self,
712
+ reduction: ReductionKernel,
713
+ index: int,
714
+ body: list[str],
715
+ *,
716
+ parallel: bool,
717
+ ) -> list[str]:
718
+ """Return a loop over the reduced members that reads their symbols and runs a body."""
719
+ reads = [
720
+ f'{INDENT * 2}{self._reduction_read(str(item), read, index)}'
721
+ for item, read in reduction.reads.items()
722
+ if read.per_member
723
+ ]
724
+ condition = reduction.condition if reduction.condition is not None else 1
725
+ printer = ExpressionPrinter('scalar', prefix=f'_r{index}cse').check().prepare()
726
+ assignments, codes = self._printed(printer, [reduction.argument, condition])
727
+ loop = 'prange' if parallel else 'range'
728
+ return [
729
+ f'{INDENT}for _m_ in {loop}(_n{index}_):',
730
+ *reads,
731
+ *(f'{INDENT * 2}{name} = {code}' for name, code in assignments),
732
+ f'{INDENT * 2}_a_ = {codes[0]}',
733
+ f'{INDENT * 2}_c_ = {codes[1]}',
734
+ *(f'{INDENT * 2}{line}' for line in body),
735
+ ]
736
+
737
+ def _shaped_weights_lines(self, reduction: ReductionKernel, weights: ReadSpec, index: int, count: str) -> list[str]:
738
+ """Return the lines of a reduction weighted by a shaped parameter, a product with its row-major block."""
739
+ entry = weights.entry if weights.entry is not None else reduction.entry
740
+ readers, size = entry.shape
741
+ vector = 'x' if weights.is_state else 'p'
742
+ start, block = f'_L{2 * self._slot(reduction.entry)}_', f'_L{2 * self._slot(entry)}_'
743
+ cnt = f'_cnt{index}_'
744
+ lines = [f'{INDENT}_values{index}_ = np.empty(_n{index}_)']
745
+ body = [f'_values{index}_[_m_] = _a_ if _c_ else 0.0', count]
746
+ lines += self._reduction_loop(reduction, index, body, parallel=True)
747
+ divisor = f' / {cnt} if {cnt} > 0.0 else 0.0' if reduction.kind == 'mean' else ''
748
+ return [
749
+ *lines,
750
+ f'{INDENT}for _i_ in prange({readers}):',
751
+ f'{INDENT * 2}_s_ = 0.0',
752
+ f'{INDENT * 2}for _k_ in range({size}):',
753
+ f'{INDENT * 3}_s_ += {vector}[{block} + _i_ * {size} + _k_] * _values{index}_[_k_]',
754
+ f'{INDENT * 2}p[{start} + _i_] = _s_{divisor}',
755
+ ]
756
+
757
+ def _log_sum_exp_lines(self, reduction: ReductionKernel, index: int, start: str) -> list[str]:
758
+ """Return the lines of a log-sum-exp reduction, a sum of exponentials shifted by the largest value."""
759
+ acc, cnt, top = f'_acc{index}_', f'_cnt{index}_', f'_top{index}_'
760
+ largest = [
761
+ f'if _c_ and ({cnt} == 0.0 or _a_ > {top}):',
762
+ f'{INDENT}{top} = _a_',
763
+ f'{cnt} += 1.0 if _c_ else 0.0',
764
+ ]
765
+ shifted = [f'{acc} += np.exp(_a_ - {top}) if _c_ else 0.0']
766
+ return [
767
+ f'{INDENT}{top} = 0.0',
768
+ *self._reduction_loop(reduction, index, largest, parallel=False),
769
+ *self._reduction_loop(reduction, index, shifted, parallel=True),
770
+ f'{INDENT}p[{start}] = {top} + np.log({acc}) if {cnt} > 0.0 else 0.0',
771
+ ]
772
+
773
+ def _reduction_lines(self, reduction: ReductionKernel, index: int) -> list[str]:
774
+ """Return the lines that compute one reduction and store it in the extended parameter vector."""
775
+ start = f'_L{2 * self._slot(reduction.entry)}_'
776
+ acc, cnt = f'_acc{index}_', f'_cnt{index}_'
777
+ lines = [f'{INDENT}_n{index}_ = {self._reduction_rows(reduction)}']
778
+ lines += [
779
+ f'{INDENT}{self._reduction_read(str(item), read, index)}'
780
+ for item, read in reduction.reads.items()
781
+ if not read.per_member
782
+ ]
783
+ lines += [f'{INDENT}{acc} = 0.0', f'{INDENT}{cnt} = 0.0']
784
+ sums = [f'{acc} += _a_ if _c_ else 0.0', f'{cnt} += 1.0 if _c_ else 0.0']
785
+ mean = f'({acc} / {cnt} if {cnt} > 0.0 else 0.0)'
786
+ if isinstance(reduction.weights, ReadSpec):
787
+ return lines + self._shaped_weights_lines(reduction, reduction.weights, index, sums[1])
788
+ if reduction.weights is not None:
789
+ weights = scipy.sparse.csr_array(reduction.weights)
790
+ for part in ('indptr', 'indices', 'data'):
791
+ self.functions_[f'_w{index}_{part}_'] = np.asarray(getattr(weights, part))
792
+ lines.append(f'{INDENT}_values{index}_ = np.empty(_n{index}_)')
793
+ body = [f'_values{index}_[_m_] = _a_ if _c_ else 0.0', sums[1]]
794
+ lines += self._reduction_loop(reduction, index, body, parallel=True)
795
+ divisor = f' / {cnt} if {cnt} > 0.0 else 0.0' if reduction.kind == 'mean' else ''
796
+ lines += [
797
+ f'{INDENT}for _i_ in prange({weights.shape[0]}):',
798
+ f'{INDENT * 2}_s_ = 0.0',
799
+ f'{INDENT * 2}for _k_ in range(_w{index}_indptr_[_i_], _w{index}_indptr_[_i_ + 1]):',
800
+ f'{INDENT * 3}_s_ += _w{index}_data_[_k_] * _values{index}_[_w{index}_indices_[_k_]]',
801
+ f'{INDENT * 2}p[{start} + _i_] = _s_{divisor}',
802
+ ]
803
+ return lines
804
+ if reduction.kind in {'max', 'min'}:
805
+ better = '>' if reduction.kind == 'max' else '<'
806
+ body = [
807
+ f'if _c_ and ({cnt} == 0.0 or _a_ {better} {acc}):',
808
+ f'{INDENT}{acc} = _a_',
809
+ f'{cnt} += 1.0 if _c_ else 0.0',
810
+ ]
811
+ lines += self._reduction_loop(reduction, index, body, parallel=False)
812
+ return [*lines, f'{INDENT}p[{start}] = {acc}']
813
+ if reduction.kind == 'logsumexp':
814
+ return lines + self._log_sum_exp_lines(reduction, index, start)
815
+ lines += self._reduction_loop(reduction, index, sums, parallel=True)
816
+ if reduction.kind == 'var':
817
+ lines.append(f'{INDENT}_mean{index}_ = {mean}')
818
+ lines.append(f'{INDENT}_sq{index}_ = 0.0')
819
+ body = [f'_sq{index}_ += (_a_ - _mean{index}_) ** 2 if _c_ else 0.0']
820
+ lines += self._reduction_loop(reduction, index, body, parallel=True)
821
+ return [*lines, f'{INDENT}p[{start}] = _sq{index}_ / {cnt} if {cnt} > 0.0 else 0.0']
822
+ value = {'sum': acc, 'count': cnt, 'mean': mean}[reduction.kind]
823
+ return [*lines, f'{INDENT}p[{start}] = {value}']
824
+
825
+ def _search_lines(self, reduction: NeighborhoodKernel, index: int) -> list[str]:
826
+ """Return the lines that find the neighbours of every member, as rows `_ip<k>_` and neighbours `_ix<k>_`."""
827
+ search = reduction.search
828
+ if isinstance(search, StaticSearch):
829
+ rows = self._data_slot(f'__neighbours_{index}_indptr', search.indptr)
830
+ neighbours = self._data_slot(f'__neighbours_{index}_indices', search.indices)
831
+ lines = [
832
+ f'{INDENT}_ip{index}_ = L[_L{2 * rows}_ : _L{2 * rows}_ + _L{2 * rows + 1}_]',
833
+ f'{INDENT}_ix{index}_ = L[_L{2 * neighbours}_ : _L{2 * neighbours}_ + _L{2 * neighbours + 1}_]',
834
+ ]
835
+ if search.edges is not None:
836
+ edges = self._data_slot(f'__neighbours_{index}_edges', search.edges)
837
+ lines.append(f'{INDENT}_ie{index}_ = L[_L{2 * edges}_ : _L{2 * edges}_ + _L{2 * edges + 1}_]')
838
+ return lines
839
+ if isinstance(search, EdgeRowSearch):
840
+ starts = ', '.join(f'_L{2 * self._slot(entry)}_' for entry in (search.source, search.target, search.active))
841
+ call = (
842
+ f'_edge_neighbours(p, ({starts}), _L{2 * self._slot(search.source) + 1}_, {search.size}, '
843
+ f'({search.directed}, {search.center}))'
844
+ )
845
+ return [f'{INDENT}_ip{index}_, _ix{index}_, _ie{index}_ = {call}']
846
+ assert isinstance(search, MetricSearch)
847
+ entry = search.positions
848
+ start, columns = f'_L{2 * self._slot(entry)}_', entry.columns
849
+ periods = search.periods if search.periods is not None else (1.0,) * columns
850
+ periodic = search.periods is not None
851
+ lines = [
852
+ (
853
+ f'{INDENT}_pos{index}_ = x[{start} : {start} + {reduction.size} * {columns}]'
854
+ f'.reshape(({reduction.size}, {columns}))'
855
+ ),
856
+ f'{INDENT}_per{index}_ = np.array([{", ".join(repr(float(item)) for item in periods)}])',
857
+ ]
858
+ neighbourhood = search.neighbourhood
859
+ center = bool(neighbourhood.center)
860
+ if isinstance(neighbourhood, NearestNeighborhood):
861
+ call = f'_nearest_neighbours(_pos{index}_, {neighbourhood.k}, _per{index}_, {periodic}, {center})'
862
+ return [*lines, f'{INDENT}_ip{index}_, _ix{index}_ = {call}']
863
+ if not isinstance(neighbourhood, ConeNeighborhood):
864
+ call = f'_radius_neighbours(_pos{index}_, {neighbourhood.radius!r}, _per{index}_, {periodic}, {center})'
865
+ return [*lines, f'{INDENT}_ip{index}_, _ix{index}_ = {call}']
866
+ direction = search.direction
867
+ assert direction is not None
868
+ first = f'_L{2 * self._slot(direction.entry)}_'
869
+ if direction.angle:
870
+ lines += [
871
+ f'{INDENT}_dr{index}_ = np.empty(({reduction.size}, 2))',
872
+ f'{INDENT}for _i_ in range({reduction.size}):',
873
+ f'{INDENT * 2}_dr{index}_[_i_, 0] = math.cos(x[{first} + _i_])',
874
+ f'{INDENT * 2}_dr{index}_[_i_, 1] = math.sin(x[{first} + _i_])',
875
+ ]
876
+ else:
877
+ lines.append(
878
+ f'{INDENT}_dr{index}_ = x[{first} : {first} + {reduction.size} * {columns}].reshape(({reduction.size}, '
879
+ f'{columns}))',
880
+ )
881
+ cosine = repr(float(np.cos(neighbourhood.angle)))
882
+ call = (
883
+ f'_cone_neighbours(_pos{index}_, _dr{index}_, ({neighbourhood.radius!r}, {cosine}), (_per{index}_, '
884
+ f'{periodic}), {center})'
885
+ )
886
+ return [*lines, f'{INDENT}_ip{index}_, _ix{index}_ = {call}']
887
+
888
+ def _pair_read_code(self, reduction: NeighborhoodKernel, item: Expression, index: int) -> str:
889
+ """Return the code of one symbol of a neighbourhood reduction for the reader `_i_` and the neighbour `_j_`."""
890
+ pair = reduction.reads[item]
891
+ read = pair.read
892
+ vector = 'x' if read.is_state else 'p'
893
+ assert read.entry is not None
894
+ start = f'_L{2 * self._slot(read.entry)}_'
895
+ if pair.side == 'shared':
896
+ return f'{vector}[{start} + {read.column}]'
897
+ member = {'reader': '_i_', 'edge': f'_ie{index}_[_e_]', 'pair': '_e_'}.get(pair.side, '_j_')
898
+ if pair.table is not None:
899
+ slot = self._data_slot(f'__neighbours_{index}_{item}', pair.table)
900
+ member = f'L[_L{2 * slot}_ + _j_]'
901
+ value = f'{vector}[{start} + {member} * {read.stride} + {read.column}]'
902
+ if not pair.image:
903
+ return value
904
+ search = reduction.search
905
+ assert isinstance(search, MetricSearch)
906
+ assert search.periods is not None
907
+ period = repr(float(search.periods[read.column]))
908
+ own = f'{vector}[{start} + _i_ * {read.stride} + {read.column}]'
909
+ del index
910
+ return f'{own} - (({own} - {value}) - {period} * np.rint(({own} - {value}) / {period}))'
911
+
912
+ def _component_lines(
913
+ self,
914
+ reduction: NeighborhoodKernel,
915
+ index: int,
916
+ assignments: Sequence[tuple[str, str]],
917
+ active: str,
918
+ ) -> list[str]:
919
+ """Return the lines that collect the active pairs of every member and write the values of their components."""
920
+ sides = {item: reduction.reads[item].side for item in reduction.symbols}
921
+ readers = [item for item in reduction.symbols if sides[item] == 'reader']
922
+ others = [item for item in reduction.symbols if sides[item] in {'other', 'edge', 'pair'}]
923
+ firsts, seconds, count = f'_cf{index}_', f'_cs{index}_', f'_cn{index}_'
924
+ target = f'_L{2 * self._slot(reduction.entry)}_'
925
+ size = reduction.size
926
+ call = f'_component_values({size}, {firsts}, {seconds}, {count}, {COMPONENT_KINDS[reduction.kind]})'
927
+ return [
928
+ f'{INDENT}{firsts} = np.empty(_ip{index}_[{size}], dtype=np.int64)',
929
+ f'{INDENT}{seconds} = np.empty(_ip{index}_[{size}], dtype=np.int64)',
930
+ f'{INDENT}{count} = 0',
931
+ f'{INDENT}for _i_ in range({size}):',
932
+ *(f'{INDENT * 2}{item} = {self._pair_read_code(reduction, item, index)}' for item in readers),
933
+ f'{INDENT * 2}for _e_ in range(_ip{index}_[_i_], _ip{index}_[_i_ + 1]):',
934
+ f'{INDENT * 3}_j_ = _ix{index}_[_e_]',
935
+ *(f'{INDENT * 3}{item} = {self._pair_read_code(reduction, item, index)}' for item in others),
936
+ *(f'{INDENT * 3}{name} = {code}' for name, code in assignments),
937
+ f'{INDENT * 3}if {active} != 0.0:',
938
+ f'{INDENT * 4}{firsts}[{count}] = _i_',
939
+ f'{INDENT * 4}{seconds}[{count}] = _j_',
940
+ f'{INDENT * 4}{count} += 1',
941
+ f'{INDENT}p[{target} : {target} + {size}] = {call}',
942
+ ]
943
+
944
+ def _neighborhood_lines(self, reduction: NeighborhoodKernel, index: int) -> list[str]:
945
+ """Return the lines that compute a neighbourhood reduction of every member into the extended parameters."""
946
+ lines = self._search_lines(reduction, index)
947
+ sides = {item: reduction.reads[item].side for item in reduction.symbols}
948
+ shared = [item for item in reduction.symbols if sides[item] == 'shared']
949
+ readers = [item for item in reduction.symbols if sides[item] == 'reader']
950
+ others = [item for item in reduction.symbols if sides[item] in {'other', 'edge', 'pair'}]
951
+ lines += [f'{INDENT}{item} = {self._pair_read_code(reduction, item, index)}' for item in shared]
952
+ printer = ExpressionPrinter('scalar', prefix=f'_n{index}cse').check().prepare()
953
+ assignments, codes = self._printed(printer, [reduction.argument, reduction.weight])
954
+ kind = reduction.kind
955
+ if kind in COMPONENT_KINDS:
956
+ return lines + self._component_lines(reduction, index, assignments, codes[0])
957
+ acc, weights, found = f'_acc{index}_', f'_ws{index}_', f'_found{index}_'
958
+ if kind == 'argmax':
959
+ accumulate = [
960
+ f'if not {found} or _w_ > {weights}:',
961
+ f'{INDENT}{acc} = _a_',
962
+ f'{INDENT}{weights} = _w_',
963
+ f'{INDENT}{found} = True',
964
+ ]
965
+ value = f'{acc} if {found} else 0.0'
966
+ elif kind in {'max', 'min'}:
967
+ better = '>' if kind == 'max' else '<'
968
+ accumulate = [
969
+ '_v_ = _w_ * _a_',
970
+ f'if not {found} or _v_ {better} {acc}:',
971
+ f'{INDENT}{acc} = _v_',
972
+ f'{INDENT}{found} = True',
973
+ ]
974
+ value = f'{acc} if {found} else 0.0'
975
+ elif kind == 'count':
976
+ accumulate = [f'{acc} += _w_ * (1.0 if _a_ != 0.0 else 0.0)']
977
+ value = acc
978
+ else:
979
+ accumulate = [f'{acc} += _w_ * _a_', f'{weights} += _w_']
980
+ count = f'(_ip{index}_[_i_ + 1] - _ip{index}_[_i_])'
981
+ value = {
982
+ 'sum': acc,
983
+ 'mean': f'{acc} / {count} if {count} > 0 else 0.0',
984
+ 'normalized-mean': f'{acc} / {weights} if {weights} != 0.0 else 0.0',
985
+ }[kind]
986
+ target = f'_L{2 * self._slot(reduction.entry)}_'
987
+ lines += [
988
+ f'{INDENT}for _i_ in prange({reduction.size}):',
989
+ *(f'{INDENT * 2}{item} = {self._pair_read_code(reduction, item, index)}' for item in readers),
990
+ f'{INDENT * 2}{acc} = 0.0',
991
+ f'{INDENT * 2}{weights} = 0.0',
992
+ f'{INDENT * 2}{found} = False',
993
+ f'{INDENT * 2}for _e_ in range(_ip{index}_[_i_], _ip{index}_[_i_ + 1]):',
994
+ f'{INDENT * 3}_j_ = _ix{index}_[_e_]',
995
+ *(f'{INDENT * 3}{item} = {self._pair_read_code(reduction, item, index)}' for item in others),
996
+ *(f'{INDENT * 3}{name} = {code}' for name, code in assignments),
997
+ f'{INDENT * 3}_a_ = {codes[0]}',
998
+ f'{INDENT * 3}_w_ = {codes[1]}',
999
+ *(f'{INDENT * 3}{line}' for line in accumulate),
1000
+ f'{INDENT * 2}p[{target} + _i_] = {value}',
1001
+ ]
1002
+ return lines
1003
+
1004
+ def _reduce_function(self, reductions: ReductionScheduleSpec, parallel: bool) -> None:
1005
+ """Add the function that returns the parameter vector extended with every reduction, in dependency order."""
1006
+ extents = [
1007
+ f'_L{2 * self._slot(item.entry)}_ + _L{2 * self._slot(item.entry) + 1}_ * {item.entry.columns}'
1008
+ for item in reductions.steps
1009
+ ]
1010
+ size = extents[0] if len(extents) == 1 else f'max({", ".join(extents)})'
1011
+ lines = [
1012
+ f'@njit(cache=CACHE, parallel={parallel})',
1013
+ 'def _reduce(t, x, p0, L):',
1014
+ f'{INDENT}p = np.empty({size})',
1015
+ f'{INDENT}p[: p0.size] = p0',
1016
+ ]
1017
+ for index, reduction in enumerate(reductions.steps):
1018
+ if isinstance(reduction, NeighborhoodKernel):
1019
+ lines += self._neighborhood_lines(reduction, index)
1020
+ else:
1021
+ lines += self._reduction_lines(reduction, index)
1022
+ lines.append(f'{INDENT}return p')
1023
+ self.code_ += ['', '', *NumbaPrinter._hoist_layout(lines)]