diff-grok 1.2.0 → 1.3.1

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 (624) hide show
  1. package/README.MD +56 -8
  2. package/dist/index.d.ts +6 -0
  3. package/{index.js → dist/index.js} +1 -0
  4. package/dist/index.js.map +1 -0
  5. package/dist/src/examples/basic-use.d.ts +10 -0
  6. package/dist/src/examples/basic-use.js.map +1 -0
  7. package/dist/src/examples/check-methods.d.ts +1 -0
  8. package/dist/src/examples/check-methods.js.map +1 -0
  9. package/dist/src/examples/corr-probs.d.ts +15 -0
  10. package/{src → dist/src}/examples/corr-probs.js +2 -2
  11. package/dist/src/examples/corr-probs.js.map +1 -0
  12. package/dist/src/examples/cyclic-model.d.ts +6 -0
  13. package/dist/src/examples/cyclic-model.js.map +1 -0
  14. package/dist/src/examples/e5.d.ts +15 -0
  15. package/dist/src/examples/e5.js.map +1 -0
  16. package/dist/src/examples/hires.d.ts +15 -0
  17. package/dist/src/examples/hires.js.map +1 -0
  18. package/dist/src/examples/index.d.ts +22 -0
  19. package/dist/src/examples/index.js.map +1 -0
  20. package/dist/src/examples/model-updates.d.ts +6 -0
  21. package/dist/src/examples/model-updates.js.map +1 -0
  22. package/dist/src/examples/orego.d.ts +15 -0
  23. package/dist/src/examples/orego.js.map +1 -0
  24. package/dist/src/examples/pipeline-use.d.ts +6 -0
  25. package/dist/src/examples/pipeline-use.js.map +1 -0
  26. package/dist/src/examples/pollution.d.ts +15 -0
  27. package/dist/src/examples/pollution.js.map +1 -0
  28. package/{src/examples/print-benchmark.ts → dist/src/examples/print-benchmark.d.ts} +8 -58
  29. package/dist/src/examples/print-benchmark.js.map +1 -0
  30. package/dist/src/examples/robertson.d.ts +15 -0
  31. package/{docs/media → dist/src/examples}/robertson.js +2 -2
  32. package/dist/src/examples/robertson.js.map +1 -0
  33. package/dist/src/examples/scripting.d.ts +1 -0
  34. package/dist/src/examples/scripting.js.map +1 -0
  35. package/dist/src/examples/vdpol.d.ts +15 -0
  36. package/dist/src/examples/vdpol.js.map +1 -0
  37. package/dist/src/latex-export/examples/advanced-to-latex.d.ts +2 -0
  38. package/dist/src/latex-export/examples/advanced-to-latex.js +41 -0
  39. package/dist/src/latex-export/examples/advanced-to-latex.js.map +1 -0
  40. package/dist/src/latex-export/examples/basic-to-latex.d.ts +2 -0
  41. package/dist/src/latex-export/examples/basic-to-latex.js +17 -0
  42. package/dist/src/latex-export/examples/basic-to-latex.js.map +1 -0
  43. package/dist/src/latex-export/examples/bioreactor-to-latex-selective.d.ts +2 -0
  44. package/dist/src/latex-export/examples/bioreactor-to-latex-selective.js +145 -0
  45. package/dist/src/latex-export/examples/bioreactor-to-latex-selective.js.map +1 -0
  46. package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.d.ts +2 -0
  47. package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.js +41 -0
  48. package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.js.map +1 -0
  49. package/dist/src/latex-export/examples/energy-n-control-to-markdown.d.ts +2 -0
  50. package/dist/src/latex-export/examples/energy-n-control-to-markdown.js +58 -0
  51. package/dist/src/latex-export/examples/energy-n-control-to-markdown.js.map +1 -0
  52. package/dist/src/latex-export/examples/extended-to-markdown.d.ts +2 -0
  53. package/dist/src/latex-export/examples/extended-to-markdown.js +37 -0
  54. package/dist/src/latex-export/examples/extended-to-markdown.js.map +1 -0
  55. package/dist/src/latex-export/examples/fermentation-to-latex.d.ts +2 -0
  56. package/dist/src/latex-export/examples/fermentation-to-latex.js +32 -0
  57. package/dist/src/latex-export/examples/fermentation-to-latex.js.map +1 -0
  58. package/dist/src/latex-export/examples/ga-production-to-markdown.d.ts +2 -0
  59. package/dist/src/latex-export/examples/ga-production-to-markdown.js +58 -0
  60. package/dist/src/latex-export/examples/ga-production-to-markdown.js.map +1 -0
  61. package/dist/src/latex-export/examples/nimotuzumab-to-latex.d.ts +2 -0
  62. package/dist/src/latex-export/examples/nimotuzumab-to-latex.js +53 -0
  63. package/dist/src/latex-export/examples/nimotuzumab-to-latex.js.map +1 -0
  64. package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.d.ts +2 -0
  65. package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.js +50 -0
  66. package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.js.map +1 -0
  67. package/dist/src/latex-export/examples/pk-to-markdown.d.ts +2 -0
  68. package/dist/src/latex-export/examples/pk-to-markdown.js +35 -0
  69. package/dist/src/latex-export/examples/pk-to-markdown.js.map +1 -0
  70. package/dist/src/latex-export/examples/pollution-to-latex.d.ts +2 -0
  71. package/dist/src/latex-export/examples/pollution-to-latex.js +141 -0
  72. package/dist/src/latex-export/examples/pollution-to-latex.js.map +1 -0
  73. package/dist/src/latex-export/examples/robertson-to-latex-no-meta.d.ts +2 -0
  74. package/dist/src/latex-export/examples/robertson-to-latex-no-meta.js +25 -0
  75. package/dist/src/latex-export/examples/robertson-to-latex-no-meta.js.map +1 -0
  76. package/dist/src/latex-export/generator/bracket-manager.d.ts +19 -0
  77. package/dist/src/latex-export/generator/bracket-manager.js +58 -0
  78. package/dist/src/latex-export/generator/bracket-manager.js.map +1 -0
  79. package/dist/src/latex-export/generator/document-builder.d.ts +13 -0
  80. package/dist/src/latex-export/generator/document-builder.js +433 -0
  81. package/dist/src/latex-export/generator/document-builder.js.map +1 -0
  82. package/dist/src/latex-export/generator/latex-generator.d.ts +26 -0
  83. package/dist/src/latex-export/generator/latex-generator.js +180 -0
  84. package/dist/src/latex-export/generator/latex-generator.js.map +1 -0
  85. package/dist/src/latex-export/index.d.ts +8 -0
  86. package/dist/src/latex-export/index.js +25 -0
  87. package/dist/src/latex-export/index.js.map +1 -0
  88. package/dist/src/latex-export/output/md-formatter.d.ts +16 -0
  89. package/dist/src/latex-export/output/md-formatter.js +27 -0
  90. package/dist/src/latex-export/output/md-formatter.js.map +1 -0
  91. package/dist/src/latex-export/output/tex-formatter.d.ts +5 -0
  92. package/dist/src/latex-export/output/tex-formatter.js +20 -0
  93. package/dist/src/latex-export/output/tex-formatter.js.map +1 -0
  94. package/dist/src/latex-export/parser/ast-parser.d.ts +7 -0
  95. package/dist/src/latex-export/parser/ast-parser.js +153 -0
  96. package/dist/src/latex-export/parser/ast-parser.js.map +1 -0
  97. package/dist/src/latex-export/parser/ivp-parser.d.ts +6 -0
  98. package/dist/src/latex-export/parser/ivp-parser.js +219 -0
  99. package/dist/src/latex-export/parser/ivp-parser.js.map +1 -0
  100. package/dist/src/latex-export/parser/line-joiner.d.ts +25 -0
  101. package/dist/src/latex-export/parser/line-joiner.js +80 -0
  102. package/dist/src/latex-export/parser/line-joiner.js.map +1 -0
  103. package/dist/src/latex-export/parser/tokenizer.d.ts +7 -0
  104. package/dist/src/latex-export/parser/tokenizer.js +143 -0
  105. package/dist/src/latex-export/parser/tokenizer.js.map +1 -0
  106. package/dist/src/latex-export/transformer/functions.d.ts +12 -0
  107. package/dist/src/latex-export/transformer/functions.js +47 -0
  108. package/dist/src/latex-export/transformer/functions.js.map +1 -0
  109. package/dist/src/latex-export/transformer/identifier.d.ts +23 -0
  110. package/dist/src/latex-export/transformer/identifier.js +194 -0
  111. package/dist/src/latex-export/transformer/identifier.js.map +1 -0
  112. package/dist/src/latex-export/transformer/operators.d.ts +9 -0
  113. package/dist/src/latex-export/transformer/operators.js +41 -0
  114. package/dist/src/latex-export/transformer/operators.js.map +1 -0
  115. package/dist/src/latex-export/types.d.ts +122 -0
  116. package/dist/src/latex-export/types.js +10 -0
  117. package/dist/src/latex-export/types.js.map +1 -0
  118. package/{src/pipeline/basic-pipeline-creator.ts → dist/src/pipeline/basic-pipeline-creator.d.ts} +11 -28
  119. package/dist/src/pipeline/basic-pipeline-creator.js.map +1 -0
  120. package/dist/src/pipeline/constants.d.ts +14 -0
  121. package/dist/src/pipeline/constants.js.map +1 -0
  122. package/dist/src/pipeline/index.d.ts +7 -0
  123. package/dist/src/pipeline/index.js.map +1 -0
  124. package/dist/src/pipeline/input.d.ts +3 -0
  125. package/dist/src/pipeline/input.js.map +1 -0
  126. package/dist/src/pipeline/loops-pipeline-creator.d.ts +124 -0
  127. package/dist/src/pipeline/loops-pipeline-creator.js.map +1 -0
  128. package/dist/src/pipeline/output.d.ts +10 -0
  129. package/{src → dist/src}/pipeline/output.js +1 -1
  130. package/dist/src/pipeline/output.js.map +1 -0
  131. package/dist/src/pipeline/pipeline-creator.d.ts +12 -0
  132. package/{src → dist/src}/pipeline/pipeline-creator.js +2 -0
  133. package/dist/src/pipeline/pipeline-creator.js.map +1 -0
  134. package/{src/pipeline/pipeline.ts → dist/src/pipeline/pipeline.d.ts} +10 -97
  135. package/dist/src/pipeline/pipeline.js.map +1 -0
  136. package/{src/pipeline/updates-pipeline-creator.ts → dist/src/pipeline/updates-pipeline-creator.d.ts} +15 -131
  137. package/dist/src/pipeline/updates-pipeline-creator.js.map +1 -0
  138. package/dist/src/scripting-tools/constants.d.ts +59 -0
  139. package/dist/src/scripting-tools/constants.js.map +1 -0
  140. package/dist/src/scripting-tools/index.d.ts +3 -0
  141. package/dist/src/scripting-tools/index.js.map +1 -0
  142. package/dist/src/scripting-tools/model-error.d.ts +10 -0
  143. package/{src → dist/src}/scripting-tools/model-error.js +2 -1
  144. package/dist/src/scripting-tools/model-error.js.map +1 -0
  145. package/dist/src/scripting-tools/scripting-tools.d.ts +277 -0
  146. package/{src → dist/src}/scripting-tools/scripting-tools.js +2 -4
  147. package/dist/src/scripting-tools/scripting-tools.js.map +1 -0
  148. package/dist/src/solver-tools/ab4-method.d.ts +46 -0
  149. package/{src → dist/src}/solver-tools/ab4-method.js +3 -3
  150. package/dist/src/solver-tools/ab4-method.js.map +1 -0
  151. package/dist/src/solver-tools/ab5-method.d.ts +46 -0
  152. package/{src → dist/src}/solver-tools/ab5-method.js +3 -3
  153. package/dist/src/solver-tools/ab5-method.js.map +1 -0
  154. package/dist/src/solver-tools/callbacks/callback-base.d.ts +8 -0
  155. package/dist/src/solver-tools/callbacks/callback-base.js.map +1 -0
  156. package/dist/src/solver-tools/callbacks/callback-tools.d.ts +6 -0
  157. package/dist/src/solver-tools/callbacks/callback-tools.js.map +1 -0
  158. package/dist/src/solver-tools/callbacks/iter-checker-callback.d.ts +12 -0
  159. package/{src → dist/src}/solver-tools/callbacks/iter-checker-callback.js +2 -0
  160. package/dist/src/solver-tools/callbacks/iter-checker-callback.js.map +1 -0
  161. package/dist/src/solver-tools/callbacks/time-checker-callback.d.ts +12 -0
  162. package/{src → dist/src}/solver-tools/callbacks/time-checker-callback.js +2 -2
  163. package/dist/src/solver-tools/callbacks/time-checker-callback.js.map +1 -0
  164. package/dist/src/solver-tools/cvode/common.d.ts +395 -0
  165. package/dist/src/solver-tools/cvode/common.js +483 -0
  166. package/dist/src/solver-tools/cvode/common.js.map +1 -0
  167. package/dist/src/solver-tools/cvode/cvode.d.ts +23 -0
  168. package/dist/src/solver-tools/cvode/cvode.js.map +1 -0
  169. package/dist/src/solver-tools/cvode/cvode_adams.d.ts +22 -0
  170. package/dist/src/solver-tools/cvode/cvode_adams.js.map +1 -0
  171. package/dist/src/solver-tools/cvode/cvode_bdf.d.ts +37 -0
  172. package/dist/src/solver-tools/cvode/cvode_bdf.js.map +1 -0
  173. package/dist/src/solver-tools/cvode/cvode_class.d.ts +116 -0
  174. package/{src → dist/src}/solver-tools/cvode/cvode_class.js +9 -4
  175. package/dist/src/solver-tools/cvode/cvode_class.js.map +1 -0
  176. package/dist/src/solver-tools/cvode/cvode_hin.d.ts +24 -0
  177. package/dist/src/solver-tools/cvode/cvode_hin.js.map +1 -0
  178. package/dist/src/solver-tools/cvode/cvode_io.d.ts +98 -0
  179. package/{src → dist/src}/solver-tools/cvode/cvode_io.js +1 -2
  180. package/dist/src/solver-tools/cvode/cvode_io.js.map +1 -0
  181. package/dist/src/solver-tools/cvode/cvode_ls.d.ts +23 -0
  182. package/dist/src/solver-tools/cvode/cvode_ls.js.map +1 -0
  183. package/dist/src/solver-tools/cvode/cvode_nls.d.ts +25 -0
  184. package/dist/src/solver-tools/cvode/cvode_nls.js.map +1 -0
  185. package/dist/src/solver-tools/cvode/cvode_root.d.ts +64 -0
  186. package/dist/src/solver-tools/cvode/cvode_root.js.map +1 -0
  187. package/dist/src/solver-tools/cvode/dense_linalg.d.ts +50 -0
  188. package/dist/src/solver-tools/cvode/dense_linalg.js.map +1 -0
  189. package/dist/src/solver-tools/cvode/index.d.ts +24 -0
  190. package/dist/src/solver-tools/cvode/index.js.map +1 -0
  191. package/dist/src/solver-tools/cvode-method.d.ts +47 -0
  192. package/dist/src/solver-tools/cvode-method.js.map +1 -0
  193. package/dist/src/solver-tools/index.d.ts +16 -0
  194. package/dist/src/solver-tools/index.js.map +1 -0
  195. package/dist/src/solver-tools/lin-alg-tools.d.ts +6 -0
  196. package/dist/src/solver-tools/lin-alg-tools.js.map +1 -0
  197. package/dist/src/solver-tools/lsoda/blas.d.ts +59 -0
  198. package/dist/src/solver-tools/lsoda/blas.js.map +1 -0
  199. package/{src/solver-tools/lsoda/index.ts → dist/src/solver-tools/lsoda/cfode.d.ts} +7 -6
  200. package/dist/src/solver-tools/lsoda/cfode.js.map +1 -0
  201. package/dist/src/solver-tools/lsoda/common.d.ts +85 -0
  202. package/dist/src/solver-tools/lsoda/common.js +96 -0
  203. package/dist/src/solver-tools/lsoda/common.js.map +1 -0
  204. package/{src/solver-tools/lsoda/corfailure.ts → dist/src/solver-tools/lsoda/corfailure.d.ts} +2 -26
  205. package/dist/src/solver-tools/lsoda/corfailure.js.map +1 -0
  206. package/dist/src/solver-tools/lsoda/correction.d.ts +23 -0
  207. package/dist/src/solver-tools/lsoda/correction.js.map +1 -0
  208. package/dist/src/solver-tools/lsoda/dense.d.ts +47 -0
  209. package/{src → dist/src}/solver-tools/lsoda/dense.js +2 -0
  210. package/dist/src/solver-tools/lsoda/dense.js.map +1 -0
  211. package/dist/src/solver-tools/lsoda/index.d.ts +16 -0
  212. package/dist/src/solver-tools/lsoda/index.js.map +1 -0
  213. package/dist/src/solver-tools/lsoda/intdy.d.ts +19 -0
  214. package/dist/src/solver-tools/lsoda/intdy.js.map +1 -0
  215. package/dist/src/solver-tools/lsoda/lsoda.d.ts +66 -0
  216. package/{src → dist/src}/solver-tools/lsoda/lsoda.js +13 -5
  217. package/dist/src/solver-tools/lsoda/lsoda.js.map +1 -0
  218. package/dist/src/solver-tools/lsoda/methodswitch.d.ts +21 -0
  219. package/dist/src/solver-tools/lsoda/methodswitch.js.map +1 -0
  220. package/dist/src/solver-tools/lsoda/orderswitch.d.ts +21 -0
  221. package/dist/src/solver-tools/lsoda/orderswitch.js.map +1 -0
  222. package/dist/src/solver-tools/lsoda/prja.d.ts +18 -0
  223. package/dist/src/solver-tools/lsoda/prja.js.map +1 -0
  224. package/dist/src/solver-tools/lsoda/scaleh.d.ts +16 -0
  225. package/dist/src/solver-tools/lsoda/scaleh.js.map +1 -0
  226. package/{src/solver-tools/lsoda/solsy.ts → dist/src/solver-tools/lsoda/solsy.d.ts} +2 -15
  227. package/dist/src/solver-tools/lsoda/solsy.js.map +1 -0
  228. package/dist/src/solver-tools/lsoda/stoda.d.ts +19 -0
  229. package/dist/src/solver-tools/lsoda/stoda.js.map +1 -0
  230. package/dist/src/solver-tools/lsoda-method.d.ts +46 -0
  231. package/dist/src/solver-tools/lsoda-method.js.map +1 -0
  232. package/dist/src/solver-tools/mrt-method.d.ts +47 -0
  233. package/{src → dist/src}/solver-tools/mrt-method.js +2 -2
  234. package/dist/src/solver-tools/mrt-method.js.map +1 -0
  235. package/dist/src/solver-tools/rk3-method.d.ts +46 -0
  236. package/{src → dist/src}/solver-tools/rk3-method.js +2 -2
  237. package/dist/src/solver-tools/rk3-method.js.map +1 -0
  238. package/dist/src/solver-tools/rk4-method.d.ts +46 -0
  239. package/{src → dist/src}/solver-tools/rk4-method.js +2 -2
  240. package/dist/src/solver-tools/rk4-method.js.map +1 -0
  241. package/dist/src/solver-tools/rkdp-method.d.ts +46 -0
  242. package/{src → dist/src}/solver-tools/rkdp-method.js +2 -2
  243. package/dist/src/solver-tools/rkdp-method.js.map +1 -0
  244. package/dist/src/solver-tools/ros34prw-method.d.ts +46 -0
  245. package/{src → dist/src}/solver-tools/ros34prw-method.js +2 -2
  246. package/dist/src/solver-tools/ros34prw-method.js.map +1 -0
  247. package/dist/src/solver-tools/ros3prw-method.d.ts +46 -0
  248. package/{src → dist/src}/solver-tools/ros3prw-method.js +2 -2
  249. package/dist/src/solver-tools/ros3prw-method.js.map +1 -0
  250. package/{src/solver-tools/solver-defs.ts → dist/src/solver-tools/solver-defs.d.ts} +45 -85
  251. package/dist/src/solver-tools/solver-defs.js.map +1 -0
  252. package/dist/src/worker-tools/index.d.ts +2 -0
  253. package/dist/src/worker-tools/index.js.map +1 -0
  254. package/{src/worker-tools/scripting.ts → dist/src/worker-tools/scripting.d.ts} +9 -91
  255. package/dist/src/worker-tools/scripting.js.map +1 -0
  256. package/dist/src/worker-tools/solving.d.ts +7 -0
  257. package/dist/src/worker-tools/solving.js.map +1 -0
  258. package/package.json +10 -11
  259. package/.claude/settings.local.json +0 -11
  260. package/.claude/skills/license-updater/SKILL.md +0 -149
  261. package/.claude/skills/license-updater/references/compatibility.md +0 -68
  262. package/.claude/skills/license-updater/references/templates.md +0 -151
  263. package/.claude/skills/license-updater/scripts/generate_license_files.py +0 -467
  264. package/.eslintrc.json +0 -45
  265. package/.github/ISSUE_TEMPLATE/bug_report.md +0 -29
  266. package/.github/ISSUE_TEMPLATE/feature_request.md +0 -20
  267. package/.github/PULL_REQUEST_TEMPLATE.md +0 -22
  268. package/.github/scripts/bump-js-api-version.sh +0 -106
  269. package/.github/scripts/check-output.sh +0 -20
  270. package/.github/scripts/iac-cfn-deploy.sh +0 -90
  271. package/.github/scripts/slack_api_request.sh +0 -65
  272. package/.github/scripts/test_package.sh +0 -270
  273. package/.github/workflows/deploy-docs.yml +0 -15
  274. package/.github/workflows/libraries.yaml +0 -305
  275. package/.github/workflows/test.yaml +0 -19
  276. package/CLAUDE.md +0 -104
  277. package/CONTRIBUTING.md +0 -74
  278. package/THIRD_PARTY_LICENSES +0 -135
  279. package/docs/.nojekyll +0 -1
  280. package/docs/assets/hierarchy.js +0 -1
  281. package/docs/assets/highlight.css +0 -99
  282. package/docs/assets/icons.js +0 -18
  283. package/docs/assets/icons.svg +0 -1
  284. package/docs/assets/main.js +0 -60
  285. package/docs/assets/navigation.js +0 -1
  286. package/docs/assets/search.js +0 -1
  287. package/docs/assets/style.css +0 -1633
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@@ -1,232 +0,0 @@
1
- /* eslint-disable max-len */
2
- import {mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda, cvode} from '../../index';
3
-
4
- export const methods = new Map([
5
- ['MRT', mrt],
6
- ['ROS3PRw', ros3prw],
7
- ['ROS34PRw', ros34prw],
8
- ['RK4', rk4],
9
- ['AB5', ab5],
10
- ['AB4', ab4],
11
- ['RKDP', rkdp],
12
- ['RK3', rk3],
13
- ['LSODA', lsoda],
14
- ['CVODE', cvode],
15
- ]);
16
-
17
- /** Implicit methods suitable for stiff performance benchmarks */
18
- export const implicitMethods = new Map([
19
- ['MRT', mrt],
20
- ['ROS3PRw', ros3prw],
21
- ['ROS34PRw', ros34prw],
22
- ['LSODA', lsoda],
23
- ['CVODE', cvode],
24
- ]);
25
-
26
- /** Performance problems to skip per method (known limitations) */
27
- export const perfExclusions = new Map<string, Set<string>>([
28
- ['CVODE', new Set(['E5'])],
29
- ]);
30
-
31
- export const MAX_MAD = 0.1;
32
- export const TIMEOUT_MS = 10000;
33
-
34
- const BASIC_MODEL = `#name: M|M|2|2
35
- #description: Modelling the system with two servers & two waiting places (EXPLAINED)
36
- #equations:
37
- dp0/dt = -la * p0 + mu * p1
38
- dp1/dt = la * p0 - (la + mu) * p1 + 2 * mu * p2
39
- dp2/dt = la * p1 - (la + 2 * mu) * p2 + 2 * mu * p3
40
- dp3/dt = la * p2 - (la + 2 * mu) * p3 + 2 * mu * p4
41
-
42
- #expressions:
43
- la = 1 / arrival
44
- mu = 1 / service
45
- p4 = 1 - p0 - p1 - p2 - p3
46
- busy = 1 - p0 - p1
47
- queue = p3 + 2 * p4
48
-
49
- #argument: t
50
- _t0 = 0 {min: 0; max: 10; caption: start; category: Time; units: min} [Initial time of simulation]
51
- _t1 = 60 {min: 20; max: 100; caption: finish; category: Time; units: min} [Final time of simulation]
52
- _h = 1 {min: 0.01; max: 0.1; caption: step; category: Time; units: min} [Time step of simulation]
53
-
54
- #inits:
55
- p0 = 1 {min: 0; max: 1; category: Initial state; caption: empty} [Probability that initially there are NO customers]
56
- p1 = 0 {min: 0; max: 1; category: Initial state; caption: single} [Probability that initially there is ONE customer]
57
- p2 = 0 {min: 0; max: 1; category: Initial state; caption: two} [Probability that initially there are TWO customers]
58
- p3 = 0 {min: 0; max: 1; category: Initial state; caption: three} [Probability that initially there are THREE customers]
59
-
60
- #output:
61
- t {caption: Time, min}
62
- p0 {caption: P(Empty)}
63
- busy {caption: P(Full load)}
64
- queue {caption: E(Queue)}
65
-
66
- #parameters:
67
- arrival = 10 {min: 1; max: 100; category: Means; caption: arrival; units: min} [Mean arrival time]
68
- service = 100 {min: 1; max: 100; category: Means; caption: service; units: min} [Mean service time]`;
69
-
70
- const BASIC_MODEL_INPUTS = {
71
- _t0: 0,
72
- _t1: 60,
73
- _h: 1,
74
- p0: 1,
75
- p1: 0,
76
- p2: 0,
77
- p3: 0,
78
- arrival: 10,
79
- service: 100,
80
- };
81
-
82
- const BASIC_MODEL_OUTPUTS = 4;
83
-
84
- const CYCLIC_MODEL = `#name: PK-PD
85
- #tags: model
86
- #description: Pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model
87
- #equations:
88
- d(depot)/dt = -KA * depot
89
- d(centr)/dt = KA * depot - CL * C2 - Q * C2 + Q * C3
90
- d(peri)/dt = Q * C2 - Q * C3
91
- d(eff)/dt = Kin - Kout * (1 - C2/(EC50 + C2)) * eff
92
-
93
- #expressions:
94
- C2 = centr / V2
95
- C3 = peri / V3
96
-
97
- #loop:
98
- _count = 10 {caption: count; category: Dosing; min: 1; max: 20} [Number of doses]
99
- depot += dose
100
-
101
- #argument: t
102
- _t0 = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1} [Begin of dosing interval]
103
- _t1 = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15} [End of dosing interval]
104
- _h = 1 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1} [Time step of simulation]
105
-
106
- #inits:
107
- depot = 0 {category: Initial values}
108
- centr = 0 {category: Initial values} [Central]
109
- peri = 0 {category: Initial values} [Peripheral]
110
- eff = 0.2 {category: Initial values} [Effective compartment rate]
111
-
112
- #parameters:
113
- dose = 1e4 {category: Dosing; min: 1e3; max: 2e4; step: 1e3} [Dosage]
114
- KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
115
- CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
116
- V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10} [Central compartment volume]
117
- Q = 1 {caption: inter rate; category: Parameters; min: 0.1; max: 1} [Intercompartmental rate]
118
- V3 = 30 {caption: peri volume; category: Parameters; min: 20; max: 40} [Peripheral compartment volume]
119
- EC50 = 8 {caption: effect; category: Parameters; min: 1; max: 10}
120
- Kin = 0.2 {caption: Kin; category: Parameters; min: 0.1; max: 0.5} [The first-order production constant]
121
- Kout = 0.2 {caption: Kout; category: Parameters; min: 0.1; max: 0.5} [The first-order dissipation rate constant]
122
-
123
- #tolerance: 1e-9`;
124
-
125
- const CYCLIC_MODEL_INPUTS = {
126
- _count: 10,
127
- _t0: 0,
128
- _t1: 16,
129
- _h: 1,
130
- depot: 0,
131
- centr: 0,
132
- peri: 0,
133
- eff: 0.2,
134
- dose: 10000,
135
- KA: 0.63,
136
- CL: 3.2,
137
- V2: 6.58,
138
- Q: 0.622,
139
- V3: 35.6,
140
- EC50: 5.41,
141
- Kin: 0.272,
142
- Kout: 0.276,
143
- };
144
-
145
- const CYCLIC_MODEL_OUTPUTS = 5;
146
-
147
- const MULTISTAGE_MODEL = `#name: GA-production
148
- #tags: model
149
- #description: Gluconic acid (GA) production by Aspergillus niger modeling
150
- #equations:
151
- dX/dt = rX
152
- dS/dt = -gamma * rX - lambda * X
153
- dO/dt = Kla * (Cod - O) - delta * rX - phi * X
154
- dP/dt = alpha * rX + beta * X
155
-
156
- #expressions:
157
- mu = muM * S / (Ks + S) * O / (Ko + O)
158
- rX = mu * X
159
-
160
- #argument: t, 1-st stage
161
- _t0 = 0 {units: h; caption: initial; category: Misc} [Start of the process]
162
- _t1 = 60 {units: h; caption: 1-st stage; category: Durations; min: 20; max: 80} [Duration of the 1-st stage]
163
- step = 0.1 {units: h; caption: step; category: Misc; min: 0.01; max: 1} [Time step of simulation]
164
-
165
- #update: 2-nd stage
166
- duration = overall - _t1
167
- S += 70
168
-
169
- #inits:
170
- X = 5 {units: kg/m³; caption: biomass; category: Initial concentrations; min: 1; max: 10} [Aspergillus niger biomass]
171
- S = 150 {units: kg/m³; caption: glucose; category: Initial concentrations; min: 50; max: 200} [Glucose]
172
- O = 7 {units: kg/m³; caption: oxygen; category: Initial concentrations; min: 1; max: 10} [Dissolved oxygen]
173
- P = 0 {units: kg/m³; caption: acid; category: Initial concentrations; min: 0; max: 0.1} [Gluconic acid]
174
-
175
- #output:
176
- t {caption: time}
177
- X {caption: biomass}
178
- S {caption: glucose}
179
- O {caption: oxygen}
180
- P {caption: acid}
181
-
182
- #parameters:
183
- overall = 100 {units: h; category: Durations; min: 100; max: 140} [Overall duration]
184
- muM = 0.668 {units: 1/h; category: Parameters} [Monod type model parameter]
185
- alpha = 2.92 {category: Parameters} [Monod type model parameter]
186
- beta = 0.131 {units: 1/h; category: Parameters} [Monod type model parameter]
187
- gamma = 2.12 {category: Parameters} [Monod type model parameter]
188
- lambda = 0.232 {units: 1/h; category: Parameters} [Monod type model parameter]
189
- delta = 0.278 {category: Parameters} [Monod type model parameter]
190
- phi = 4.87e-3 {units: 1/h; category: Parameters} [Monod type model parameter]
191
- Ks = 1.309e2 {units: g/L; category: Parameters} [Monod type model parameter]
192
- Ko = 3.63e-4 {units: g/L; category: Parameters} [Monod type model parameter]
193
- Kla = 1.7e-2 {units: 1/s; category: Parameters} [Volumetric mass transfer coefficient]
194
- Cod = 15 {units: kg/m³; category: Parameters} [Liquid phase dissolved oxygen saturation concentration]
195
-
196
- #tolerance: 1e-9`;
197
-
198
- const MULTISTAGE_MODEL_INPUTS = {
199
- _t0: 0,
200
- _t1: 60,
201
- _h: 1,
202
- X: 5,
203
- S: 150,
204
- O: 7,
205
- P: 0,
206
- overall: 100,
207
- muM: 0.668,
208
- alpha: 2.92,
209
- beta: 0.131,
210
- gamma: 2.12,
211
- lambda: 0.232,
212
- delta: 0.278,
213
- phi: 4.87e-3,
214
- Ks: 1.309e2,
215
- Ko: 3.63e-4,
216
- Kla: 1.7e-2,
217
- Cod: 15,
218
- };
219
-
220
- const MULTISTAGE_MODEL_OUTPUTS = 5;
221
-
222
- type TestProblem = {
223
- model: string,
224
- inputs: Record<string, number>,
225
- outputsCount: number,
226
- };
227
-
228
- export const problems = new Map<string, TestProblem>([
229
- ['basic', {model: BASIC_MODEL, inputs: BASIC_MODEL_INPUTS, outputsCount: BASIC_MODEL_OUTPUTS}],
230
- ['cyclic', {model: CYCLIC_MODEL, inputs: CYCLIC_MODEL_INPUTS, outputsCount: CYCLIC_MODEL_OUTPUTS}],
231
- ['multistage', {model: MULTISTAGE_MODEL, inputs: MULTISTAGE_MODEL_INPUTS, outputsCount: MULTISTAGE_MODEL_OUTPUTS}],
232
- ]);
@@ -1,28 +0,0 @@
1
- import { getIVP, getIvp2WebWorker, getInputVector, getPipelineCreator, applyPipeline } from '../../index';
2
- /** Return numerical solution error: maximum absolute deviation between approximate & exact solutions */
3
- export function getError(method, corProb) {
4
- let error = 0;
5
- // Get numerical solution
6
- const approxSolution = method(corProb.odes);
7
- const exact = corProb.exact;
8
- const arg = approxSolution[0];
9
- const pointsCount = arg.length;
10
- const funcsCount = approxSolution.length - 1;
11
- // Compute error
12
- for (let i = 0; i < pointsCount; ++i) {
13
- const exactSolution = exact(arg[i]);
14
- for (let j = 0; j < funcsCount; ++j)
15
- error = Math.max(error, Math.abs(exactSolution[j] - approxSolution[j + 1][i]));
16
- }
17
- return error;
18
- } // getError
19
- /** Evaluate model */
20
- export function evalModel(model, inputs) {
21
- const ivp = getIVP(model);
22
- const ivpWW = getIvp2WebWorker(ivp);
23
- const inputVector = getInputVector(inputs, ivp);
24
- const creator = getPipelineCreator(ivp);
25
- const pipeline = creator.getPipeline(inputVector);
26
- return applyPipeline(pipeline, ivpWW, inputVector);
27
- } // evalModel
28
- //# sourceMappingURL=test-utils.js.map
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@@ -1,37 +0,0 @@
1
- import {ODEs, CorrProblem, getIVP, getIvp2WebWorker, getInputVector, getPipelineCreator,
2
- applyPipeline} from '../../index';
3
-
4
- /** Return numerical solution error: maximum absolute deviation between approximate & exact solutions */
5
- export function getError(method: (odes: ODEs) => Float64Array[], corProb: CorrProblem): number {
6
- let error = 0;
7
-
8
- // Get numerical solution
9
- const approxSolution = method(corProb.odes);
10
-
11
- const exact = corProb.exact;
12
-
13
- const arg = approxSolution[0];
14
-
15
- const pointsCount = arg.length;
16
- const funcsCount = approxSolution.length - 1;
17
-
18
- // Compute error
19
- for (let i = 0; i < pointsCount; ++i) {
20
- const exactSolution = exact(arg[i]);
21
-
22
- for (let j = 0; j < funcsCount; ++j)
23
- error = Math.max(error, Math.abs(exactSolution[j] - approxSolution[j + 1][i]));
24
- }
25
-
26
- return error;
27
- } // getError
28
-
29
- /** Evaluate model */
30
- export function evalModel(model: string, inputs: Record<string, number>): Float64Array[] {
31
- const ivp = getIVP(model);
32
- const ivpWW = getIvp2WebWorker(ivp);
33
- const inputVector = getInputVector(inputs, ivp);
34
- const creator = getPipelineCreator(ivp);
35
- const pipeline = creator.getPipeline(inputVector);
36
- return applyPipeline(pipeline, ivpWW, inputVector);
37
- } // evalModel
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@@ -1,2 +0,0 @@
1
- export {IVP2WebWorker, getIvp2WebWorker} from './scripting';
2
- export {solveIvp} from './solving';
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@@ -1 +0,0 @@
1
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@@ -1,86 +0,0 @@
1
- // Tools for solving IVPs in web-workers
2
-
3
- import {SolverMethod, mrt, ros3prw, ros34prw, ODEs, getCallback,
4
- rk4, ab5, ab4, rkdp, rk3, lsoda, cvode} from '../solver-tools';
5
- import {Func} from '../solver-tools/solver-defs';
6
- import {IVP2WebWorker, getFunc} from './scripting';
7
-
8
- const ARG_INIT = 0;
9
- const ARG_FINAL = 1;
10
- const ARG_STEP = 2;
11
- const ARG_INP_COUNT = 3;
12
-
13
- /** Return method for solving IVP */
14
- function getMethod(name: string | undefined): SolverMethod {
15
- switch (name) {
16
- case 'mrt':
17
- return mrt;
18
-
19
- case 'ros3prw':
20
- return ros3prw;
21
-
22
- case 'rk4':
23
- return rk4;
24
-
25
- case 'ab5':
26
- return ab5;
27
-
28
- case 'ab4':
29
- return ab4;
30
-
31
- case 'rkdp':
32
- return rkdp;
33
-
34
- case 'rk3':
35
- return rk3;
36
-
37
- case 'lsoda':
38
- return lsoda;
39
-
40
- case 'cvode':
41
- return cvode;
42
-
43
- default:
44
- return ros34prw;
45
- }
46
- }
47
-
48
- /** Check the correspondence of inputs to IVP */
49
- function checkInputs(ivp: IVP2WebWorker, inputs: Float64Array): void {
50
- const expected = ARG_INP_COUNT + ivp.deqsCount + ivp.paramNames.length;
51
-
52
- if (expected > inputs.length)
53
- throw new Error(`Incorrect inputs count, expected: ${expected}, current: ${inputs.length}`);
54
- }
55
-
56
- /** Return solution of IVP with a specified inputs
57
- * @param ivp - initial value problem to be solved
58
- * @param inputs - vector of input values
59
- * @returns solution of the given initial value problem
60
- */
61
- export function solveIvp(ivp: IVP2WebWorker, inputs: Float64Array): Float64Array[] {
62
- checkInputs(ivp, inputs);
63
- const nonParamInputsCount = inputs.length - ivp.paramNames.length;
64
-
65
- const funcCode = getFunc(ivp, inputs.slice(nonParamInputsCount));
66
- const func = new Function(funcCode) as Func;
67
-
68
- const odes: ODEs = {
69
- name: '',
70
- arg: {
71
- name: '',
72
- start: inputs[ARG_INIT],
73
- finish: inputs[ARG_FINAL],
74
- step: inputs[ARG_STEP],
75
- },
76
- initial: inputs.slice(ARG_STEP + 1, nonParamInputsCount),
77
- func: func,
78
- tolerance: ivp.tolerance,
79
- solutionColNames: [],
80
- };
81
-
82
- const method = getMethod(ivp.solverOpts.method);
83
- const callback = getCallback(ivp.solverOpts);
84
-
85
- return method(odes, callback);
86
- }
package/tsconfig.json DELETED
@@ -1,71 +0,0 @@
1
- {
2
- "compilerOptions": {
3
- /* Visit https://aka.ms/tsconfig.json to read more about this file */
4
-
5
- /* Basic Options */
6
- // "incremental": true, /* Enable incremental compilation */
7
- "target": "es6", /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
8
- "module": "es2020", /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
9
- "lib": ["ES2022", "dom"], /* Specify library files to be included in the compilation. */
10
- // "allowJs": true, /* Allow javascript files to be compiled. */
11
- // "checkJs": true, /* Report errors in .js files. */
12
- // "jsx": "preserve", /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
13
- // "declaration": true, /* Generates corresponding '.d.ts' file. */
14
- // "declarationMap": true, /* Generates a sourcemap for each corresponding '.d.ts' file. */
15
- "sourceMap": true, /* Generates corresponding '.map' file. */
16
- // "outFile": "./", /* Concatenate and emit output to single file. */
17
- // "outDir": "./dist", /* Redirect output structure to the directory. */
18
- // "rootDir": "./", /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */
19
- // "composite": true, /* Enable project compilation */
20
- // "tsBuildInfoFile": "./", /* Specify file to store incremental compilation information */
21
- // "removeComments": true, /* Do not emit comments to output. */
22
- // "noEmit": true, /* Do not emit outputs. */
23
- // "importHelpers": true, /* Import emit helpers from 'tslib'. */
24
- // "downlevelIteration": true, /* Provide full support for iterables in 'for-of', spread, and destructuring when targeting 'ES5' or 'ES3'. */
25
- // "isolatedModules": true, /* Transpile each file as a separate module (similar to 'ts.transpileModule'). */
26
-
27
- /* Strict Type-Checking Options */
28
- "strict": true, /* Enable all strict type-checking options. */
29
- // "noImplicitAny": true, /* Raise error on expressions and declarations with an implied 'any' type. */
30
- // "strictNullChecks": true, /* Enable strict null checks. */
31
- // "strictFunctionTypes": true, /* Enable strict checking of function types. */
32
- // "strictBindCallApply": true, /* Enable strict 'bind', 'call', and 'apply' methods on functions. */
33
- // "strictPropertyInitialization": true, /* Enable strict checking of property initialization in classes. */
34
- // "noImplicitThis": true, /* Raise error on 'this' expressions with an implied 'any' type. */
35
- // "alwaysStrict": true, /* Parse in strict mode and emit "use strict" for each source file. */
36
-
37
- /* Additional Checks */
38
- // "noUnusedLocals": true, /* Report errors on unused locals. */
39
- // "noUnusedParameters": true, /* Report errors on unused parameters. */
40
- // "noImplicitReturns": true, /* Report error when not all code paths in function return a value. */
41
- // "noFallthroughCasesInSwitch": true, /* Report errors for fallthrough cases in switch statement. */
42
- // "noUncheckedIndexedAccess": true, /* Include 'undefined' in index signature results */
43
- // "noPropertyAccessFromIndexSignature": true, /* Require undeclared properties from index signatures to use element accesses. */
44
-
45
- /* Module Resolution Options */
46
- "moduleResolution": "node", /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */
47
- // "baseUrl": "./", /* Base directory to resolve non-absolute module names. */
48
- // "paths": {}, /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */
49
- // "rootDirs": [], /* List of root folders whose combined content represents the structure of the project at runtime. */
50
- // "typeRoots": [], /* List of folders to include type definitions from. */
51
- "types": ["jest", "node"], /* Type declaration files to be included in compilation. */
52
- // "allowSyntheticDefaultImports": true, /* Allow default imports from modules with no default export. This does not affect code emit, just typechecking. */
53
- "esModuleInterop": true, /* Enables emit interoperability between CommonJS and ES Modules via creation of namespace objects for all imports. Implies 'allowSyntheticDefaultImports'. */
54
- // "preserveSymlinks": true, /* Do not resolve the real path of symlinks. */
55
- // "allowUmdGlobalAccess": true, /* Allow accessing UMD globals from modules. */
56
-
57
- /* Source Map Options */
58
- // "sourceRoot": "", /* Specify the location where debugger should locate TypeScript files instead of source locations. */
59
- // "mapRoot": "", /* Specify the location where debugger should locate map files instead of generated locations. */
60
- // "inlineSourceMap": true, /* Emit a single file with source maps instead of having a separate file. */
61
- // "inlineSources": true, /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */
62
-
63
- /* Experimental Options */
64
- // "experimentalDecorators": true, /* Enables experimental support for ES7 decorators. */
65
- // "emitDecoratorMetadata": true, /* Enables experimental support for emitting type metadata for decorators. */
66
-
67
- /* Advanced Options */
68
- "skipLibCheck": true, /* Skip type checking of declaration files. */
69
- "forceConsistentCasingInFileNames": true /* Disallow inconsistently-cased references to the same file. */
70
- }
71
- }
package/typedoc.json DELETED
@@ -1,8 +0,0 @@
1
- {
2
- "entryPoints": ["index.ts"],
3
- "out": "docs",
4
- "includeVersion": true,
5
- "excludePrivate": true,
6
- "excludeProtected": true,
7
- "excludeInternal": true
8
- }
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