opentrons 8.6.0__py3-none-any.whl

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  1. opentrons/__init__.py +150 -0
  2. opentrons/_version.py +34 -0
  3. opentrons/calibration_storage/__init__.py +54 -0
  4. opentrons/calibration_storage/deck_configuration.py +62 -0
  5. opentrons/calibration_storage/encoder_decoder.py +31 -0
  6. opentrons/calibration_storage/file_operators.py +142 -0
  7. opentrons/calibration_storage/helpers.py +103 -0
  8. opentrons/calibration_storage/ot2/__init__.py +34 -0
  9. opentrons/calibration_storage/ot2/deck_attitude.py +85 -0
  10. opentrons/calibration_storage/ot2/mark_bad_calibration.py +27 -0
  11. opentrons/calibration_storage/ot2/models/__init__.py +0 -0
  12. opentrons/calibration_storage/ot2/models/v1.py +149 -0
  13. opentrons/calibration_storage/ot2/pipette_offset.py +129 -0
  14. opentrons/calibration_storage/ot2/tip_length.py +281 -0
  15. opentrons/calibration_storage/ot3/__init__.py +31 -0
  16. opentrons/calibration_storage/ot3/deck_attitude.py +83 -0
  17. opentrons/calibration_storage/ot3/gripper_offset.py +156 -0
  18. opentrons/calibration_storage/ot3/models/__init__.py +0 -0
  19. opentrons/calibration_storage/ot3/models/v1.py +122 -0
  20. opentrons/calibration_storage/ot3/module_offset.py +138 -0
  21. opentrons/calibration_storage/ot3/pipette_offset.py +95 -0
  22. opentrons/calibration_storage/types.py +45 -0
  23. opentrons/cli/__init__.py +21 -0
  24. opentrons/cli/__main__.py +5 -0
  25. opentrons/cli/analyze.py +557 -0
  26. opentrons/config/__init__.py +631 -0
  27. opentrons/config/advanced_settings.py +871 -0
  28. opentrons/config/defaults_ot2.py +214 -0
  29. opentrons/config/defaults_ot3.py +499 -0
  30. opentrons/config/feature_flags.py +86 -0
  31. opentrons/config/gripper_config.py +55 -0
  32. opentrons/config/reset.py +203 -0
  33. opentrons/config/robot_configs.py +187 -0
  34. opentrons/config/types.py +183 -0
  35. opentrons/drivers/__init__.py +0 -0
  36. opentrons/drivers/absorbance_reader/__init__.py +11 -0
  37. opentrons/drivers/absorbance_reader/abstract.py +72 -0
  38. opentrons/drivers/absorbance_reader/async_byonoy.py +352 -0
  39. opentrons/drivers/absorbance_reader/driver.py +81 -0
  40. opentrons/drivers/absorbance_reader/hid_protocol.py +161 -0
  41. opentrons/drivers/absorbance_reader/simulator.py +84 -0
  42. opentrons/drivers/asyncio/__init__.py +0 -0
  43. opentrons/drivers/asyncio/communication/__init__.py +22 -0
  44. opentrons/drivers/asyncio/communication/async_serial.py +187 -0
  45. opentrons/drivers/asyncio/communication/errors.py +88 -0
  46. opentrons/drivers/asyncio/communication/serial_connection.py +557 -0
  47. opentrons/drivers/command_builder.py +102 -0
  48. opentrons/drivers/flex_stacker/__init__.py +13 -0
  49. opentrons/drivers/flex_stacker/abstract.py +214 -0
  50. opentrons/drivers/flex_stacker/driver.py +768 -0
  51. opentrons/drivers/flex_stacker/errors.py +68 -0
  52. opentrons/drivers/flex_stacker/simulator.py +309 -0
  53. opentrons/drivers/flex_stacker/types.py +367 -0
  54. opentrons/drivers/flex_stacker/utils.py +19 -0
  55. opentrons/drivers/heater_shaker/__init__.py +5 -0
  56. opentrons/drivers/heater_shaker/abstract.py +76 -0
  57. opentrons/drivers/heater_shaker/driver.py +204 -0
  58. opentrons/drivers/heater_shaker/simulator.py +94 -0
  59. opentrons/drivers/mag_deck/__init__.py +6 -0
  60. opentrons/drivers/mag_deck/abstract.py +44 -0
  61. opentrons/drivers/mag_deck/driver.py +208 -0
  62. opentrons/drivers/mag_deck/simulator.py +63 -0
  63. opentrons/drivers/rpi_drivers/__init__.py +33 -0
  64. opentrons/drivers/rpi_drivers/dev_types.py +94 -0
  65. opentrons/drivers/rpi_drivers/gpio.py +282 -0
  66. opentrons/drivers/rpi_drivers/gpio_simulator.py +127 -0
  67. opentrons/drivers/rpi_drivers/interfaces.py +15 -0
  68. opentrons/drivers/rpi_drivers/types.py +364 -0
  69. opentrons/drivers/rpi_drivers/usb.py +102 -0
  70. opentrons/drivers/rpi_drivers/usb_simulator.py +22 -0
  71. opentrons/drivers/serial_communication.py +151 -0
  72. opentrons/drivers/smoothie_drivers/__init__.py +4 -0
  73. opentrons/drivers/smoothie_drivers/connection.py +51 -0
  74. opentrons/drivers/smoothie_drivers/constants.py +121 -0
  75. opentrons/drivers/smoothie_drivers/driver_3_0.py +1933 -0
  76. opentrons/drivers/smoothie_drivers/errors.py +49 -0
  77. opentrons/drivers/smoothie_drivers/parse_utils.py +143 -0
  78. opentrons/drivers/smoothie_drivers/simulator.py +99 -0
  79. opentrons/drivers/smoothie_drivers/types.py +16 -0
  80. opentrons/drivers/temp_deck/__init__.py +10 -0
  81. opentrons/drivers/temp_deck/abstract.py +54 -0
  82. opentrons/drivers/temp_deck/driver.py +197 -0
  83. opentrons/drivers/temp_deck/simulator.py +57 -0
  84. opentrons/drivers/thermocycler/__init__.py +12 -0
  85. opentrons/drivers/thermocycler/abstract.py +99 -0
  86. opentrons/drivers/thermocycler/driver.py +395 -0
  87. opentrons/drivers/thermocycler/simulator.py +126 -0
  88. opentrons/drivers/types.py +107 -0
  89. opentrons/drivers/utils.py +222 -0
  90. opentrons/execute.py +742 -0
  91. opentrons/hardware_control/__init__.py +65 -0
  92. opentrons/hardware_control/__main__.py +77 -0
  93. opentrons/hardware_control/adapters.py +98 -0
  94. opentrons/hardware_control/api.py +1347 -0
  95. opentrons/hardware_control/backends/__init__.py +7 -0
  96. opentrons/hardware_control/backends/controller.py +400 -0
  97. opentrons/hardware_control/backends/errors.py +9 -0
  98. opentrons/hardware_control/backends/estop_state.py +164 -0
  99. opentrons/hardware_control/backends/flex_protocol.py +497 -0
  100. opentrons/hardware_control/backends/ot3controller.py +1930 -0
  101. opentrons/hardware_control/backends/ot3simulator.py +900 -0
  102. opentrons/hardware_control/backends/ot3utils.py +664 -0
  103. opentrons/hardware_control/backends/simulator.py +442 -0
  104. opentrons/hardware_control/backends/status_bar_state.py +240 -0
  105. opentrons/hardware_control/backends/subsystem_manager.py +431 -0
  106. opentrons/hardware_control/backends/tip_presence_manager.py +173 -0
  107. opentrons/hardware_control/backends/types.py +14 -0
  108. opentrons/hardware_control/constants.py +6 -0
  109. opentrons/hardware_control/dev_types.py +125 -0
  110. opentrons/hardware_control/emulation/__init__.py +0 -0
  111. opentrons/hardware_control/emulation/abstract_emulator.py +21 -0
  112. opentrons/hardware_control/emulation/app.py +56 -0
  113. opentrons/hardware_control/emulation/connection_handler.py +38 -0
  114. opentrons/hardware_control/emulation/heater_shaker.py +150 -0
  115. opentrons/hardware_control/emulation/magdeck.py +60 -0
  116. opentrons/hardware_control/emulation/module_server/__init__.py +8 -0
  117. opentrons/hardware_control/emulation/module_server/client.py +78 -0
  118. opentrons/hardware_control/emulation/module_server/helpers.py +130 -0
  119. opentrons/hardware_control/emulation/module_server/models.py +31 -0
  120. opentrons/hardware_control/emulation/module_server/server.py +110 -0
  121. opentrons/hardware_control/emulation/parser.py +74 -0
  122. opentrons/hardware_control/emulation/proxy.py +241 -0
  123. opentrons/hardware_control/emulation/run_emulator.py +68 -0
  124. opentrons/hardware_control/emulation/scripts/__init__.py +0 -0
  125. opentrons/hardware_control/emulation/scripts/run_app.py +54 -0
  126. opentrons/hardware_control/emulation/scripts/run_module_emulator.py +72 -0
  127. opentrons/hardware_control/emulation/scripts/run_smoothie.py +37 -0
  128. opentrons/hardware_control/emulation/settings.py +119 -0
  129. opentrons/hardware_control/emulation/simulations.py +133 -0
  130. opentrons/hardware_control/emulation/smoothie.py +192 -0
  131. opentrons/hardware_control/emulation/tempdeck.py +69 -0
  132. opentrons/hardware_control/emulation/thermocycler.py +128 -0
  133. opentrons/hardware_control/emulation/types.py +10 -0
  134. opentrons/hardware_control/emulation/util.py +38 -0
  135. opentrons/hardware_control/errors.py +43 -0
  136. opentrons/hardware_control/execution_manager.py +164 -0
  137. opentrons/hardware_control/instruments/__init__.py +5 -0
  138. opentrons/hardware_control/instruments/instrument_abc.py +39 -0
  139. opentrons/hardware_control/instruments/ot2/__init__.py +0 -0
  140. opentrons/hardware_control/instruments/ot2/instrument_calibration.py +152 -0
  141. opentrons/hardware_control/instruments/ot2/pipette.py +777 -0
  142. opentrons/hardware_control/instruments/ot2/pipette_handler.py +995 -0
  143. opentrons/hardware_control/instruments/ot3/__init__.py +0 -0
  144. opentrons/hardware_control/instruments/ot3/gripper.py +420 -0
  145. opentrons/hardware_control/instruments/ot3/gripper_handler.py +173 -0
  146. opentrons/hardware_control/instruments/ot3/instrument_calibration.py +214 -0
  147. opentrons/hardware_control/instruments/ot3/pipette.py +858 -0
  148. opentrons/hardware_control/instruments/ot3/pipette_handler.py +1030 -0
  149. opentrons/hardware_control/module_control.py +332 -0
  150. opentrons/hardware_control/modules/__init__.py +69 -0
  151. opentrons/hardware_control/modules/absorbance_reader.py +373 -0
  152. opentrons/hardware_control/modules/errors.py +7 -0
  153. opentrons/hardware_control/modules/flex_stacker.py +948 -0
  154. opentrons/hardware_control/modules/heater_shaker.py +426 -0
  155. opentrons/hardware_control/modules/lid_temp_status.py +35 -0
  156. opentrons/hardware_control/modules/magdeck.py +233 -0
  157. opentrons/hardware_control/modules/mod_abc.py +245 -0
  158. opentrons/hardware_control/modules/module_calibration.py +93 -0
  159. opentrons/hardware_control/modules/plate_temp_status.py +61 -0
  160. opentrons/hardware_control/modules/tempdeck.py +299 -0
  161. opentrons/hardware_control/modules/thermocycler.py +731 -0
  162. opentrons/hardware_control/modules/types.py +417 -0
  163. opentrons/hardware_control/modules/update.py +255 -0
  164. opentrons/hardware_control/modules/utils.py +73 -0
  165. opentrons/hardware_control/motion_utilities.py +318 -0
  166. opentrons/hardware_control/nozzle_manager.py +422 -0
  167. opentrons/hardware_control/ot3_calibration.py +1171 -0
  168. opentrons/hardware_control/ot3api.py +3227 -0
  169. opentrons/hardware_control/pause_manager.py +31 -0
  170. opentrons/hardware_control/poller.py +112 -0
  171. opentrons/hardware_control/protocols/__init__.py +106 -0
  172. opentrons/hardware_control/protocols/asyncio_configurable.py +11 -0
  173. opentrons/hardware_control/protocols/calibratable.py +45 -0
  174. opentrons/hardware_control/protocols/chassis_accessory_manager.py +90 -0
  175. opentrons/hardware_control/protocols/configurable.py +48 -0
  176. opentrons/hardware_control/protocols/event_sourcer.py +18 -0
  177. opentrons/hardware_control/protocols/execution_controllable.py +33 -0
  178. opentrons/hardware_control/protocols/flex_calibratable.py +96 -0
  179. opentrons/hardware_control/protocols/flex_instrument_configurer.py +52 -0
  180. opentrons/hardware_control/protocols/gripper_controller.py +55 -0
  181. opentrons/hardware_control/protocols/hardware_manager.py +51 -0
  182. opentrons/hardware_control/protocols/identifiable.py +16 -0
  183. opentrons/hardware_control/protocols/instrument_configurer.py +206 -0
  184. opentrons/hardware_control/protocols/liquid_handler.py +266 -0
  185. opentrons/hardware_control/protocols/module_provider.py +16 -0
  186. opentrons/hardware_control/protocols/motion_controller.py +243 -0
  187. opentrons/hardware_control/protocols/position_estimator.py +45 -0
  188. opentrons/hardware_control/protocols/simulatable.py +10 -0
  189. opentrons/hardware_control/protocols/stoppable.py +9 -0
  190. opentrons/hardware_control/protocols/types.py +27 -0
  191. opentrons/hardware_control/robot_calibration.py +224 -0
  192. opentrons/hardware_control/scripts/README.md +28 -0
  193. opentrons/hardware_control/scripts/__init__.py +1 -0
  194. opentrons/hardware_control/scripts/gripper_control.py +208 -0
  195. opentrons/hardware_control/scripts/ot3gripper +7 -0
  196. opentrons/hardware_control/scripts/ot3repl +7 -0
  197. opentrons/hardware_control/scripts/repl.py +187 -0
  198. opentrons/hardware_control/scripts/tc_control.py +97 -0
  199. opentrons/hardware_control/scripts/update_module_fw.py +274 -0
  200. opentrons/hardware_control/simulator_setup.py +260 -0
  201. opentrons/hardware_control/thread_manager.py +431 -0
  202. opentrons/hardware_control/threaded_async_lock.py +97 -0
  203. opentrons/hardware_control/types.py +792 -0
  204. opentrons/hardware_control/util.py +234 -0
  205. opentrons/legacy_broker.py +53 -0
  206. opentrons/legacy_commands/__init__.py +1 -0
  207. opentrons/legacy_commands/commands.py +483 -0
  208. opentrons/legacy_commands/helpers.py +153 -0
  209. opentrons/legacy_commands/module_commands.py +276 -0
  210. opentrons/legacy_commands/protocol_commands.py +54 -0
  211. opentrons/legacy_commands/publisher.py +155 -0
  212. opentrons/legacy_commands/robot_commands.py +51 -0
  213. opentrons/legacy_commands/types.py +1186 -0
  214. opentrons/motion_planning/__init__.py +32 -0
  215. opentrons/motion_planning/adjacent_slots_getters.py +168 -0
  216. opentrons/motion_planning/deck_conflict.py +501 -0
  217. opentrons/motion_planning/errors.py +35 -0
  218. opentrons/motion_planning/types.py +42 -0
  219. opentrons/motion_planning/waypoints.py +218 -0
  220. opentrons/ordered_set.py +138 -0
  221. opentrons/protocol_api/__init__.py +105 -0
  222. opentrons/protocol_api/_liquid.py +157 -0
  223. opentrons/protocol_api/_liquid_properties.py +814 -0
  224. opentrons/protocol_api/_nozzle_layout.py +31 -0
  225. opentrons/protocol_api/_parameter_context.py +300 -0
  226. opentrons/protocol_api/_parameters.py +31 -0
  227. opentrons/protocol_api/_transfer_liquid_validation.py +108 -0
  228. opentrons/protocol_api/_types.py +43 -0
  229. opentrons/protocol_api/config.py +23 -0
  230. opentrons/protocol_api/core/__init__.py +23 -0
  231. opentrons/protocol_api/core/common.py +33 -0
  232. opentrons/protocol_api/core/core_map.py +74 -0
  233. opentrons/protocol_api/core/engine/__init__.py +22 -0
  234. opentrons/protocol_api/core/engine/_default_labware_versions.py +179 -0
  235. opentrons/protocol_api/core/engine/deck_conflict.py +400 -0
  236. opentrons/protocol_api/core/engine/exceptions.py +19 -0
  237. opentrons/protocol_api/core/engine/instrument.py +2391 -0
  238. opentrons/protocol_api/core/engine/labware.py +238 -0
  239. opentrons/protocol_api/core/engine/load_labware_params.py +73 -0
  240. opentrons/protocol_api/core/engine/module_core.py +1027 -0
  241. opentrons/protocol_api/core/engine/overlap_versions.py +20 -0
  242. opentrons/protocol_api/core/engine/pipette_movement_conflict.py +358 -0
  243. opentrons/protocol_api/core/engine/point_calculations.py +64 -0
  244. opentrons/protocol_api/core/engine/protocol.py +1153 -0
  245. opentrons/protocol_api/core/engine/robot.py +139 -0
  246. opentrons/protocol_api/core/engine/stringify.py +74 -0
  247. opentrons/protocol_api/core/engine/transfer_components_executor.py +1006 -0
  248. opentrons/protocol_api/core/engine/well.py +241 -0
  249. opentrons/protocol_api/core/instrument.py +459 -0
  250. opentrons/protocol_api/core/labware.py +151 -0
  251. opentrons/protocol_api/core/legacy/__init__.py +11 -0
  252. opentrons/protocol_api/core/legacy/_labware_geometry.py +37 -0
  253. opentrons/protocol_api/core/legacy/deck.py +369 -0
  254. opentrons/protocol_api/core/legacy/labware_offset_provider.py +108 -0
  255. opentrons/protocol_api/core/legacy/legacy_instrument_core.py +709 -0
  256. opentrons/protocol_api/core/legacy/legacy_labware_core.py +235 -0
  257. opentrons/protocol_api/core/legacy/legacy_module_core.py +592 -0
  258. opentrons/protocol_api/core/legacy/legacy_protocol_core.py +612 -0
  259. opentrons/protocol_api/core/legacy/legacy_well_core.py +162 -0
  260. opentrons/protocol_api/core/legacy/load_info.py +67 -0
  261. opentrons/protocol_api/core/legacy/module_geometry.py +547 -0
  262. opentrons/protocol_api/core/legacy/well_geometry.py +148 -0
  263. opentrons/protocol_api/core/legacy_simulator/__init__.py +16 -0
  264. opentrons/protocol_api/core/legacy_simulator/legacy_instrument_core.py +624 -0
  265. opentrons/protocol_api/core/legacy_simulator/legacy_protocol_core.py +85 -0
  266. opentrons/protocol_api/core/module.py +484 -0
  267. opentrons/protocol_api/core/protocol.py +311 -0
  268. opentrons/protocol_api/core/robot.py +51 -0
  269. opentrons/protocol_api/core/well.py +116 -0
  270. opentrons/protocol_api/core/well_grid.py +45 -0
  271. opentrons/protocol_api/create_protocol_context.py +177 -0
  272. opentrons/protocol_api/deck.py +223 -0
  273. opentrons/protocol_api/disposal_locations.py +244 -0
  274. opentrons/protocol_api/instrument_context.py +3272 -0
  275. opentrons/protocol_api/labware.py +1579 -0
  276. opentrons/protocol_api/module_contexts.py +1447 -0
  277. opentrons/protocol_api/module_validation_and_errors.py +61 -0
  278. opentrons/protocol_api/protocol_context.py +1688 -0
  279. opentrons/protocol_api/robot_context.py +303 -0
  280. opentrons/protocol_api/validation.py +761 -0
  281. opentrons/protocol_engine/__init__.py +155 -0
  282. opentrons/protocol_engine/actions/__init__.py +65 -0
  283. opentrons/protocol_engine/actions/action_dispatcher.py +30 -0
  284. opentrons/protocol_engine/actions/action_handler.py +13 -0
  285. opentrons/protocol_engine/actions/actions.py +302 -0
  286. opentrons/protocol_engine/actions/get_state_update.py +38 -0
  287. opentrons/protocol_engine/clients/__init__.py +5 -0
  288. opentrons/protocol_engine/clients/sync_client.py +174 -0
  289. opentrons/protocol_engine/clients/transports.py +197 -0
  290. opentrons/protocol_engine/commands/__init__.py +757 -0
  291. opentrons/protocol_engine/commands/absorbance_reader/__init__.py +61 -0
  292. opentrons/protocol_engine/commands/absorbance_reader/close_lid.py +154 -0
  293. opentrons/protocol_engine/commands/absorbance_reader/common.py +6 -0
  294. opentrons/protocol_engine/commands/absorbance_reader/initialize.py +151 -0
  295. opentrons/protocol_engine/commands/absorbance_reader/open_lid.py +154 -0
  296. opentrons/protocol_engine/commands/absorbance_reader/read.py +226 -0
  297. opentrons/protocol_engine/commands/air_gap_in_place.py +162 -0
  298. opentrons/protocol_engine/commands/aspirate.py +244 -0
  299. opentrons/protocol_engine/commands/aspirate_in_place.py +184 -0
  300. opentrons/protocol_engine/commands/aspirate_while_tracking.py +211 -0
  301. opentrons/protocol_engine/commands/blow_out.py +146 -0
  302. opentrons/protocol_engine/commands/blow_out_in_place.py +119 -0
  303. opentrons/protocol_engine/commands/calibration/__init__.py +60 -0
  304. opentrons/protocol_engine/commands/calibration/calibrate_gripper.py +166 -0
  305. opentrons/protocol_engine/commands/calibration/calibrate_module.py +117 -0
  306. opentrons/protocol_engine/commands/calibration/calibrate_pipette.py +96 -0
  307. opentrons/protocol_engine/commands/calibration/move_to_maintenance_position.py +156 -0
  308. opentrons/protocol_engine/commands/command.py +308 -0
  309. opentrons/protocol_engine/commands/command_unions.py +974 -0
  310. opentrons/protocol_engine/commands/comment.py +57 -0
  311. opentrons/protocol_engine/commands/configure_for_volume.py +108 -0
  312. opentrons/protocol_engine/commands/configure_nozzle_layout.py +115 -0
  313. opentrons/protocol_engine/commands/custom.py +67 -0
  314. opentrons/protocol_engine/commands/dispense.py +194 -0
  315. opentrons/protocol_engine/commands/dispense_in_place.py +179 -0
  316. opentrons/protocol_engine/commands/dispense_while_tracking.py +204 -0
  317. opentrons/protocol_engine/commands/drop_tip.py +232 -0
  318. opentrons/protocol_engine/commands/drop_tip_in_place.py +205 -0
  319. opentrons/protocol_engine/commands/flex_stacker/__init__.py +64 -0
  320. opentrons/protocol_engine/commands/flex_stacker/common.py +900 -0
  321. opentrons/protocol_engine/commands/flex_stacker/empty.py +293 -0
  322. opentrons/protocol_engine/commands/flex_stacker/fill.py +281 -0
  323. opentrons/protocol_engine/commands/flex_stacker/retrieve.py +339 -0
  324. opentrons/protocol_engine/commands/flex_stacker/set_stored_labware.py +328 -0
  325. opentrons/protocol_engine/commands/flex_stacker/store.py +339 -0
  326. opentrons/protocol_engine/commands/generate_command_schema.py +61 -0
  327. opentrons/protocol_engine/commands/get_next_tip.py +134 -0
  328. opentrons/protocol_engine/commands/get_tip_presence.py +87 -0
  329. opentrons/protocol_engine/commands/hash_command_params.py +38 -0
  330. opentrons/protocol_engine/commands/heater_shaker/__init__.py +102 -0
  331. opentrons/protocol_engine/commands/heater_shaker/close_labware_latch.py +83 -0
  332. opentrons/protocol_engine/commands/heater_shaker/deactivate_heater.py +82 -0
  333. opentrons/protocol_engine/commands/heater_shaker/deactivate_shaker.py +84 -0
  334. opentrons/protocol_engine/commands/heater_shaker/open_labware_latch.py +110 -0
  335. opentrons/protocol_engine/commands/heater_shaker/set_and_wait_for_shake_speed.py +125 -0
  336. opentrons/protocol_engine/commands/heater_shaker/set_target_temperature.py +90 -0
  337. opentrons/protocol_engine/commands/heater_shaker/wait_for_temperature.py +102 -0
  338. opentrons/protocol_engine/commands/home.py +100 -0
  339. opentrons/protocol_engine/commands/identify_module.py +86 -0
  340. opentrons/protocol_engine/commands/labware_handling_common.py +29 -0
  341. opentrons/protocol_engine/commands/liquid_probe.py +464 -0
  342. opentrons/protocol_engine/commands/load_labware.py +210 -0
  343. opentrons/protocol_engine/commands/load_lid.py +154 -0
  344. opentrons/protocol_engine/commands/load_lid_stack.py +272 -0
  345. opentrons/protocol_engine/commands/load_liquid.py +95 -0
  346. opentrons/protocol_engine/commands/load_liquid_class.py +144 -0
  347. opentrons/protocol_engine/commands/load_module.py +223 -0
  348. opentrons/protocol_engine/commands/load_pipette.py +167 -0
  349. opentrons/protocol_engine/commands/magnetic_module/__init__.py +32 -0
  350. opentrons/protocol_engine/commands/magnetic_module/disengage.py +97 -0
  351. opentrons/protocol_engine/commands/magnetic_module/engage.py +119 -0
  352. opentrons/protocol_engine/commands/move_labware.py +546 -0
  353. opentrons/protocol_engine/commands/move_relative.py +102 -0
  354. opentrons/protocol_engine/commands/move_to_addressable_area.py +176 -0
  355. opentrons/protocol_engine/commands/move_to_addressable_area_for_drop_tip.py +198 -0
  356. opentrons/protocol_engine/commands/move_to_coordinates.py +107 -0
  357. opentrons/protocol_engine/commands/move_to_well.py +119 -0
  358. opentrons/protocol_engine/commands/movement_common.py +338 -0
  359. opentrons/protocol_engine/commands/pick_up_tip.py +241 -0
  360. opentrons/protocol_engine/commands/pipetting_common.py +443 -0
  361. opentrons/protocol_engine/commands/prepare_to_aspirate.py +121 -0
  362. opentrons/protocol_engine/commands/pressure_dispense.py +155 -0
  363. opentrons/protocol_engine/commands/reload_labware.py +90 -0
  364. opentrons/protocol_engine/commands/retract_axis.py +75 -0
  365. opentrons/protocol_engine/commands/robot/__init__.py +70 -0
  366. opentrons/protocol_engine/commands/robot/close_gripper_jaw.py +96 -0
  367. opentrons/protocol_engine/commands/robot/common.py +18 -0
  368. opentrons/protocol_engine/commands/robot/move_axes_relative.py +101 -0
  369. opentrons/protocol_engine/commands/robot/move_axes_to.py +100 -0
  370. opentrons/protocol_engine/commands/robot/move_to.py +94 -0
  371. opentrons/protocol_engine/commands/robot/open_gripper_jaw.py +86 -0
  372. opentrons/protocol_engine/commands/save_position.py +109 -0
  373. opentrons/protocol_engine/commands/seal_pipette_to_tip.py +353 -0
  374. opentrons/protocol_engine/commands/set_rail_lights.py +67 -0
  375. opentrons/protocol_engine/commands/set_status_bar.py +89 -0
  376. opentrons/protocol_engine/commands/temperature_module/__init__.py +46 -0
  377. opentrons/protocol_engine/commands/temperature_module/deactivate.py +86 -0
  378. opentrons/protocol_engine/commands/temperature_module/set_target_temperature.py +97 -0
  379. opentrons/protocol_engine/commands/temperature_module/wait_for_temperature.py +104 -0
  380. opentrons/protocol_engine/commands/thermocycler/__init__.py +152 -0
  381. opentrons/protocol_engine/commands/thermocycler/close_lid.py +87 -0
  382. opentrons/protocol_engine/commands/thermocycler/deactivate_block.py +80 -0
  383. opentrons/protocol_engine/commands/thermocycler/deactivate_lid.py +80 -0
  384. opentrons/protocol_engine/commands/thermocycler/open_lid.py +87 -0
  385. opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py +171 -0
  386. opentrons/protocol_engine/commands/thermocycler/run_profile.py +124 -0
  387. opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py +140 -0
  388. opentrons/protocol_engine/commands/thermocycler/set_target_lid_temperature.py +100 -0
  389. opentrons/protocol_engine/commands/thermocycler/wait_for_block_temperature.py +93 -0
  390. opentrons/protocol_engine/commands/thermocycler/wait_for_lid_temperature.py +89 -0
  391. opentrons/protocol_engine/commands/touch_tip.py +189 -0
  392. opentrons/protocol_engine/commands/unsafe/__init__.py +161 -0
  393. opentrons/protocol_engine/commands/unsafe/unsafe_blow_out_in_place.py +100 -0
  394. opentrons/protocol_engine/commands/unsafe/unsafe_drop_tip_in_place.py +121 -0
  395. opentrons/protocol_engine/commands/unsafe/unsafe_engage_axes.py +82 -0
  396. opentrons/protocol_engine/commands/unsafe/unsafe_place_labware.py +208 -0
  397. opentrons/protocol_engine/commands/unsafe/unsafe_stacker_close_latch.py +94 -0
  398. opentrons/protocol_engine/commands/unsafe/unsafe_stacker_manual_retrieve.py +295 -0
  399. opentrons/protocol_engine/commands/unsafe/unsafe_stacker_open_latch.py +91 -0
  400. opentrons/protocol_engine/commands/unsafe/unsafe_stacker_prepare_shuttle.py +136 -0
  401. opentrons/protocol_engine/commands/unsafe/unsafe_ungrip_labware.py +77 -0
  402. opentrons/protocol_engine/commands/unsafe/update_position_estimators.py +90 -0
  403. opentrons/protocol_engine/commands/unseal_pipette_from_tip.py +153 -0
  404. opentrons/protocol_engine/commands/verify_tip_presence.py +100 -0
  405. opentrons/protocol_engine/commands/wait_for_duration.py +76 -0
  406. opentrons/protocol_engine/commands/wait_for_resume.py +75 -0
  407. opentrons/protocol_engine/create_protocol_engine.py +193 -0
  408. opentrons/protocol_engine/engine_support.py +28 -0
  409. opentrons/protocol_engine/error_recovery_policy.py +81 -0
  410. opentrons/protocol_engine/errors/__init__.py +191 -0
  411. opentrons/protocol_engine/errors/error_occurrence.py +182 -0
  412. opentrons/protocol_engine/errors/exceptions.py +1308 -0
  413. opentrons/protocol_engine/execution/__init__.py +50 -0
  414. opentrons/protocol_engine/execution/command_executor.py +216 -0
  415. opentrons/protocol_engine/execution/create_queue_worker.py +102 -0
  416. opentrons/protocol_engine/execution/door_watcher.py +119 -0
  417. opentrons/protocol_engine/execution/equipment.py +819 -0
  418. opentrons/protocol_engine/execution/error_recovery_hardware_state_synchronizer.py +101 -0
  419. opentrons/protocol_engine/execution/gantry_mover.py +686 -0
  420. opentrons/protocol_engine/execution/hardware_stopper.py +147 -0
  421. opentrons/protocol_engine/execution/heater_shaker_movement_flagger.py +207 -0
  422. opentrons/protocol_engine/execution/labware_movement.py +297 -0
  423. opentrons/protocol_engine/execution/movement.py +350 -0
  424. opentrons/protocol_engine/execution/pipetting.py +607 -0
  425. opentrons/protocol_engine/execution/queue_worker.py +86 -0
  426. opentrons/protocol_engine/execution/rail_lights.py +25 -0
  427. opentrons/protocol_engine/execution/run_control.py +33 -0
  428. opentrons/protocol_engine/execution/status_bar.py +34 -0
  429. opentrons/protocol_engine/execution/thermocycler_movement_flagger.py +188 -0
  430. opentrons/protocol_engine/execution/thermocycler_plate_lifter.py +81 -0
  431. opentrons/protocol_engine/execution/tip_handler.py +550 -0
  432. opentrons/protocol_engine/labware_offset_standardization.py +194 -0
  433. opentrons/protocol_engine/notes/__init__.py +17 -0
  434. opentrons/protocol_engine/notes/notes.py +59 -0
  435. opentrons/protocol_engine/plugins.py +104 -0
  436. opentrons/protocol_engine/protocol_engine.py +683 -0
  437. opentrons/protocol_engine/resources/__init__.py +26 -0
  438. opentrons/protocol_engine/resources/deck_configuration_provider.py +232 -0
  439. opentrons/protocol_engine/resources/deck_data_provider.py +94 -0
  440. opentrons/protocol_engine/resources/file_provider.py +161 -0
  441. opentrons/protocol_engine/resources/fixture_validation.py +68 -0
  442. opentrons/protocol_engine/resources/labware_data_provider.py +106 -0
  443. opentrons/protocol_engine/resources/labware_validation.py +73 -0
  444. opentrons/protocol_engine/resources/model_utils.py +32 -0
  445. opentrons/protocol_engine/resources/module_data_provider.py +44 -0
  446. opentrons/protocol_engine/resources/ot3_validation.py +21 -0
  447. opentrons/protocol_engine/resources/pipette_data_provider.py +379 -0
  448. opentrons/protocol_engine/slot_standardization.py +128 -0
  449. opentrons/protocol_engine/state/__init__.py +1 -0
  450. opentrons/protocol_engine/state/_abstract_store.py +27 -0
  451. opentrons/protocol_engine/state/_axis_aligned_bounding_box.py +50 -0
  452. opentrons/protocol_engine/state/_labware_origin_math.py +636 -0
  453. opentrons/protocol_engine/state/_move_types.py +83 -0
  454. opentrons/protocol_engine/state/_well_math.py +193 -0
  455. opentrons/protocol_engine/state/addressable_areas.py +699 -0
  456. opentrons/protocol_engine/state/command_history.py +309 -0
  457. opentrons/protocol_engine/state/commands.py +1164 -0
  458. opentrons/protocol_engine/state/config.py +39 -0
  459. opentrons/protocol_engine/state/files.py +57 -0
  460. opentrons/protocol_engine/state/fluid_stack.py +138 -0
  461. opentrons/protocol_engine/state/geometry.py +2408 -0
  462. opentrons/protocol_engine/state/inner_well_math_utils.py +548 -0
  463. opentrons/protocol_engine/state/labware.py +1432 -0
  464. opentrons/protocol_engine/state/liquid_classes.py +82 -0
  465. opentrons/protocol_engine/state/liquids.py +73 -0
  466. opentrons/protocol_engine/state/module_substates/__init__.py +45 -0
  467. opentrons/protocol_engine/state/module_substates/absorbance_reader_substate.py +35 -0
  468. opentrons/protocol_engine/state/module_substates/flex_stacker_substate.py +112 -0
  469. opentrons/protocol_engine/state/module_substates/heater_shaker_module_substate.py +115 -0
  470. opentrons/protocol_engine/state/module_substates/magnetic_block_substate.py +17 -0
  471. opentrons/protocol_engine/state/module_substates/magnetic_module_substate.py +65 -0
  472. opentrons/protocol_engine/state/module_substates/temperature_module_substate.py +67 -0
  473. opentrons/protocol_engine/state/module_substates/thermocycler_module_substate.py +163 -0
  474. opentrons/protocol_engine/state/modules.py +1515 -0
  475. opentrons/protocol_engine/state/motion.py +373 -0
  476. opentrons/protocol_engine/state/pipettes.py +905 -0
  477. opentrons/protocol_engine/state/state.py +421 -0
  478. opentrons/protocol_engine/state/state_summary.py +36 -0
  479. opentrons/protocol_engine/state/tips.py +420 -0
  480. opentrons/protocol_engine/state/update_types.py +904 -0
  481. opentrons/protocol_engine/state/wells.py +290 -0
  482. opentrons/protocol_engine/types/__init__.py +310 -0
  483. opentrons/protocol_engine/types/automatic_tip_selection.py +39 -0
  484. opentrons/protocol_engine/types/command_annotations.py +53 -0
  485. opentrons/protocol_engine/types/deck_configuration.py +81 -0
  486. opentrons/protocol_engine/types/execution.py +96 -0
  487. opentrons/protocol_engine/types/hardware_passthrough.py +25 -0
  488. opentrons/protocol_engine/types/instrument.py +47 -0
  489. opentrons/protocol_engine/types/instrument_sensors.py +47 -0
  490. opentrons/protocol_engine/types/labware.py +131 -0
  491. opentrons/protocol_engine/types/labware_movement.py +22 -0
  492. opentrons/protocol_engine/types/labware_offset_location.py +111 -0
  493. opentrons/protocol_engine/types/labware_offset_vector.py +16 -0
  494. opentrons/protocol_engine/types/liquid.py +40 -0
  495. opentrons/protocol_engine/types/liquid_class.py +59 -0
  496. opentrons/protocol_engine/types/liquid_handling.py +13 -0
  497. opentrons/protocol_engine/types/liquid_level_detection.py +191 -0
  498. opentrons/protocol_engine/types/location.py +194 -0
  499. opentrons/protocol_engine/types/module.py +310 -0
  500. opentrons/protocol_engine/types/partial_tip_configuration.py +76 -0
  501. opentrons/protocol_engine/types/run_time_parameters.py +133 -0
  502. opentrons/protocol_engine/types/tip.py +18 -0
  503. opentrons/protocol_engine/types/util.py +21 -0
  504. opentrons/protocol_engine/types/well_position.py +124 -0
  505. opentrons/protocol_reader/__init__.py +37 -0
  506. opentrons/protocol_reader/extract_labware_definitions.py +66 -0
  507. opentrons/protocol_reader/file_format_validator.py +152 -0
  508. opentrons/protocol_reader/file_hasher.py +27 -0
  509. opentrons/protocol_reader/file_identifier.py +284 -0
  510. opentrons/protocol_reader/file_reader_writer.py +90 -0
  511. opentrons/protocol_reader/input_file.py +16 -0
  512. opentrons/protocol_reader/protocol_files_invalid_error.py +6 -0
  513. opentrons/protocol_reader/protocol_reader.py +188 -0
  514. opentrons/protocol_reader/protocol_source.py +124 -0
  515. opentrons/protocol_reader/role_analyzer.py +86 -0
  516. opentrons/protocol_runner/__init__.py +26 -0
  517. opentrons/protocol_runner/create_simulating_orchestrator.py +118 -0
  518. opentrons/protocol_runner/json_file_reader.py +55 -0
  519. opentrons/protocol_runner/json_translator.py +314 -0
  520. opentrons/protocol_runner/legacy_command_mapper.py +852 -0
  521. opentrons/protocol_runner/legacy_context_plugin.py +116 -0
  522. opentrons/protocol_runner/protocol_runner.py +530 -0
  523. opentrons/protocol_runner/python_protocol_wrappers.py +179 -0
  524. opentrons/protocol_runner/run_orchestrator.py +496 -0
  525. opentrons/protocol_runner/task_queue.py +95 -0
  526. opentrons/protocols/__init__.py +6 -0
  527. opentrons/protocols/advanced_control/__init__.py +0 -0
  528. opentrons/protocols/advanced_control/common.py +38 -0
  529. opentrons/protocols/advanced_control/mix.py +60 -0
  530. opentrons/protocols/advanced_control/transfers/__init__.py +0 -0
  531. opentrons/protocols/advanced_control/transfers/common.py +180 -0
  532. opentrons/protocols/advanced_control/transfers/transfer.py +972 -0
  533. opentrons/protocols/advanced_control/transfers/transfer_liquid_utils.py +231 -0
  534. opentrons/protocols/api_support/__init__.py +0 -0
  535. opentrons/protocols/api_support/constants.py +8 -0
  536. opentrons/protocols/api_support/deck_type.py +110 -0
  537. opentrons/protocols/api_support/definitions.py +18 -0
  538. opentrons/protocols/api_support/instrument.py +151 -0
  539. opentrons/protocols/api_support/labware_like.py +233 -0
  540. opentrons/protocols/api_support/tip_tracker.py +175 -0
  541. opentrons/protocols/api_support/types.py +32 -0
  542. opentrons/protocols/api_support/util.py +403 -0
  543. opentrons/protocols/bundle.py +89 -0
  544. opentrons/protocols/duration/__init__.py +4 -0
  545. opentrons/protocols/duration/errors.py +5 -0
  546. opentrons/protocols/duration/estimator.py +628 -0
  547. opentrons/protocols/execution/__init__.py +0 -0
  548. opentrons/protocols/execution/dev_types.py +181 -0
  549. opentrons/protocols/execution/errors.py +40 -0
  550. opentrons/protocols/execution/execute.py +84 -0
  551. opentrons/protocols/execution/execute_json_v3.py +275 -0
  552. opentrons/protocols/execution/execute_json_v4.py +359 -0
  553. opentrons/protocols/execution/execute_json_v5.py +28 -0
  554. opentrons/protocols/execution/execute_python.py +169 -0
  555. opentrons/protocols/execution/json_dispatchers.py +87 -0
  556. opentrons/protocols/execution/types.py +7 -0
  557. opentrons/protocols/geometry/__init__.py +0 -0
  558. opentrons/protocols/geometry/planning.py +297 -0
  559. opentrons/protocols/labware.py +312 -0
  560. opentrons/protocols/models/__init__.py +0 -0
  561. opentrons/protocols/models/json_protocol.py +679 -0
  562. opentrons/protocols/parameters/__init__.py +0 -0
  563. opentrons/protocols/parameters/csv_parameter_definition.py +77 -0
  564. opentrons/protocols/parameters/csv_parameter_interface.py +96 -0
  565. opentrons/protocols/parameters/exceptions.py +34 -0
  566. opentrons/protocols/parameters/parameter_definition.py +272 -0
  567. opentrons/protocols/parameters/types.py +17 -0
  568. opentrons/protocols/parameters/validation.py +267 -0
  569. opentrons/protocols/parse.py +671 -0
  570. opentrons/protocols/types.py +159 -0
  571. opentrons/py.typed +0 -0
  572. opentrons/resources/scripts/lpc21isp +0 -0
  573. opentrons/resources/smoothie-edge-8414642.hex +23010 -0
  574. opentrons/simulate.py +1065 -0
  575. opentrons/system/__init__.py +6 -0
  576. opentrons/system/camera.py +51 -0
  577. opentrons/system/log_control.py +59 -0
  578. opentrons/system/nmcli.py +856 -0
  579. opentrons/system/resin.py +24 -0
  580. opentrons/system/smoothie_update.py +15 -0
  581. opentrons/system/wifi.py +204 -0
  582. opentrons/tools/__init__.py +0 -0
  583. opentrons/tools/args_handler.py +22 -0
  584. opentrons/tools/write_pipette_memory.py +157 -0
  585. opentrons/types.py +618 -0
  586. opentrons/util/__init__.py +1 -0
  587. opentrons/util/async_helpers.py +166 -0
  588. opentrons/util/broker.py +84 -0
  589. opentrons/util/change_notifier.py +47 -0
  590. opentrons/util/entrypoint_util.py +278 -0
  591. opentrons/util/get_union_elements.py +26 -0
  592. opentrons/util/helpers.py +6 -0
  593. opentrons/util/linal.py +178 -0
  594. opentrons/util/logging_config.py +265 -0
  595. opentrons/util/logging_queue_handler.py +61 -0
  596. opentrons/util/performance_helpers.py +157 -0
  597. opentrons-8.6.0.dist-info/METADATA +37 -0
  598. opentrons-8.6.0.dist-info/RECORD +601 -0
  599. opentrons-8.6.0.dist-info/WHEEL +4 -0
  600. opentrons-8.6.0.dist-info/entry_points.txt +3 -0
  601. opentrons-8.6.0.dist-info/licenses/LICENSE +202 -0
@@ -0,0 +1,664 @@
1
+ """Shared utilities for ot3 hardware control."""
2
+ from typing import Dict, Iterable, List, Set, Tuple, TypeVar, cast, Sequence, Optional
3
+ from typing_extensions import Literal
4
+ from logging import getLogger
5
+ from opentrons.config.defaults_ot3 import (
6
+ DEFAULT_EMULSIFYING_PIPETTE_AXIS_MAX_SPEED,
7
+ )
8
+ from opentrons.config.types import OT3MotionSettings, OT3CurrentSettings, GantryLoad
9
+ from opentrons.hardware_control.types import (
10
+ Axis,
11
+ OT3AxisKind,
12
+ OT3AxisMap,
13
+ CurrentConfig,
14
+ SubSystem,
15
+ OT3Mount,
16
+ InstrumentProbeType,
17
+ PipetteSubType,
18
+ UpdateState,
19
+ UpdateStatus,
20
+ GripperJawState,
21
+ )
22
+ import numpy as np
23
+
24
+ from opentrons_hardware.firmware_bindings.constants import (
25
+ NodeId,
26
+ FirmwareTarget,
27
+ PipetteType,
28
+ SensorId,
29
+ PipetteTipActionType,
30
+ USBTarget,
31
+ GripperJawState as FirmwareGripperjawState,
32
+ )
33
+ from opentrons_hardware.firmware_update.types import FirmwareUpdateStatus, StatusElement
34
+ from opentrons_hardware.hardware_control import network
35
+ from opentrons_hardware.hardware_control.motion_planning import (
36
+ AxisConstraints,
37
+ SystemConstraints,
38
+ Coordinates,
39
+ Move,
40
+ CoordinateValue,
41
+ )
42
+ from opentrons_hardware.hardware_control.tool_sensors import (
43
+ InstrumentProbeTarget,
44
+ PipetteProbeTarget,
45
+ )
46
+ from opentrons_hardware.hardware_control.motion_planning.move_utils import (
47
+ unit_vector_multiplication,
48
+ )
49
+ from opentrons_hardware.hardware_control.motion import (
50
+ create_step,
51
+ NodeIdMotionValues,
52
+ create_home_step,
53
+ create_backoff_step,
54
+ create_tip_action_backoff_step,
55
+ MoveGroup,
56
+ MoveType,
57
+ MoveStopCondition,
58
+ create_gripper_jaw_step,
59
+ create_tip_action_step,
60
+ )
61
+ from opentrons_hardware.hardware_control.constants import interrupts_per_sec
62
+
63
+ GRIPPER_JAW_HOME_TIME: float = 10
64
+ GRIPPER_JAW_GRIP_TIME: float = 10
65
+
66
+ LIMIT_SWITCH_OVERTRAVEL_DISTANCE: float = 1
67
+
68
+ PipetteAction = Literal["clamp", "home"]
69
+
70
+ # TODO: These methods exist to defer uses of NodeId to inside
71
+ # method bodies, which won't be evaluated until called. This is needed
72
+ # because the robot server doesn't have opentrons_ot3_firmware as a dep
73
+ # which is where they're defined, and therefore you can't have references
74
+ # to NodeId that are interpreted at import time because then the robot
75
+ # server tests fail when importing hardware controller. This is obviously
76
+ # terrible and needs to be fixed.
77
+
78
+ SUBSYSTEM_NODEID: Dict[SubSystem, NodeId] = {
79
+ SubSystem.gantry_x: NodeId.gantry_x,
80
+ SubSystem.gantry_y: NodeId.gantry_y,
81
+ SubSystem.head: NodeId.head,
82
+ SubSystem.pipette_left: NodeId.pipette_left,
83
+ SubSystem.pipette_right: NodeId.pipette_right,
84
+ SubSystem.gripper: NodeId.gripper,
85
+ SubSystem.hepa_uv: NodeId.hepa_uv,
86
+ }
87
+
88
+ NODEID_SUBSYSTEM = {node: subsystem for subsystem, node in SUBSYSTEM_NODEID.items()}
89
+
90
+ SUBSYSTEM_USB: Dict[SubSystem, USBTarget] = {SubSystem.rear_panel: USBTarget.rear_panel}
91
+
92
+ USB_SUBSYSTEM = {target: subsystem for subsystem, target in SUBSYSTEM_USB.items()}
93
+
94
+ LOG = getLogger(__name__)
95
+
96
+
97
+ def axis_nodes() -> List["NodeId"]:
98
+ return [
99
+ NodeId.gantry_x,
100
+ NodeId.gantry_y,
101
+ NodeId.head_l,
102
+ NodeId.head_r,
103
+ NodeId.pipette_left,
104
+ NodeId.pipette_right,
105
+ NodeId.gripper_z,
106
+ NodeId.gripper_g,
107
+ ]
108
+
109
+
110
+ def node_axes() -> List[Axis]:
111
+ return Axis.node_axes()
112
+
113
+
114
+ def home_axes() -> List[Axis]:
115
+ return [
116
+ Axis.P_L,
117
+ Axis.P_R,
118
+ Axis.G,
119
+ Axis.Z_L,
120
+ Axis.Z_R,
121
+ Axis.Z_G,
122
+ Axis.X,
123
+ Axis.Y,
124
+ ]
125
+
126
+
127
+ def axis_to_node(axis: Axis) -> "NodeId":
128
+ anm = {
129
+ Axis.X: NodeId.gantry_x,
130
+ Axis.Y: NodeId.gantry_y,
131
+ Axis.Z_L: NodeId.head_l,
132
+ Axis.Z_R: NodeId.head_r,
133
+ Axis.P_L: NodeId.pipette_left,
134
+ Axis.P_R: NodeId.pipette_right,
135
+ Axis.Z_G: NodeId.gripper_z,
136
+ Axis.G: NodeId.gripper_g,
137
+ Axis.Q: NodeId.pipette_left,
138
+ }
139
+ return anm[axis]
140
+
141
+
142
+ def node_to_axis(node: "NodeId") -> Axis:
143
+ nam = {
144
+ NodeId.gantry_x: Axis.X,
145
+ NodeId.gantry_y: Axis.Y,
146
+ NodeId.head_l: Axis.Z_L,
147
+ NodeId.head_r: Axis.Z_R,
148
+ NodeId.pipette_left: Axis.P_L,
149
+ NodeId.pipette_right: Axis.P_R,
150
+ NodeId.gripper_z: Axis.Z_G,
151
+ NodeId.gripper_g: Axis.G,
152
+ }
153
+ return nam[node]
154
+
155
+
156
+ def node_is_axis(node: "NodeId") -> bool:
157
+ try:
158
+ node_to_axis(node)
159
+ return True
160
+ except KeyError:
161
+ return False
162
+
163
+
164
+ def axis_is_node(axis: Axis) -> bool:
165
+ try:
166
+ axis_to_node(axis)
167
+ return True
168
+ except KeyError:
169
+ return False
170
+
171
+
172
+ def sub_system_to_nodeid(sub_sys: SubSystem) -> "NodeId":
173
+ """Convert a sub system to a NodeId."""
174
+ return SUBSYSTEM_NODEID[sub_sys]
175
+
176
+
177
+ def node_id_to_subsystem(node_id: NodeId) -> "SubSystem":
178
+ """Convert a NodeId to a Subsystem"""
179
+ return NODEID_SUBSYSTEM[node_id.application_for()]
180
+
181
+
182
+ def usb_to_subsystem(target: USBTarget) -> SubSystem:
183
+ return USB_SUBSYSTEM[target]
184
+
185
+
186
+ def subsystem_to_usb(subsystem: SubSystem) -> USBTarget:
187
+ return SUBSYSTEM_USB[subsystem]
188
+
189
+
190
+ def target_to_subsystem(target: FirmwareTarget) -> SubSystem:
191
+ if isinstance(target, USBTarget):
192
+ return usb_to_subsystem(target)
193
+ elif isinstance(target, NodeId):
194
+ return node_id_to_subsystem(target)
195
+ else:
196
+ raise KeyError(target)
197
+
198
+
199
+ def subsystem_to_target(subsystem: SubSystem) -> FirmwareTarget:
200
+ try:
201
+ return sub_system_to_nodeid(subsystem)
202
+ except KeyError:
203
+ return subsystem_to_usb(subsystem)
204
+
205
+
206
+ def get_current_settings(
207
+ config: OT3CurrentSettings,
208
+ gantry_load: GantryLoad,
209
+ ) -> OT3AxisMap[CurrentConfig]:
210
+ conf_by_pip = config.by_gantry_load(gantry_load)
211
+ currents = {}
212
+ for axis_kind in conf_by_pip["hold_current"].keys():
213
+ for axis in Axis.of_kind(axis_kind):
214
+ currents[axis] = CurrentConfig(
215
+ hold_current=conf_by_pip["hold_current"][axis_kind],
216
+ run_current=conf_by_pip["run_current"][axis_kind],
217
+ )
218
+ if gantry_load in [GantryLoad.HIGH_THROUGHPUT_1000, GantryLoad.HIGH_THROUGHPUT_200]:
219
+ # In high-throughput configuration, the right mount doesn't do anything: the
220
+ # lead screw nut is disconnected from the carriage, and it just hangs out
221
+ # up at the top of the axis. We should therefore not give it a lot of current.
222
+ # TODO: think of a better way to do this
223
+ lt_config = config.by_gantry_load(GantryLoad.LOW_THROUGHPUT)
224
+ currents[Axis.Z_R] = CurrentConfig(
225
+ hold_current=lt_config["hold_current"][OT3AxisKind.Z],
226
+ # not a typo: keep that current low
227
+ run_current=lt_config["hold_current"][OT3AxisKind.Z],
228
+ )
229
+ return currents
230
+
231
+
232
+ def get_system_constraints(
233
+ config: OT3MotionSettings,
234
+ gantry_load: GantryLoad,
235
+ ) -> "SystemConstraints[Axis]":
236
+ conf_by_pip = config.by_gantry_load(gantry_load)
237
+ constraints = {}
238
+ axis_kind_list = [
239
+ OT3AxisKind.P,
240
+ OT3AxisKind.X,
241
+ OT3AxisKind.Y,
242
+ OT3AxisKind.Z,
243
+ OT3AxisKind.Z_G,
244
+ ]
245
+ if gantry_load in [GantryLoad.HIGH_THROUGHPUT_1000, GantryLoad.HIGH_THROUGHPUT_200]:
246
+ axis_kind_list.append(OT3AxisKind.Q)
247
+ for axis_kind in axis_kind_list:
248
+ for axis in Axis.of_kind(axis_kind):
249
+ constraints[axis] = AxisConstraints.build(
250
+ conf_by_pip["acceleration"][axis_kind],
251
+ conf_by_pip["max_speed_discontinuity"][axis_kind],
252
+ conf_by_pip["direction_change_speed_discontinuity"][axis_kind],
253
+ conf_by_pip["default_max_speed"][axis_kind],
254
+ )
255
+ return constraints
256
+
257
+
258
+ def get_system_constraints_for_plunger_acceleration(
259
+ config: OT3MotionSettings,
260
+ gantry_load: GantryLoad,
261
+ mount: OT3Mount,
262
+ acceleration: float,
263
+ high_speed_pipette: bool = False,
264
+ ) -> "SystemConstraints[Axis]":
265
+ old_constraints = config.by_gantry_load(gantry_load)
266
+ new_constraints = {}
267
+ axis_kinds = set([k for _, v in old_constraints.items() for k in v.keys()])
268
+
269
+ def _get_axis_max_speed(ax: Axis) -> float:
270
+ if ax == Axis.of_main_tool_actuator(mount) and high_speed_pipette:
271
+ _max_speed = float(DEFAULT_EMULSIFYING_PIPETTE_AXIS_MAX_SPEED)
272
+ else:
273
+ _max_speed = old_constraints["default_max_speed"][axis_kind]
274
+ return _max_speed
275
+
276
+ for axis_kind in axis_kinds:
277
+ for axis in Axis.of_kind(axis_kind):
278
+ _default_max_speed = _get_axis_max_speed(axis)
279
+ if axis == Axis.of_main_tool_actuator(mount):
280
+ _accel = acceleration
281
+ else:
282
+ _accel = old_constraints["acceleration"][axis_kind]
283
+ new_constraints[axis] = AxisConstraints.build(
284
+ _accel,
285
+ old_constraints["max_speed_discontinuity"][axis_kind],
286
+ old_constraints["direction_change_speed_discontinuity"][axis_kind],
287
+ _default_max_speed,
288
+ )
289
+ return new_constraints
290
+
291
+
292
+ def get_system_constraints_for_emulsifying_pipette(
293
+ config: OT3MotionSettings,
294
+ gantry_load: GantryLoad,
295
+ mount: OT3Mount,
296
+ ) -> "SystemConstraints[Axis]":
297
+ old_constraints = config.by_gantry_load(gantry_load)
298
+ new_constraints = {}
299
+ axis_kinds = set([k for _, v in old_constraints.items() for k in v.keys()])
300
+ for axis_kind in axis_kinds:
301
+ for axis in Axis.of_kind(axis_kind):
302
+ if axis == Axis.of_main_tool_actuator(mount):
303
+ _max_speed = float(DEFAULT_EMULSIFYING_PIPETTE_AXIS_MAX_SPEED)
304
+ else:
305
+ _max_speed = old_constraints["default_max_speed"][axis_kind]
306
+ new_constraints[axis] = AxisConstraints.build(
307
+ max_acceleration=old_constraints["acceleration"][axis_kind],
308
+ max_speed_discont=old_constraints["max_speed_discontinuity"][axis_kind],
309
+ max_direction_change_speed_discont=old_constraints[
310
+ "direction_change_speed_discontinuity"
311
+ ][axis_kind],
312
+ max_speed=_max_speed,
313
+ )
314
+ return new_constraints
315
+
316
+
317
+ def _convert_to_node_id_dict(
318
+ axis_pos: Coordinates[Axis, CoordinateValue],
319
+ ) -> NodeIdMotionValues:
320
+ target: NodeIdMotionValues = {}
321
+ for axis, pos in axis_pos.items():
322
+ if axis_is_node(axis):
323
+ target[axis_to_node(axis)] = np.float64(pos)
324
+ return target
325
+
326
+
327
+ def replace_head_node(targets: Set[FirmwareTarget]) -> Set[FirmwareTarget]:
328
+ """Replace the head core node with its two sides.
329
+
330
+ The node ID for the head central controller is what shows up in a network probe,
331
+ but what we actually send commands to an overwhelming majority of the time is
332
+ the head_l and head_r synthetic node IDs, and those are what we want in the
333
+ network map.
334
+ """
335
+ if NodeId.head in targets:
336
+ targets.remove(NodeId.head)
337
+ targets.add(NodeId.head_r)
338
+ targets.add(NodeId.head_l)
339
+ return targets
340
+
341
+
342
+ def replace_gripper_node(targets: Set[FirmwareTarget]) -> Set[FirmwareTarget]:
343
+ """Replace the gripper core node with its two axes.
344
+
345
+ The node ID for the gripper controller is what shows up in a network probe,
346
+ but what we actually send most commands to is the gripper_z and gripper_g
347
+ synthetic nodes, so we should have them in the network map instead.
348
+ """
349
+ if NodeId.gripper in targets:
350
+ targets.remove(NodeId.gripper)
351
+ targets.add(NodeId.gripper_z)
352
+ targets.add(NodeId.gripper_g)
353
+ return targets
354
+
355
+
356
+ def motor_nodes(devices: Set[FirmwareTarget]) -> Set[NodeId]:
357
+ # do the replacement of head and gripper devices
358
+ motor_nodes = replace_gripper_node(devices)
359
+ motor_nodes = replace_head_node(motor_nodes)
360
+ bootloader_nodes = {
361
+ NodeId.pipette_left_bootloader,
362
+ NodeId.pipette_right_bootloader,
363
+ NodeId.gantry_x_bootloader,
364
+ NodeId.gantry_y_bootloader,
365
+ NodeId.head_bootloader,
366
+ NodeId.gripper_bootloader,
367
+ }
368
+ hepa_uv_nodes = {
369
+ NodeId.hepa_uv,
370
+ NodeId.hepa_uv_bootloader,
371
+ }
372
+ # remove any bootloader nodes
373
+ motor_nodes -= bootloader_nodes
374
+ motor_nodes -= hepa_uv_nodes
375
+ # filter out usb nodes
376
+ return {NodeId(target) for target in motor_nodes if target in NodeId}
377
+
378
+
379
+ def create_move_group(
380
+ origin: Coordinates[Axis, CoordinateValue],
381
+ moves: List[Move[Axis]],
382
+ present_nodes: Iterable[NodeId],
383
+ stop_condition: MoveStopCondition = MoveStopCondition.none,
384
+ ) -> Tuple[MoveGroup, Dict[NodeId, float]]:
385
+ pos = _convert_to_node_id_dict(origin)
386
+ move_group: MoveGroup = []
387
+ for move in moves:
388
+ unit_vector = move.unit_vector
389
+ for block in move.blocks:
390
+ if block.time < (3.0 / interrupts_per_sec):
391
+ LOG.info(
392
+ f"Skipping move block with time {block.time} (<{3.0/interrupts_per_sec})"
393
+ )
394
+ continue
395
+ distances = unit_vector_multiplication(unit_vector, block.distance)
396
+ node_id_distances = _convert_to_node_id_dict(distances)
397
+ velocities = unit_vector_multiplication(unit_vector, block.initial_speed)
398
+ accelerations = unit_vector_multiplication(unit_vector, block.acceleration)
399
+ step = create_step(
400
+ distance=node_id_distances,
401
+ velocity=_convert_to_node_id_dict(velocities),
402
+ acceleration=_convert_to_node_id_dict(accelerations),
403
+ duration=block.time,
404
+ present_nodes=present_nodes,
405
+ stop_condition=stop_condition,
406
+ )
407
+ for ax in pos.keys():
408
+ pos[ax] += node_id_distances.get(ax, 0)
409
+ move_group.append(step)
410
+ return move_group, {k: float(v) for k, v in pos.items()}
411
+
412
+
413
+ def create_home_groups(
414
+ distance: Dict[Axis, float], velocity: Dict[Axis, float]
415
+ ) -> List[MoveGroup]:
416
+ node_id_distances = _convert_to_node_id_dict(distance)
417
+ node_id_velocities = _convert_to_node_id_dict(velocity)
418
+ home_group = [
419
+ create_home_step(distance=node_id_distances, velocity=node_id_velocities)
420
+ ]
421
+ # halve the homing speed for backoff
422
+ backoff_velocities = {k: v / 2 for k, v in node_id_velocities.items()}
423
+ backoff_group = [create_backoff_step(backoff_velocities)]
424
+ return [home_group, backoff_group]
425
+
426
+
427
+ def create_tip_action_group(
428
+ moves: Sequence[Move[Axis]],
429
+ present_nodes: Iterable[NodeId],
430
+ action: str,
431
+ ) -> MoveGroup:
432
+ move_group: MoveGroup = []
433
+ for move in moves:
434
+ unit_vector = move.unit_vector
435
+ for block in move.blocks:
436
+ if block.time < (3.0 / interrupts_per_sec):
437
+ continue
438
+ velocities = unit_vector_multiplication(unit_vector, block.initial_speed)
439
+ accelerations = unit_vector_multiplication(unit_vector, block.acceleration)
440
+ step = create_tip_action_step(
441
+ velocity=_convert_to_node_id_dict(velocities),
442
+ acceleration=_convert_to_node_id_dict(accelerations),
443
+ duration=block.time,
444
+ present_nodes=present_nodes,
445
+ action=PipetteTipActionType[action],
446
+ )
447
+ move_group.append(step)
448
+ return move_group
449
+
450
+
451
+ def create_tip_motor_home_group(
452
+ distance: float,
453
+ velocity: float,
454
+ backoff: Optional[bool] = False,
455
+ ) -> MoveGroup:
456
+ move_group: MoveGroup = []
457
+ home_step = create_tip_action_step(
458
+ velocity={NodeId.pipette_left: np.float64(-1 * velocity)},
459
+ acceleration={NodeId.pipette_left: np.float64(0)},
460
+ duration=np.float64(distance / velocity),
461
+ present_nodes=[NodeId.pipette_left],
462
+ action=PipetteTipActionType.home,
463
+ )
464
+ move_group.append(home_step)
465
+
466
+ if backoff:
467
+ backoff_group = create_tip_action_backoff_step(
468
+ velocity={
469
+ node_id: np.float64(velocity / 2) for node_id in [NodeId.pipette_left]
470
+ }
471
+ )
472
+ move_group.append(backoff_group)
473
+ return move_group
474
+
475
+
476
+ def create_gripper_jaw_grip_group(
477
+ duty_cycle: float,
478
+ stop_condition: MoveStopCondition = MoveStopCondition.none,
479
+ stay_engaged: bool = True,
480
+ ) -> MoveGroup:
481
+ step = create_gripper_jaw_step(
482
+ duration=np.float64(GRIPPER_JAW_GRIP_TIME),
483
+ duty_cycle=np.float32(round(duty_cycle)),
484
+ stop_condition=stop_condition,
485
+ move_type=MoveType.grip,
486
+ stay_engaged=stay_engaged,
487
+ )
488
+ move_group: MoveGroup = [step]
489
+ return move_group
490
+
491
+
492
+ def create_gripper_jaw_home_group(dc: float) -> MoveGroup:
493
+ step = create_gripper_jaw_step(
494
+ duration=np.float64(GRIPPER_JAW_HOME_TIME),
495
+ duty_cycle=np.float32(dc),
496
+ stop_condition=MoveStopCondition.limit_switch,
497
+ move_type=MoveType.home,
498
+ )
499
+ move_group: MoveGroup = [step]
500
+ return move_group
501
+
502
+
503
+ def create_gripper_jaw_hold_group(encoder_position_um: int) -> MoveGroup:
504
+ step = create_gripper_jaw_step(
505
+ duration=np.float64(GRIPPER_JAW_GRIP_TIME),
506
+ duty_cycle=np.float32(0),
507
+ encoder_position_um=np.int32(encoder_position_um),
508
+ stop_condition=MoveStopCondition.encoder_position,
509
+ move_type=MoveType.linear,
510
+ )
511
+ move_group: MoveGroup = [step]
512
+ return move_group
513
+
514
+
515
+ def moving_pipettes_in_move_group(
516
+ all_nodes: Set[NodeId], moving_nodes: Set[NodeId]
517
+ ) -> List[NodeId]:
518
+ """Utility function to get which pipette nodes are moving either in z or their plunger."""
519
+ pipettes_moving: List[NodeId] = [
520
+ k for k in moving_nodes if k in [NodeId.pipette_left, NodeId.pipette_right]
521
+ ]
522
+ if NodeId.head_l in moving_nodes and NodeId.pipette_left in all_nodes:
523
+ pipettes_moving.append(NodeId.pipette_left)
524
+ if NodeId.head_r in moving_nodes and NodeId.pipette_right in all_nodes:
525
+ pipettes_moving.append(NodeId.pipette_right)
526
+ return pipettes_moving
527
+
528
+
529
+ AxisMapPayload = TypeVar("AxisMapPayload")
530
+
531
+
532
+ def axis_convert(
533
+ axis_map: Dict["NodeId", AxisMapPayload], default_value: AxisMapPayload
534
+ ) -> OT3AxisMap[AxisMapPayload]:
535
+ ret: OT3AxisMap[AxisMapPayload] = {k: default_value for k in node_axes()}
536
+ for node, value in axis_map.items():
537
+ if node_is_axis(node):
538
+ ret[node_to_axis(node)] = value
539
+ return ret
540
+
541
+
542
+ _sensor_node_lookup: Dict[OT3Mount, InstrumentProbeTarget] = {
543
+ OT3Mount.LEFT: NodeId.pipette_left,
544
+ OT3Mount.RIGHT: NodeId.pipette_right,
545
+ OT3Mount.GRIPPER: NodeId.gripper,
546
+ }
547
+
548
+ _sensor_node_lookup_pipettes_only: Dict[OT3Mount, PipetteProbeTarget] = {
549
+ OT3Mount.LEFT: NodeId.pipette_left,
550
+ OT3Mount.RIGHT: NodeId.pipette_right,
551
+ }
552
+
553
+
554
+ def sensor_node_for_mount(mount: OT3Mount) -> InstrumentProbeTarget:
555
+ return _sensor_node_lookup[mount]
556
+
557
+
558
+ def sensor_node_for_pipette(mount: OT3Mount) -> PipetteProbeTarget:
559
+ return _sensor_node_lookup_pipettes_only[mount]
560
+
561
+
562
+ _instr_sensor_id_lookup: Dict[InstrumentProbeType, SensorId] = {
563
+ InstrumentProbeType.PRIMARY: SensorId.S0,
564
+ InstrumentProbeType.SECONDARY: SensorId.S1,
565
+ InstrumentProbeType.BOTH: SensorId.BOTH,
566
+ }
567
+
568
+
569
+ def sensor_id_for_instrument(probe: InstrumentProbeType) -> SensorId:
570
+ return _instr_sensor_id_lookup[probe]
571
+
572
+
573
+ _pipette_channels_to_sensor_map = {
574
+ PipetteType.pipette_single: [SensorId.S0],
575
+ PipetteType.pipette_multi: [SensorId.S0, SensorId.S1],
576
+ PipetteType.pipette_96: [SensorId.S0, SensorId.S1],
577
+ }
578
+
579
+
580
+ def map_pipette_type_to_sensor_id(
581
+ available_instruments: List[NodeId],
582
+ device_info: Dict[SubSystem, network.DeviceInfoCache],
583
+ ) -> Dict[PipetteProbeTarget, List[SensorId]]:
584
+ return_map = {}
585
+ for node in available_instruments:
586
+ node_info = device_info[node_id_to_subsystem(node)]
587
+ return_map[cast(PipetteProbeTarget, node)] = _pipette_channels_to_sensor_map[
588
+ PipetteType(node_info.subidentifier)
589
+ ]
590
+ return return_map
591
+
592
+
593
+ _pipette_subtype_lookup = {
594
+ PipetteSubType.pipette_single: PipetteType.pipette_single,
595
+ PipetteSubType.pipette_multi: PipetteType.pipette_multi,
596
+ PipetteSubType.pipette_96: PipetteType.pipette_96,
597
+ }
598
+
599
+
600
+ def pipette_type_for_subtype(pipette_subtype: PipetteSubType) -> PipetteType:
601
+ return _pipette_subtype_lookup[pipette_subtype]
602
+
603
+
604
+ _update_state_lookup = {
605
+ FirmwareUpdateStatus.queued: UpdateState.queued,
606
+ FirmwareUpdateStatus.updating: UpdateState.updating,
607
+ FirmwareUpdateStatus.done: UpdateState.done,
608
+ }
609
+
610
+
611
+ def fw_update_state_from_status(state: FirmwareUpdateStatus) -> UpdateState:
612
+ return _update_state_lookup[state]
613
+
614
+
615
+ class UpdateProgress:
616
+ """Class to keep track of Update progress."""
617
+
618
+ def __init__(self, targets: Set[FirmwareTarget]):
619
+ self._tracker: Dict[FirmwareTarget, UpdateStatus] = {}
620
+ self._total_progress = 0
621
+ for target in targets:
622
+ subsystem = (
623
+ node_id_to_subsystem(NodeId(target))
624
+ if isinstance(target, NodeId)
625
+ else SubSystem.rear_panel
626
+ )
627
+ self._tracker[target] = UpdateStatus(subsystem, UpdateState.queued, 0)
628
+
629
+ @property
630
+ def targets(self) -> Set[FirmwareTarget]:
631
+ """Gets the set of update Targets queued or updating."""
632
+ return set(self._tracker)
633
+
634
+ def get_progress(self) -> Set[UpdateStatus]:
635
+ """Gets the update status and total progress"""
636
+ return set(self._tracker.values())
637
+
638
+ def update(
639
+ self, target: FirmwareTarget, status_element: StatusElement
640
+ ) -> Set[UpdateStatus]:
641
+ """Update internal states/progress of firmware updates."""
642
+ fw_update_status, progress = status_element
643
+ subsystem = (
644
+ node_id_to_subsystem(NodeId(target))
645
+ if isinstance(target, NodeId)
646
+ else SubSystem.rear_panel
647
+ )
648
+ state = fw_update_state_from_status(fw_update_status)
649
+ progress = int(progress * 100)
650
+ self._tracker[target] = UpdateStatus(subsystem, state, progress)
651
+ return set(self._tracker.values())
652
+
653
+
654
+ _gripper_jaw_state_lookup: Dict[FirmwareGripperjawState, GripperJawState] = {
655
+ FirmwareGripperjawState.unhomed: GripperJawState.UNHOMED,
656
+ FirmwareGripperjawState.force_controlling_home: GripperJawState.HOMED_READY,
657
+ FirmwareGripperjawState.force_controlling: GripperJawState.GRIPPING,
658
+ FirmwareGripperjawState.position_controlling: GripperJawState.HOLDING,
659
+ FirmwareGripperjawState.stopped: GripperJawState.STOPPED,
660
+ }
661
+
662
+
663
+ def gripper_jaw_state_from_fw(state: FirmwareGripperjawState) -> GripperJawState:
664
+ return _gripper_jaw_state_lookup[state]