opentrons 8.1.0a0__py2.py3-none-any.whl → 8.2.0a0__py2.py3-none-any.whl

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Files changed (230) hide show
  1. opentrons/cli/analyze.py +71 -7
  2. opentrons/config/__init__.py +9 -0
  3. opentrons/config/advanced_settings.py +22 -0
  4. opentrons/config/defaults_ot3.py +14 -36
  5. opentrons/config/feature_flags.py +4 -0
  6. opentrons/config/types.py +6 -17
  7. opentrons/drivers/absorbance_reader/abstract.py +27 -3
  8. opentrons/drivers/absorbance_reader/async_byonoy.py +207 -154
  9. opentrons/drivers/absorbance_reader/driver.py +24 -15
  10. opentrons/drivers/absorbance_reader/hid_protocol.py +79 -50
  11. opentrons/drivers/absorbance_reader/simulator.py +32 -6
  12. opentrons/drivers/types.py +23 -1
  13. opentrons/execute.py +2 -2
  14. opentrons/hardware_control/api.py +18 -10
  15. opentrons/hardware_control/backends/controller.py +3 -2
  16. opentrons/hardware_control/backends/flex_protocol.py +11 -5
  17. opentrons/hardware_control/backends/ot3controller.py +18 -50
  18. opentrons/hardware_control/backends/ot3simulator.py +7 -6
  19. opentrons/hardware_control/instruments/ot2/pipette_handler.py +22 -82
  20. opentrons/hardware_control/instruments/ot3/pipette_handler.py +10 -2
  21. opentrons/hardware_control/module_control.py +43 -2
  22. opentrons/hardware_control/modules/__init__.py +7 -1
  23. opentrons/hardware_control/modules/absorbance_reader.py +230 -83
  24. opentrons/hardware_control/modules/errors.py +7 -0
  25. opentrons/hardware_control/modules/heater_shaker.py +8 -3
  26. opentrons/hardware_control/modules/magdeck.py +12 -3
  27. opentrons/hardware_control/modules/mod_abc.py +27 -2
  28. opentrons/hardware_control/modules/tempdeck.py +15 -7
  29. opentrons/hardware_control/modules/thermocycler.py +69 -3
  30. opentrons/hardware_control/modules/types.py +11 -5
  31. opentrons/hardware_control/modules/update.py +11 -5
  32. opentrons/hardware_control/modules/utils.py +3 -1
  33. opentrons/hardware_control/ot3_calibration.py +6 -6
  34. opentrons/hardware_control/ot3api.py +126 -89
  35. opentrons/hardware_control/poller.py +15 -11
  36. opentrons/hardware_control/protocols/__init__.py +1 -7
  37. opentrons/hardware_control/protocols/instrument_configurer.py +14 -2
  38. opentrons/hardware_control/protocols/liquid_handler.py +5 -0
  39. opentrons/motion_planning/__init__.py +2 -0
  40. opentrons/motion_planning/waypoints.py +32 -0
  41. opentrons/protocol_api/__init__.py +2 -1
  42. opentrons/protocol_api/_liquid.py +87 -1
  43. opentrons/protocol_api/_parameter_context.py +10 -1
  44. opentrons/protocol_api/core/engine/deck_conflict.py +0 -297
  45. opentrons/protocol_api/core/engine/instrument.py +29 -25
  46. opentrons/protocol_api/core/engine/labware.py +10 -2
  47. opentrons/protocol_api/core/engine/module_core.py +129 -17
  48. opentrons/protocol_api/core/engine/pipette_movement_conflict.py +355 -0
  49. opentrons/protocol_api/core/engine/protocol.py +55 -2
  50. opentrons/protocol_api/core/instrument.py +2 -0
  51. opentrons/protocol_api/core/legacy/legacy_instrument_core.py +2 -0
  52. opentrons/protocol_api/core/legacy/legacy_protocol_core.py +5 -2
  53. opentrons/protocol_api/core/legacy_simulator/legacy_instrument_core.py +2 -0
  54. opentrons/protocol_api/core/module.py +22 -4
  55. opentrons/protocol_api/core/protocol.py +5 -2
  56. opentrons/protocol_api/instrument_context.py +52 -20
  57. opentrons/protocol_api/labware.py +13 -1
  58. opentrons/protocol_api/module_contexts.py +68 -13
  59. opentrons/protocol_api/protocol_context.py +38 -4
  60. opentrons/protocol_api/validation.py +5 -3
  61. opentrons/protocol_engine/__init__.py +10 -9
  62. opentrons/protocol_engine/actions/__init__.py +5 -0
  63. opentrons/protocol_engine/actions/actions.py +42 -25
  64. opentrons/protocol_engine/actions/get_state_update.py +38 -0
  65. opentrons/protocol_engine/clients/sync_client.py +7 -1
  66. opentrons/protocol_engine/clients/transports.py +1 -1
  67. opentrons/protocol_engine/commands/__init__.py +0 -4
  68. opentrons/protocol_engine/commands/absorbance_reader/__init__.py +41 -11
  69. opentrons/protocol_engine/commands/absorbance_reader/close_lid.py +161 -0
  70. opentrons/protocol_engine/commands/absorbance_reader/initialize.py +53 -9
  71. opentrons/protocol_engine/commands/absorbance_reader/open_lid.py +160 -0
  72. opentrons/protocol_engine/commands/absorbance_reader/read.py +196 -0
  73. opentrons/protocol_engine/commands/aspirate.py +29 -16
  74. opentrons/protocol_engine/commands/aspirate_in_place.py +32 -15
  75. opentrons/protocol_engine/commands/blow_out.py +63 -14
  76. opentrons/protocol_engine/commands/blow_out_in_place.py +55 -13
  77. opentrons/protocol_engine/commands/calibration/calibrate_gripper.py +2 -5
  78. opentrons/protocol_engine/commands/calibration/calibrate_module.py +3 -4
  79. opentrons/protocol_engine/commands/calibration/calibrate_pipette.py +2 -5
  80. opentrons/protocol_engine/commands/calibration/move_to_maintenance_position.py +6 -4
  81. opentrons/protocol_engine/commands/command.py +28 -17
  82. opentrons/protocol_engine/commands/command_unions.py +37 -24
  83. opentrons/protocol_engine/commands/comment.py +5 -3
  84. opentrons/protocol_engine/commands/configure_for_volume.py +11 -14
  85. opentrons/protocol_engine/commands/configure_nozzle_layout.py +9 -15
  86. opentrons/protocol_engine/commands/custom.py +5 -3
  87. opentrons/protocol_engine/commands/dispense.py +42 -20
  88. opentrons/protocol_engine/commands/dispense_in_place.py +32 -14
  89. opentrons/protocol_engine/commands/drop_tip.py +68 -15
  90. opentrons/protocol_engine/commands/drop_tip_in_place.py +52 -11
  91. opentrons/protocol_engine/commands/get_tip_presence.py +5 -3
  92. opentrons/protocol_engine/commands/heater_shaker/close_labware_latch.py +6 -6
  93. opentrons/protocol_engine/commands/heater_shaker/deactivate_heater.py +6 -6
  94. opentrons/protocol_engine/commands/heater_shaker/deactivate_shaker.py +6 -6
  95. opentrons/protocol_engine/commands/heater_shaker/open_labware_latch.py +8 -6
  96. opentrons/protocol_engine/commands/heater_shaker/set_and_wait_for_shake_speed.py +8 -4
  97. opentrons/protocol_engine/commands/heater_shaker/set_target_temperature.py +6 -4
  98. opentrons/protocol_engine/commands/heater_shaker/wait_for_temperature.py +6 -6
  99. opentrons/protocol_engine/commands/home.py +11 -5
  100. opentrons/protocol_engine/commands/liquid_probe.py +146 -88
  101. opentrons/protocol_engine/commands/load_labware.py +19 -5
  102. opentrons/protocol_engine/commands/load_liquid.py +18 -7
  103. opentrons/protocol_engine/commands/load_module.py +43 -6
  104. opentrons/protocol_engine/commands/load_pipette.py +18 -17
  105. opentrons/protocol_engine/commands/magnetic_module/disengage.py +6 -6
  106. opentrons/protocol_engine/commands/magnetic_module/engage.py +6 -4
  107. opentrons/protocol_engine/commands/move_labware.py +106 -19
  108. opentrons/protocol_engine/commands/move_relative.py +15 -3
  109. opentrons/protocol_engine/commands/move_to_addressable_area.py +29 -4
  110. opentrons/protocol_engine/commands/move_to_addressable_area_for_drop_tip.py +13 -4
  111. opentrons/protocol_engine/commands/move_to_coordinates.py +11 -5
  112. opentrons/protocol_engine/commands/move_to_well.py +37 -10
  113. opentrons/protocol_engine/commands/pick_up_tip.py +50 -29
  114. opentrons/protocol_engine/commands/pipetting_common.py +39 -15
  115. opentrons/protocol_engine/commands/prepare_to_aspirate.py +62 -15
  116. opentrons/protocol_engine/commands/reload_labware.py +13 -4
  117. opentrons/protocol_engine/commands/retract_axis.py +6 -3
  118. opentrons/protocol_engine/commands/save_position.py +2 -3
  119. opentrons/protocol_engine/commands/set_rail_lights.py +5 -3
  120. opentrons/protocol_engine/commands/set_status_bar.py +5 -3
  121. opentrons/protocol_engine/commands/temperature_module/deactivate.py +6 -4
  122. opentrons/protocol_engine/commands/temperature_module/set_target_temperature.py +3 -4
  123. opentrons/protocol_engine/commands/temperature_module/wait_for_temperature.py +6 -6
  124. opentrons/protocol_engine/commands/thermocycler/__init__.py +19 -0
  125. opentrons/protocol_engine/commands/thermocycler/close_lid.py +8 -8
  126. opentrons/protocol_engine/commands/thermocycler/deactivate_block.py +6 -4
  127. opentrons/protocol_engine/commands/thermocycler/deactivate_lid.py +6 -4
  128. opentrons/protocol_engine/commands/thermocycler/open_lid.py +8 -4
  129. opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py +165 -0
  130. opentrons/protocol_engine/commands/thermocycler/run_profile.py +6 -6
  131. opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py +3 -4
  132. opentrons/protocol_engine/commands/thermocycler/set_target_lid_temperature.py +3 -4
  133. opentrons/protocol_engine/commands/thermocycler/wait_for_block_temperature.py +6 -4
  134. opentrons/protocol_engine/commands/thermocycler/wait_for_lid_temperature.py +6 -4
  135. opentrons/protocol_engine/commands/touch_tip.py +19 -7
  136. opentrons/protocol_engine/commands/unsafe/__init__.py +30 -0
  137. opentrons/protocol_engine/commands/unsafe/unsafe_blow_out_in_place.py +6 -4
  138. opentrons/protocol_engine/commands/unsafe/unsafe_drop_tip_in_place.py +12 -4
  139. opentrons/protocol_engine/commands/unsafe/unsafe_engage_axes.py +5 -3
  140. opentrons/protocol_engine/commands/unsafe/unsafe_place_labware.py +194 -0
  141. opentrons/protocol_engine/commands/unsafe/unsafe_ungrip_labware.py +75 -0
  142. opentrons/protocol_engine/commands/unsafe/update_position_estimators.py +5 -3
  143. opentrons/protocol_engine/commands/verify_tip_presence.py +5 -5
  144. opentrons/protocol_engine/commands/wait_for_duration.py +5 -3
  145. opentrons/protocol_engine/commands/wait_for_resume.py +5 -3
  146. opentrons/protocol_engine/create_protocol_engine.py +41 -8
  147. opentrons/protocol_engine/engine_support.py +2 -1
  148. opentrons/protocol_engine/error_recovery_policy.py +14 -3
  149. opentrons/protocol_engine/errors/__init__.py +18 -0
  150. opentrons/protocol_engine/errors/exceptions.py +114 -2
  151. opentrons/protocol_engine/execution/__init__.py +2 -0
  152. opentrons/protocol_engine/execution/command_executor.py +22 -13
  153. opentrons/protocol_engine/execution/create_queue_worker.py +5 -1
  154. opentrons/protocol_engine/execution/door_watcher.py +1 -1
  155. opentrons/protocol_engine/execution/equipment.py +2 -1
  156. opentrons/protocol_engine/execution/error_recovery_hardware_state_synchronizer.py +101 -0
  157. opentrons/protocol_engine/execution/gantry_mover.py +4 -2
  158. opentrons/protocol_engine/execution/hardware_stopper.py +3 -3
  159. opentrons/protocol_engine/execution/heater_shaker_movement_flagger.py +1 -4
  160. opentrons/protocol_engine/execution/labware_movement.py +6 -3
  161. opentrons/protocol_engine/execution/movement.py +8 -3
  162. opentrons/protocol_engine/execution/pipetting.py +7 -4
  163. opentrons/protocol_engine/execution/queue_worker.py +6 -2
  164. opentrons/protocol_engine/execution/run_control.py +1 -1
  165. opentrons/protocol_engine/execution/thermocycler_movement_flagger.py +1 -1
  166. opentrons/protocol_engine/execution/thermocycler_plate_lifter.py +2 -1
  167. opentrons/protocol_engine/execution/tip_handler.py +77 -43
  168. opentrons/protocol_engine/notes/__init__.py +14 -2
  169. opentrons/protocol_engine/notes/notes.py +18 -1
  170. opentrons/protocol_engine/plugins.py +1 -1
  171. opentrons/protocol_engine/protocol_engine.py +54 -31
  172. opentrons/protocol_engine/resources/__init__.py +2 -0
  173. opentrons/protocol_engine/resources/deck_data_provider.py +58 -5
  174. opentrons/protocol_engine/resources/file_provider.py +157 -0
  175. opentrons/protocol_engine/resources/fixture_validation.py +5 -0
  176. opentrons/protocol_engine/resources/labware_validation.py +10 -0
  177. opentrons/protocol_engine/state/__init__.py +0 -70
  178. opentrons/protocol_engine/state/addressable_areas.py +1 -1
  179. opentrons/protocol_engine/state/command_history.py +21 -2
  180. opentrons/protocol_engine/state/commands.py +110 -31
  181. opentrons/protocol_engine/state/files.py +59 -0
  182. opentrons/protocol_engine/state/frustum_helpers.py +440 -0
  183. opentrons/protocol_engine/state/geometry.py +359 -15
  184. opentrons/protocol_engine/state/labware.py +166 -63
  185. opentrons/protocol_engine/state/liquids.py +1 -1
  186. opentrons/protocol_engine/state/module_substates/absorbance_reader_substate.py +19 -3
  187. opentrons/protocol_engine/state/modules.py +167 -85
  188. opentrons/protocol_engine/state/motion.py +16 -9
  189. opentrons/protocol_engine/state/pipettes.py +157 -317
  190. opentrons/protocol_engine/state/state.py +30 -1
  191. opentrons/protocol_engine/state/state_summary.py +3 -0
  192. opentrons/protocol_engine/state/tips.py +69 -114
  193. opentrons/protocol_engine/state/update_types.py +408 -0
  194. opentrons/protocol_engine/state/wells.py +236 -0
  195. opentrons/protocol_engine/types.py +90 -0
  196. opentrons/protocol_reader/file_format_validator.py +83 -15
  197. opentrons/protocol_runner/json_translator.py +21 -5
  198. opentrons/protocol_runner/legacy_command_mapper.py +27 -6
  199. opentrons/protocol_runner/legacy_context_plugin.py +27 -71
  200. opentrons/protocol_runner/protocol_runner.py +6 -3
  201. opentrons/protocol_runner/run_orchestrator.py +26 -6
  202. opentrons/protocols/advanced_control/mix.py +3 -5
  203. opentrons/protocols/advanced_control/transfers.py +125 -56
  204. opentrons/protocols/api_support/constants.py +1 -1
  205. opentrons/protocols/api_support/definitions.py +1 -1
  206. opentrons/protocols/api_support/labware_like.py +4 -4
  207. opentrons/protocols/api_support/tip_tracker.py +2 -2
  208. opentrons/protocols/api_support/types.py +15 -2
  209. opentrons/protocols/api_support/util.py +30 -42
  210. opentrons/protocols/duration/errors.py +1 -1
  211. opentrons/protocols/duration/estimator.py +50 -29
  212. opentrons/protocols/execution/dev_types.py +2 -2
  213. opentrons/protocols/execution/execute_json_v4.py +15 -10
  214. opentrons/protocols/execution/execute_python.py +8 -3
  215. opentrons/protocols/geometry/planning.py +12 -12
  216. opentrons/protocols/labware.py +17 -33
  217. opentrons/simulate.py +3 -3
  218. opentrons/types.py +30 -3
  219. opentrons/util/logging_config.py +34 -0
  220. {opentrons-8.1.0a0.dist-info → opentrons-8.2.0a0.dist-info}/METADATA +5 -4
  221. {opentrons-8.1.0a0.dist-info → opentrons-8.2.0a0.dist-info}/RECORD +227 -215
  222. opentrons/protocol_engine/commands/absorbance_reader/measure.py +0 -94
  223. opentrons/protocol_engine/commands/configuring_common.py +0 -26
  224. opentrons/protocol_runner/thread_async_queue.py +0 -174
  225. /opentrons/protocol_engine/state/{abstract_store.py → _abstract_store.py} +0 -0
  226. /opentrons/protocol_engine/state/{move_types.py → _move_types.py} +0 -0
  227. {opentrons-8.1.0a0.dist-info → opentrons-8.2.0a0.dist-info}/LICENSE +0 -0
  228. {opentrons-8.1.0a0.dist-info → opentrons-8.2.0a0.dist-info}/WHEEL +0 -0
  229. {opentrons-8.1.0a0.dist-info → opentrons-8.2.0a0.dist-info}/entry_points.txt +0 -0
  230. {opentrons-8.1.0a0.dist-info → opentrons-8.2.0a0.dist-info}/top_level.txt +0 -0
@@ -5,10 +5,17 @@ from typing import Any, Dict
5
5
 
6
6
  from opentrons.config import CONFIG, ARCHITECTURE, SystemArchitecture
7
7
 
8
+ if ARCHITECTURE is SystemArchitecture.BUILDROOT:
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+ from opentrons_hardware.sensors import SENSOR_LOG_NAME
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+ else:
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+ # we don't use the sensor log on ot2 or host
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+ SENSOR_LOG_NAME = "unused"
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+
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9
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  def _host_config(level_value: int) -> Dict[str, Any]:
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  serial_log_filename = CONFIG["serial_log_file"]
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  api_log_filename = CONFIG["api_log_file"]
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+ sensor_log_filename = CONFIG["sensor_log_file"]
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  return {
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  "version": 1,
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  "disable_existing_loggers": False,
@@ -41,6 +48,14 @@ def _host_config(level_value: int) -> Dict[str, Any]:
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  "level": logging.DEBUG,
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  "backupCount": 5,
43
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  },
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+ "sensor": {
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+ "class": "logging.handlers.RotatingFileHandler",
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+ "formatter": "basic",
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+ "filename": sensor_log_filename,
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+ "maxBytes": 1000000,
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+ "level": logging.DEBUG,
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+ "backupCount": 5,
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+ },
44
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  },
45
60
  "loggers": {
46
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  "opentrons": {
@@ -66,6 +81,11 @@ def _host_config(level_value: int) -> Dict[str, Any]:
66
81
  "level": logging.DEBUG,
67
82
  "propagate": False,
68
83
  },
84
+ SENSOR_LOG_NAME: {
85
+ "handlers": ["sensor"],
86
+ "level": logging.DEBUG,
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+ "propagate": False,
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+ },
69
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  "__main__": {"handlers": ["api"], "level": level_value},
70
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  },
71
91
  }
@@ -75,6 +95,7 @@ def _buildroot_config(level_value: int) -> Dict[str, Any]:
75
95
  # Import systemd.journald here since it is generally unavailble on non
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  # linux systems and we probably don't want to use it on linux desktops
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  # either
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+ sensor_log_filename = CONFIG["sensor_log_file"]
78
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  return {
79
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  "version": 1,
80
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  "disable_existing_loggers": False,
@@ -106,6 +127,14 @@ def _buildroot_config(level_value: int) -> Dict[str, Any]:
106
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  "formatter": "message_only",
107
128
  "SYSLOG_IDENTIFIER": "opentrons-api-serial-usbbin",
108
129
  },
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+ "sensor": {
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+ "class": "logging.handlers.RotatingFileHandler",
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+ "formatter": "message_only",
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+ "filename": sensor_log_filename,
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+ "maxBytes": 1000000,
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+ "level": logging.DEBUG,
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+ "backupCount": 3,
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+ },
109
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  },
110
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  "loggers": {
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  "opentrons.drivers.asyncio.communication.serial_connection": {
@@ -131,6 +160,11 @@ def _buildroot_config(level_value: int) -> Dict[str, Any]:
131
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  "level": logging.DEBUG,
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  "propagate": False,
133
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  },
163
+ SENSOR_LOG_NAME: {
164
+ "handlers": ["sensor"],
165
+ "level": logging.DEBUG,
166
+ "propagate": False,
167
+ },
134
168
  "__main__": {"handlers": ["api"], "level": level_value},
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  },
136
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  }
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
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2
  Name: opentrons
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- Version: 8.1.0a0
3
+ Version: 8.2.0a0
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  Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
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  Author: Opentrons
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  Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
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  Classifier: Topic :: Scientific/Engineering
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  Requires-Python: >=3.10
23
23
  License-File: ../LICENSE
24
- Requires-Dist: opentrons-shared-data ==8.1.0a0
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+ Requires-Dist: opentrons-shared-data ==8.2.0a0
25
25
  Requires-Dist: aionotify ==0.3.1
26
26
  Requires-Dist: anyio <4.0.0,>=3.6.1
27
27
  Requires-Dist: jsonschema <4.18.0,>=3.0.1
@@ -30,12 +30,13 @@ Requires-Dist: pydantic <2.0.0,>=1.10.9
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  Requires-Dist: pyserial >=3.5
31
31
  Requires-Dist: typing-extensions <5,>=4.0.0
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  Requires-Dist: click <9,>=8.0.0
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+ Requires-Dist: pyusb ==1.2.1
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34
  Requires-Dist: packaging >=21.0
34
35
  Requires-Dist: importlib-metadata >=1.0 ; python_version < "3.8"
35
36
  Provides-Extra: flex-hardware
36
- Requires-Dist: opentrons-hardware[flex] ==8.1.0a0 ; extra == 'flex-hardware'
37
+ Requires-Dist: opentrons-hardware[flex] ==8.2.0a0 ; extra == 'flex-hardware'
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  Provides-Extra: ot2-hardware
38
- Requires-Dist: opentrons-hardware ==8.1.0a0 ; extra == 'ot2-hardware'
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+ Requires-Dist: opentrons-hardware ==8.2.0a0 ; extra == 'ot2-hardware'
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  .. _Full API Documentation: http://docs.opentrons.com
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