vivarium-engine 5.0.0__tar.gz

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  1. vivarium_engine-5.0.0/.readthedocs.yaml +27 -0
  2. vivarium_engine-5.0.0/.zenodo.json +67 -0
  3. vivarium_engine-5.0.0/CHANGELOG.rst +1098 -0
  4. vivarium_engine-5.0.0/Jenkinsfile +40 -0
  5. vivarium_engine-5.0.0/LICENSE +27 -0
  6. vivarium_engine-5.0.0/Makefile +92 -0
  7. vivarium_engine-5.0.0/PKG-INFO +108 -0
  8. vivarium_engine-5.0.0/README.rst +55 -0
  9. vivarium_engine-5.0.0/docs/Makefile +19 -0
  10. vivarium_engine-5.0.0/docs/nitpick-exceptions +83 -0
  11. vivarium_engine-5.0.0/docs/source/_static/boids.mp4 +0 -0
  12. vivarium_engine-5.0.0/docs/source/_static/style.css +3 -0
  13. vivarium_engine-5.0.0/docs/source/api_reference/component.rst +1 -0
  14. vivarium_engine-5.0.0/docs/source/api_reference/exceptions.rst +1 -0
  15. vivarium_engine-5.0.0/docs/source/api_reference/framework/artifact/index.rst +11 -0
  16. vivarium_engine-5.0.0/docs/source/api_reference/framework/artifact/interface.rst +1 -0
  17. vivarium_engine-5.0.0/docs/source/api_reference/framework/artifact/manager.rst +1 -0
  18. vivarium_engine-5.0.0/docs/source/api_reference/framework/components/index.rst +11 -0
  19. vivarium_engine-5.0.0/docs/source/api_reference/framework/components/interface.rst +1 -0
  20. vivarium_engine-5.0.0/docs/source/api_reference/framework/components/manager.rst +1 -0
  21. vivarium_engine-5.0.0/docs/source/api_reference/framework/components/parser.rst +1 -0
  22. vivarium_engine-5.0.0/docs/source/api_reference/framework/configuration.rst +1 -0
  23. vivarium_engine-5.0.0/docs/source/api_reference/framework/engine.rst +1 -0
  24. vivarium_engine-5.0.0/docs/source/api_reference/framework/event/index.rst +11 -0
  25. vivarium_engine-5.0.0/docs/source/api_reference/framework/event/interface.rst +1 -0
  26. vivarium_engine-5.0.0/docs/source/api_reference/framework/event/manager.rst +1 -0
  27. vivarium_engine-5.0.0/docs/source/api_reference/framework/index.rst +12 -0
  28. vivarium_engine-5.0.0/docs/source/api_reference/framework/lifecycle/constraint_maker.rst +1 -0
  29. vivarium_engine-5.0.0/docs/source/api_reference/framework/lifecycle/entities.rst +1 -0
  30. vivarium_engine-5.0.0/docs/source/api_reference/framework/lifecycle/exceptions.rst +1 -0
  31. vivarium_engine-5.0.0/docs/source/api_reference/framework/lifecycle/index.rst +11 -0
  32. vivarium_engine-5.0.0/docs/source/api_reference/framework/lifecycle/interface.rst +1 -0
  33. vivarium_engine-5.0.0/docs/source/api_reference/framework/lifecycle/lifecycle_states.rst +1 -0
  34. vivarium_engine-5.0.0/docs/source/api_reference/framework/lifecycle/manager.rst +1 -0
  35. vivarium_engine-5.0.0/docs/source/api_reference/framework/logging/index.rst +11 -0
  36. vivarium_engine-5.0.0/docs/source/api_reference/framework/logging/interface.rst +1 -0
  37. vivarium_engine-5.0.0/docs/source/api_reference/framework/logging/manager.rst +1 -0
  38. vivarium_engine-5.0.0/docs/source/api_reference/framework/logging/utilities.rst +1 -0
  39. vivarium_engine-5.0.0/docs/source/api_reference/framework/lookup/index.rst +11 -0
  40. vivarium_engine-5.0.0/docs/source/api_reference/framework/lookup/interface.rst +1 -0
  41. vivarium_engine-5.0.0/docs/source/api_reference/framework/lookup/interpolation.rst +1 -0
  42. vivarium_engine-5.0.0/docs/source/api_reference/framework/lookup/manager.rst +1 -0
  43. vivarium_engine-5.0.0/docs/source/api_reference/framework/lookup/table.rst +1 -0
  44. vivarium_engine-5.0.0/docs/source/api_reference/framework/plugins.rst +1 -0
  45. vivarium_engine-5.0.0/docs/source/api_reference/framework/population/exceptions.rst +1 -0
  46. vivarium_engine-5.0.0/docs/source/api_reference/framework/population/index.rst +11 -0
  47. vivarium_engine-5.0.0/docs/source/api_reference/framework/population/interface.rst +1 -0
  48. vivarium_engine-5.0.0/docs/source/api_reference/framework/population/manager.rst +1 -0
  49. vivarium_engine-5.0.0/docs/source/api_reference/framework/population/population_view.rst +1 -0
  50. vivarium_engine-5.0.0/docs/source/api_reference/framework/population/utilities.rst +1 -0
  51. vivarium_engine-5.0.0/docs/source/api_reference/framework/randomness/exceptions.rst +1 -0
  52. vivarium_engine-5.0.0/docs/source/api_reference/framework/randomness/index.rst +11 -0
  53. vivarium_engine-5.0.0/docs/source/api_reference/framework/randomness/index_map.rst +1 -0
  54. vivarium_engine-5.0.0/docs/source/api_reference/framework/randomness/interface.rst +1 -0
  55. vivarium_engine-5.0.0/docs/source/api_reference/framework/randomness/manager.rst +1 -0
  56. vivarium_engine-5.0.0/docs/source/api_reference/framework/randomness/stream.rst +1 -0
  57. vivarium_engine-5.0.0/docs/source/api_reference/framework/resource/exceptions.rst +1 -0
  58. vivarium_engine-5.0.0/docs/source/api_reference/framework/resource/index.rst +11 -0
  59. vivarium_engine-5.0.0/docs/source/api_reference/framework/resource/interface.rst +1 -0
  60. vivarium_engine-5.0.0/docs/source/api_reference/framework/resource/manager.rst +1 -0
  61. vivarium_engine-5.0.0/docs/source/api_reference/framework/resource/resource.rst +1 -0
  62. vivarium_engine-5.0.0/docs/source/api_reference/framework/results/context.rst +1 -0
  63. vivarium_engine-5.0.0/docs/source/api_reference/framework/results/index.rst +11 -0
  64. vivarium_engine-5.0.0/docs/source/api_reference/framework/results/interface.rst +1 -0
  65. vivarium_engine-5.0.0/docs/source/api_reference/framework/results/manager.rst +1 -0
  66. vivarium_engine-5.0.0/docs/source/api_reference/framework/results/observation.rst +1 -0
  67. vivarium_engine-5.0.0/docs/source/api_reference/framework/results/observer.rst +1 -0
  68. vivarium_engine-5.0.0/docs/source/api_reference/framework/results/stratification.rst +1 -0
  69. vivarium_engine-5.0.0/docs/source/api_reference/framework/state_machine.rst +1 -0
  70. vivarium_engine-5.0.0/docs/source/api_reference/framework/time/index.rst +11 -0
  71. vivarium_engine-5.0.0/docs/source/api_reference/framework/time/interface.rst +1 -0
  72. vivarium_engine-5.0.0/docs/source/api_reference/framework/time/manager.rst +1 -0
  73. vivarium_engine-5.0.0/docs/source/api_reference/framework/utilities.rst +1 -0
  74. vivarium_engine-5.0.0/docs/source/api_reference/framework/values/combiners.rst +1 -0
  75. vivarium_engine-5.0.0/docs/source/api_reference/framework/values/exceptions.rst +1 -0
  76. vivarium_engine-5.0.0/docs/source/api_reference/framework/values/index.rst +11 -0
  77. vivarium_engine-5.0.0/docs/source/api_reference/framework/values/interface.rst +1 -0
  78. vivarium_engine-5.0.0/docs/source/api_reference/framework/values/manager.rst +1 -0
  79. vivarium_engine-5.0.0/docs/source/api_reference/framework/values/pipeline.rst +1 -0
  80. vivarium_engine-5.0.0/docs/source/api_reference/framework/values/post_processors.rst +1 -0
  81. vivarium_engine-5.0.0/docs/source/api_reference/index.rst +11 -0
  82. vivarium_engine-5.0.0/docs/source/api_reference/interface/cli.rst +1 -0
  83. vivarium_engine-5.0.0/docs/source/api_reference/interface/index.rst +11 -0
  84. vivarium_engine-5.0.0/docs/source/api_reference/interface/interactive.rst +1 -0
  85. vivarium_engine-5.0.0/docs/source/api_reference/interface/utilities.rst +1 -0
  86. vivarium_engine-5.0.0/docs/source/api_reference/manager.rst +1 -0
  87. vivarium_engine-5.0.0/docs/source/api_reference/testing_utilities.rst +1 -0
  88. vivarium_engine-5.0.0/docs/source/concepts/builder.rst +59 -0
  89. vivarium_engine-5.0.0/docs/source/concepts/components.rst +24 -0
  90. vivarium_engine-5.0.0/docs/source/concepts/configuration.rst +16 -0
  91. vivarium_engine-5.0.0/docs/source/concepts/crn.rst +223 -0
  92. vivarium_engine-5.0.0/docs/source/concepts/data.rst +17 -0
  93. vivarium_engine-5.0.0/docs/source/concepts/entry_points.rst +136 -0
  94. vivarium_engine-5.0.0/docs/source/concepts/event.rst +177 -0
  95. vivarium_engine-5.0.0/docs/source/concepts/index.rst +14 -0
  96. vivarium_engine-5.0.0/docs/source/concepts/interpolation.rst +9 -0
  97. vivarium_engine-5.0.0/docs/source/concepts/lifecycle.rst +201 -0
  98. vivarium_engine-5.0.0/docs/source/concepts/logging.rst +9 -0
  99. vivarium_engine-5.0.0/docs/source/concepts/lookup.rst +346 -0
  100. vivarium_engine-5.0.0/docs/source/concepts/model_specification/index.rst +127 -0
  101. vivarium_engine-5.0.0/docs/source/concepts/model_specification/yaml_basics.rst +148 -0
  102. vivarium_engine-5.0.0/docs/source/concepts/population.rst +223 -0
  103. vivarium_engine-5.0.0/docs/source/concepts/resource.rst +9 -0
  104. vivarium_engine-5.0.0/docs/source/concepts/results.rst +410 -0
  105. vivarium_engine-5.0.0/docs/source/concepts/time.rst +76 -0
  106. vivarium_engine-5.0.0/docs/source/concepts/values.rst +167 -0
  107. vivarium_engine-5.0.0/docs/source/conf.py +146 -0
  108. vivarium_engine-5.0.0/docs/source/glossary.rst +76 -0
  109. vivarium_engine-5.0.0/docs/source/images/crn_compare_cubes.jpg +0 -0
  110. vivarium_engine-5.0.0/docs/source/images/crn_cube.jpg +0 -0
  111. vivarium_engine-5.0.0/docs/source/images/crn_sim_alignment.jpg +0 -0
  112. vivarium_engine-5.0.0/docs/source/images/pipeline.jpg +0 -0
  113. vivarium_engine-5.0.0/docs/source/index.rst +21 -0
  114. vivarium_engine-5.0.0/docs/source/installation.rst +65 -0
  115. vivarium_engine-5.0.0/docs/source/tutorials/boids.rst +632 -0
  116. vivarium_engine-5.0.0/docs/source/tutorials/disease_model.rst +1010 -0
  117. vivarium_engine-5.0.0/docs/source/tutorials/exploration.rst +401 -0
  118. vivarium_engine-5.0.0/docs/source/tutorials/getting_started.rst +95 -0
  119. vivarium_engine-5.0.0/docs/source/tutorials/index.rst +18 -0
  120. vivarium_engine-5.0.0/docs/source/tutorials/running_a_simulation/cli.rst +126 -0
  121. vivarium_engine-5.0.0/docs/source/tutorials/running_a_simulation/index.rst +17 -0
  122. vivarium_engine-5.0.0/docs/source/tutorials/running_a_simulation/interactive.rst +412 -0
  123. vivarium_engine-5.0.0/pyproject.toml +143 -0
  124. vivarium_engine-5.0.0/python_versions.json +1 -0
  125. vivarium_engine-5.0.0/setup.cfg +4 -0
  126. vivarium_engine-5.0.0/src/vivarium/__init__.py +75 -0
  127. vivarium_engine-5.0.0/src/vivarium/engine/__init__.py +58 -0
  128. vivarium_engine-5.0.0/src/vivarium/engine/component.py +701 -0
  129. vivarium_engine-5.0.0/src/vivarium/engine/examples/__init__.py +0 -0
  130. vivarium_engine-5.0.0/src/vivarium/engine/examples/boids/__init__.py +5 -0
  131. vivarium_engine-5.0.0/src/vivarium/engine/examples/boids/forces.py +184 -0
  132. vivarium_engine-5.0.0/src/vivarium/engine/examples/boids/movement.py +104 -0
  133. vivarium_engine-5.0.0/src/vivarium/engine/examples/boids/neighbors.py +70 -0
  134. vivarium_engine-5.0.0/src/vivarium/engine/examples/boids/population.py +52 -0
  135. vivarium_engine-5.0.0/src/vivarium/engine/examples/boids/visualization.py +50 -0
  136. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/__init__.py +24 -0
  137. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/disease.py +241 -0
  138. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/disease_model.yaml +45 -0
  139. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/intervention.py +57 -0
  140. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/mortality.py +104 -0
  141. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/observer.py +82 -0
  142. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/population.py +182 -0
  143. vivarium_engine-5.0.0/src/vivarium/engine/examples/disease_model/risk.py +147 -0
  144. vivarium_engine-5.0.0/src/vivarium/engine/exceptions.py +15 -0
  145. vivarium_engine-5.0.0/src/vivarium/engine/framework/__init__.py +0 -0
  146. vivarium_engine-5.0.0/src/vivarium/engine/framework/artifact/__init__.py +9 -0
  147. vivarium_engine-5.0.0/src/vivarium/engine/framework/artifact/interface.py +59 -0
  148. vivarium_engine-5.0.0/src/vivarium/engine/framework/artifact/manager.py +217 -0
  149. vivarium_engine-5.0.0/src/vivarium/engine/framework/components/__init__.py +7 -0
  150. vivarium_engine-5.0.0/src/vivarium/engine/framework/components/interface.py +118 -0
  151. vivarium_engine-5.0.0/src/vivarium/engine/framework/components/manager.py +371 -0
  152. vivarium_engine-5.0.0/src/vivarium/engine/framework/components/parser.py +282 -0
  153. vivarium_engine-5.0.0/src/vivarium/engine/framework/configuration.py +97 -0
  154. vivarium_engine-5.0.0/src/vivarium/engine/framework/engine.py +450 -0
  155. vivarium_engine-5.0.0/src/vivarium/engine/framework/event/__init__.py +2 -0
  156. vivarium_engine-5.0.0/src/vivarium/engine/framework/event/interface.py +92 -0
  157. vivarium_engine-5.0.0/src/vivarium/engine/framework/event/manager.py +276 -0
  158. vivarium_engine-5.0.0/src/vivarium/engine/framework/lifecycle/__init__.py +36 -0
  159. vivarium_engine-5.0.0/src/vivarium/engine/framework/lifecycle/constraint_maker.py +150 -0
  160. vivarium_engine-5.0.0/src/vivarium/engine/framework/lifecycle/entities.py +275 -0
  161. vivarium_engine-5.0.0/src/vivarium/engine/framework/lifecycle/exceptions.py +29 -0
  162. vivarium_engine-5.0.0/src/vivarium/engine/framework/lifecycle/interface.py +87 -0
  163. vivarium_engine-5.0.0/src/vivarium/engine/framework/lifecycle/lifecycle_states.py +39 -0
  164. vivarium_engine-5.0.0/src/vivarium/engine/framework/lifecycle/manager.py +191 -0
  165. vivarium_engine-5.0.0/src/vivarium/engine/framework/logging/__init__.py +14 -0
  166. vivarium_engine-5.0.0/src/vivarium/engine/framework/logging/interface.py +25 -0
  167. vivarium_engine-5.0.0/src/vivarium/engine/framework/logging/manager.py +50 -0
  168. vivarium_engine-5.0.0/src/vivarium/engine/framework/logging/utilities.py +164 -0
  169. vivarium_engine-5.0.0/src/vivarium/engine/framework/lookup/__init__.py +4 -0
  170. vivarium_engine-5.0.0/src/vivarium/engine/framework/lookup/interface.py +95 -0
  171. vivarium_engine-5.0.0/src/vivarium/engine/framework/lookup/interpolation.py +384 -0
  172. vivarium_engine-5.0.0/src/vivarium/engine/framework/lookup/manager.py +163 -0
  173. vivarium_engine-5.0.0/src/vivarium/engine/framework/lookup/table.py +292 -0
  174. vivarium_engine-5.0.0/src/vivarium/engine/framework/plugins.py +269 -0
  175. vivarium_engine-5.0.0/src/vivarium/engine/framework/population/__init__.py +17 -0
  176. vivarium_engine-5.0.0/src/vivarium/engine/framework/population/exceptions.py +15 -0
  177. vivarium_engine-5.0.0/src/vivarium/engine/framework/population/interface.py +124 -0
  178. vivarium_engine-5.0.0/src/vivarium/engine/framework/population/manager.py +798 -0
  179. vivarium_engine-5.0.0/src/vivarium/engine/framework/population/population_view.py +688 -0
  180. vivarium_engine-5.0.0/src/vivarium/engine/framework/population/utilities.py +45 -0
  181. vivarium_engine-5.0.0/src/vivarium/engine/framework/randomness/__init__.py +36 -0
  182. vivarium_engine-5.0.0/src/vivarium/engine/framework/randomness/exceptions.py +16 -0
  183. vivarium_engine-5.0.0/src/vivarium/engine/framework/randomness/index_map.py +270 -0
  184. vivarium_engine-5.0.0/src/vivarium/engine/framework/randomness/interface.py +85 -0
  185. vivarium_engine-5.0.0/src/vivarium/engine/framework/randomness/manager.py +250 -0
  186. vivarium_engine-5.0.0/src/vivarium/engine/framework/randomness/stream.py +515 -0
  187. vivarium_engine-5.0.0/src/vivarium/engine/framework/resource/__init__.py +25 -0
  188. vivarium_engine-5.0.0/src/vivarium/engine/framework/resource/exceptions.py +7 -0
  189. vivarium_engine-5.0.0/src/vivarium/engine/framework/resource/interface.py +91 -0
  190. vivarium_engine-5.0.0/src/vivarium/engine/framework/resource/manager.py +207 -0
  191. vivarium_engine-5.0.0/src/vivarium/engine/framework/resource/resource.py +159 -0
  192. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/__init__.py +4 -0
  193. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/context.py +479 -0
  194. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/exceptions.py +15 -0
  195. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/interface.py +458 -0
  196. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/manager.py +414 -0
  197. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/observation.py +560 -0
  198. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/observer.py +79 -0
  199. vivarium_engine-5.0.0/src/vivarium/engine/framework/results/stratification.py +166 -0
  200. vivarium_engine-5.0.0/src/vivarium/engine/framework/state_machine.py +682 -0
  201. vivarium_engine-5.0.0/src/vivarium/engine/framework/time/__init__.py +7 -0
  202. vivarium_engine-5.0.0/src/vivarium/engine/framework/time/interface.py +75 -0
  203. vivarium_engine-5.0.0/src/vivarium/engine/framework/time/manager.py +300 -0
  204. vivarium_engine-5.0.0/src/vivarium/engine/framework/utilities.py +250 -0
  205. vivarium_engine-5.0.0/src/vivarium/engine/framework/values/__init__.py +37 -0
  206. vivarium_engine-5.0.0/src/vivarium/engine/framework/values/combiners.py +138 -0
  207. vivarium_engine-5.0.0/src/vivarium/engine/framework/values/exceptions.py +7 -0
  208. vivarium_engine-5.0.0/src/vivarium/engine/framework/values/interface.py +291 -0
  209. vivarium_engine-5.0.0/src/vivarium/engine/framework/values/manager.py +462 -0
  210. vivarium_engine-5.0.0/src/vivarium/engine/framework/values/pipeline.py +395 -0
  211. vivarium_engine-5.0.0/src/vivarium/engine/framework/values/post_processors.py +185 -0
  212. vivarium_engine-5.0.0/src/vivarium/engine/interface/__init__.py +1 -0
  213. vivarium_engine-5.0.0/src/vivarium/engine/interface/cli.py +169 -0
  214. vivarium_engine-5.0.0/src/vivarium/engine/interface/interactive.py +326 -0
  215. vivarium_engine-5.0.0/src/vivarium/engine/interface/utilities.py +166 -0
  216. vivarium_engine-5.0.0/src/vivarium/engine/manager.py +91 -0
  217. vivarium_engine-5.0.0/src/vivarium/engine/py.typed +1 -0
  218. vivarium_engine-5.0.0/src/vivarium/engine/testing_utilities.py +291 -0
  219. vivarium_engine-5.0.0/src/vivarium/engine/types.py +47 -0
  220. vivarium_engine-5.0.0/src/vivarium_engine.egg-info/PKG-INFO +108 -0
  221. vivarium_engine-5.0.0/src/vivarium_engine.egg-info/SOURCES.txt +282 -0
  222. vivarium_engine-5.0.0/src/vivarium_engine.egg-info/dependency_links.txt +1 -0
  223. vivarium_engine-5.0.0/src/vivarium_engine.egg-info/entry_points.txt +2 -0
  224. vivarium_engine-5.0.0/src/vivarium_engine.egg-info/requires.txt +31 -0
  225. vivarium_engine-5.0.0/src/vivarium_engine.egg-info/top_level.txt +1 -0
  226. vivarium_engine-5.0.0/tests/__init__.py +0 -0
  227. vivarium_engine-5.0.0/tests/conftest.py +115 -0
  228. vivarium_engine-5.0.0/tests/examples/__init__.py +0 -0
  229. vivarium_engine-5.0.0/tests/examples/test_boids_model.py +7 -0
  230. vivarium_engine-5.0.0/tests/examples/test_disease_model.py +111 -0
  231. vivarium_engine-5.0.0/tests/framework/__init__.py +0 -0
  232. vivarium_engine-5.0.0/tests/framework/artifact/test_manager.py +176 -0
  233. vivarium_engine-5.0.0/tests/framework/components/__init__.py +0 -0
  234. vivarium_engine-5.0.0/tests/framework/components/test_component.py +391 -0
  235. vivarium_engine-5.0.0/tests/framework/components/test_manager.py +350 -0
  236. vivarium_engine-5.0.0/tests/framework/components/test_parser.py +180 -0
  237. vivarium_engine-5.0.0/tests/framework/lookup/__init__.py +0 -0
  238. vivarium_engine-5.0.0/tests/framework/lookup/test_interpolation.py +574 -0
  239. vivarium_engine-5.0.0/tests/framework/lookup/test_lookup.py +868 -0
  240. vivarium_engine-5.0.0/tests/framework/population/__init__.py +0 -0
  241. vivarium_engine-5.0.0/tests/framework/population/conftest.py +101 -0
  242. vivarium_engine-5.0.0/tests/framework/population/helpers.py +53 -0
  243. vivarium_engine-5.0.0/tests/framework/population/test_manager.py +539 -0
  244. vivarium_engine-5.0.0/tests/framework/population/test_population_view.py +1126 -0
  245. vivarium_engine-5.0.0/tests/framework/population/test_utilities.py +100 -0
  246. vivarium_engine-5.0.0/tests/framework/randomness/__init__.py +0 -0
  247. vivarium_engine-5.0.0/tests/framework/randomness/conftest.py +35 -0
  248. vivarium_engine-5.0.0/tests/framework/randomness/test_crn.py +349 -0
  249. vivarium_engine-5.0.0/tests/framework/randomness/test_index_map.py +224 -0
  250. vivarium_engine-5.0.0/tests/framework/randomness/test_manager.py +164 -0
  251. vivarium_engine-5.0.0/tests/framework/randomness/test_reproducibility.py +33 -0
  252. vivarium_engine-5.0.0/tests/framework/randomness/test_stream.py +365 -0
  253. vivarium_engine-5.0.0/tests/framework/resource/__init__.py +0 -0
  254. vivarium_engine-5.0.0/tests/framework/resource/test_interface.py +42 -0
  255. vivarium_engine-5.0.0/tests/framework/resource/test_manager.py +243 -0
  256. vivarium_engine-5.0.0/tests/framework/resource/test_resource.py +7 -0
  257. vivarium_engine-5.0.0/tests/framework/results/__init__.py +0 -0
  258. vivarium_engine-5.0.0/tests/framework/results/helpers.py +362 -0
  259. vivarium_engine-5.0.0/tests/framework/results/test_context.py +850 -0
  260. vivarium_engine-5.0.0/tests/framework/results/test_interface.py +525 -0
  261. vivarium_engine-5.0.0/tests/framework/results/test_manager.py +884 -0
  262. vivarium_engine-5.0.0/tests/framework/results/test_observation.py +286 -0
  263. vivarium_engine-5.0.0/tests/framework/results/test_observer.py +98 -0
  264. vivarium_engine-5.0.0/tests/framework/results/test_stratification.py +218 -0
  265. vivarium_engine-5.0.0/tests/framework/test_configuration.py +131 -0
  266. vivarium_engine-5.0.0/tests/framework/test_engine.py +568 -0
  267. vivarium_engine-5.0.0/tests/framework/test_event.py +146 -0
  268. vivarium_engine-5.0.0/tests/framework/test_lifecycle.py +438 -0
  269. vivarium_engine-5.0.0/tests/framework/test_plugins.py +143 -0
  270. vivarium_engine-5.0.0/tests/framework/test_state_machine.py +248 -0
  271. vivarium_engine-5.0.0/tests/framework/test_time.py +569 -0
  272. vivarium_engine-5.0.0/tests/framework/test_utilities.py +169 -0
  273. vivarium_engine-5.0.0/tests/framework/test_values.py +1191 -0
  274. vivarium_engine-5.0.0/tests/helpers.py +476 -0
  275. vivarium_engine-5.0.0/tests/interface/__init__.py +0 -0
  276. vivarium_engine-5.0.0/tests/interface/test_cli.py +73 -0
  277. vivarium_engine-5.0.0/tests/interface/test_interactive.py +368 -0
  278. vivarium_engine-5.0.0/tests/interface/test_utilities.py +73 -0
  279. vivarium_engine-5.0.0/tests/test_data/bad_model_specification.txt +17 -0
  280. vivarium_engine-5.0.0/tests/test_data/mock_model_specification.yaml +17 -0
  281. vivarium_engine-5.0.0/tests/test_data/mock_model_specification.yml +17 -0
  282. vivarium_engine-5.0.0/tests/test_data/mock_user_config.yaml +2 -0
  283. vivarium_engine-5.0.0/tests/test_data/mock_user_config.yml +2 -0
  284. vivarium_engine-5.0.0/tests/test_package.py +213 -0
@@ -0,0 +1,27 @@
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+ # Paths are repo-root-relative even when this file lives in a subdirectory,
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+ # so the package path must be qualified with libs/engine/.
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+ #
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+ # This file is read by RTD only when the vivarium-engine RTD project's
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+ # Admin > Advanced Settings > "Path for .readthedocs.yaml" points here. The
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+ # root-level /.readthedocs.yaml is a placeholder used by the import wizard
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+ # and ignored for any project that has overridden the path.
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+ version: 2
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+
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+ sphinx:
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+ configuration: libs/engine/docs/source/conf.py
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+ fail_on_warning: true
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+
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+ build:
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+ os: ubuntu-22.04
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+ tools:
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+ python: "3.13"
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+
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+ python:
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+ install:
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+ - method: pip
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+ path: libs/engine
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+ extra_requirements:
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+ - docs
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+
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+ formats:
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+ - pdf
@@ -0,0 +1,67 @@
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+ {
2
+ "license": "BSD-3-Clause",
3
+ "title": "ihmeuw/vivarium: Archival release",
4
+ "upload_type": "software",
5
+ "creators": [
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+ {
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+ "orcid": "0000-0001-7633-7804",
8
+ "affiliation": "Institute for Health Metrics and Evaluation",
9
+ "name": "James Collins"
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+ },
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+ {
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+ "affiliation": "Institute for Health Metrics and Evaluation",
13
+ "name": "Alec Deason"
14
+ },
15
+ {
16
+ "orcid": "0000-0002-6538-2615",
17
+ "affiliation": "Institute for Health Metrics and Evaluation",
18
+ "name": "Kate Wilson"
19
+ },
20
+ {
21
+ "affiliation": "Institute for Health Metrics and Evaluation",
22
+ "name": "Everett Mumford"
23
+ },
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+ {
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+ "orcid": "0000-0001-6033-4713",
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+ "affiliation": "Institute for Health Metrics and Evaluation",
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+ "name": "Abraham Flaxman"
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+ },
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+ {
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+ "orcid": "0000-0001-8649-7561",
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+ "affiliation": "Institute for Health Metrics and Evaluation",
32
+ "name": "Rajan Mudambi"
33
+ },
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+ {
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+ "orcid": "0000-0003-0778-295X",
36
+ "affiliation": "Institute for Health Metrics and Evaluation",
37
+ "name": "Kjell Swedin"
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+ },
39
+ {
40
+ "affiliation": "University of Melbourne",
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+ "name": "Patrick Andersen"
42
+ },
43
+ {
44
+ "affiliation": "Institute for Health Metrics and Evaluation",
45
+ "name": "Cody Horst"
46
+ },
47
+ {
48
+ "affiliation": "Institute for Health Metrics and Evaluation",
49
+ "name": "Jonathan Joseph"
50
+ },
51
+ {
52
+ "affiliation": "Institute for Health Metrics and Evaluation",
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+ "name": "Michelle Park"
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+ },
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+ {
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+ "affiliation": "Institute for Health Metrics and Evaluation",
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+ "name": "Reed Sorensen"
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+ },
59
+ {
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+ "orcid": "0000-0003-2430-5661",
61
+ "affiliation": "Institute for Health Metrics and Evaluation",
62
+ "name": "Matthew Kappel"
63
+ }
64
+ ],
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+ "access_right": "open",
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+ "description": "Vivarium is a simulation framework written using standard scientific Python tools."
67
+ }