opentrons 8.7.0a5__py3-none-any.whl → 8.7.0a7__py3-none-any.whl

opentrons/protocol_engine/commands/__init__.py

@@ -271,6 +271,22 @@ from .wait_for_duration import (
     WaitForDurationCommandType,
 )
 
+from .create_timer import (
+    CreateTimer,
+    CreateTimerCreate,
+    CreateTimerParams,
+    CreateTimerResult,
+    CreateTimerCommandType,
+)
+
+from .wait_for_tasks import (
+    WaitForTasks,
+    WaitForTasksCreate,
+    WaitForTasksParams,
+    WaitForTasksResult,
+    WaitForTasksCommandType,
+)
+
 from .pick_up_tip import (
     PickUpTip,
     PickUpTipParams,
@@ -384,6 +400,14 @@ from .get_next_tip import (
     GetNextTipCommandType,
 )
 
+from .set_tip_state import (
+    SetTipState,
+    SetTipStateCreate,
+    SetTipStateParams,
+    SetTipStateResult,
+    SetTipStateCommandType,
+)
+
 from .liquid_probe import (
     LiquidProbe,
     LiquidProbeParams,
@@ -619,6 +643,12 @@ __all__ = [
     "WaitForDurationCreate",
     "WaitForDurationResult",
     "WaitForDurationCommandType",
+    # Timer command models
+    "CreateTimer",
+    "CreateTimerCreate",
+    "CreateTimerParams",
+    "CreateTimerResult",
+    "CreateTimerCommandType",
     # pick up tip command models
     "PickUpTip",
     "PickUpTipCreate",
@@ -725,6 +755,12 @@ __all__ = [
     "GetNextTipParams",
     "GetNextTipResult",
     "GetNextTipCommandType",
+    # set tip state command bundle
+    "SetTipState",
+    "SetTipStateCreate",
+    "SetTipStateParams",
+    "SetTipStateResult",
+    "SetTipStateCommandType",
     # liquid probe command bundle
     "LiquidProbe",
     "LiquidProbeParams",
@@ -754,4 +790,10 @@ __all__ = [
     "PressureDispenseCreate",
     "PressureDispenseResult",
     "PressureDispenseCommandType",
+    # wait for tasks command bundle
+    "WaitForTasks",
+    "WaitForTasksCreate",
+    "WaitForTasksParams",
+    "WaitForTasksResult",
+    "WaitForTasksCommandType",
 ]

opentrons/protocol_engine/commands/absorbance_reader/close_lid.py

@@ -102,25 +102,12 @@ class CloseLidImpl(AbstractCommandImpl[CloseLidParams, SuccessData[CloseLidResul
                 )
             )
 
-            # The lid's labware definition stores gripper offsets for itself in the
-            # space normally meant for offsets for labware stacked atop it.
-            lid_gripper_offsets = self._state_view.labware.get_child_gripper_offsets(
-                labware_definition=lid_definition,
-                slot_name=None,
-            )
-            if lid_gripper_offsets is None:
-                raise ValueError(
-                    "Gripper Offset values for Absorbance Reader Lid labware must not be None."
-                )
-
             await self._labware_movement.move_labware_with_gripper(
                 labware_definition=lid_definition,
                 current_location=current_location,
                 new_location=new_location,
-                user_pick_up_offset=Point.from_xyz_attrs(
-                    lid_gripper_offsets.pickUpOffset
-                ),
-                user_drop_offset=Point.from_xyz_attrs(lid_gripper_offsets.dropOffset),
+                user_pick_up_offset=Point(),
+                user_drop_offset=Point(),
                 post_drop_slide_offset=None,
                 gripper_z_offset=LID_Z_CLEARANCE,
             )

opentrons/protocol_engine/commands/absorbance_reader/open_lid.py

@@ -103,25 +103,12 @@ class OpenLidImpl(AbstractCommandImpl[OpenLidParams, SuccessData[OpenLidResult]]
                 mod_substate.module_id
             )
 
-            # The lid's labware definition stores gripper offsets for itself in the
-            # space normally meant for offsets for labware stacked atop it.
-            lid_gripper_offsets = self._state_view.labware.get_child_gripper_offsets(
-                labware_definition=lid_definition,
-                slot_name=None,
-            )
-            if lid_gripper_offsets is None:
-                raise ValueError(
-                    "Gripper Offset values for Absorbance Reader Lid labware must not be None."
-                )
-
             await self._labware_movement.move_labware_with_gripper(
                 labware_definition=lid_definition,
                 current_location=current_location,
                 new_location=new_location,
-                user_pick_up_offset=Point.from_xyz_attrs(
-                    lid_gripper_offsets.pickUpOffset
-                ),
-                user_drop_offset=Point.from_xyz_attrs(lid_gripper_offsets.dropOffset),
+                user_pick_up_offset=Point(),
+                user_drop_offset=Point(),
                 post_drop_slide_offset=None,
                 gripper_z_offset=LID_Z_CLEARANCE,
             )

opentrons/protocol_engine/commands/aspirate.py

@@ -161,6 +161,7 @@ class AspirateImplementation(AbstractCommandImpl[AspirateParams, _ExecuteReturn]
             well_location=well_location,
             current_well=current_well,
             operation_volume=-params.volume,
+            offset_pipette_for_reservoir_subwells=False,
         )
         state_update.append(move_result.state_update)
         if isinstance(move_result, DefinedErrorData):

opentrons/protocol_engine/commands/command.py

@@ -185,6 +185,7 @@ class AbstractCommandImpl(
         tip_handler: execution.TipHandler,
         run_control: execution.RunControlHandler,
         rail_lights: execution.RailLightsHandler,
+        task_handler: execution.TaskHandler,
         model_utils: ModelUtils,
         status_bar: execution.StatusBarHandler,
         command_note_adder: CommandNoteAdder,

opentrons/protocol_engine/commands/command_unions.py

@@ -267,6 +267,22 @@ from .wait_for_duration import (
     WaitForDurationCommandType,
 )
 
+from .create_timer import (
+    CreateTimer,
+    CreateTimerCreate,
+    CreateTimerParams,
+    CreateTimerResult,
+    CreateTimerCommandType,
+)
+
+from .wait_for_tasks import (
+    WaitForTasks,
+    WaitForTasksCreate,
+    WaitForTasksParams,
+    WaitForTasksResult,
+    WaitForTasksCommandType,
+)
+
 from .pick_up_tip import (
     PickUpTip,
     PickUpTipParams,
@@ -372,6 +388,14 @@ from .get_next_tip import (
     GetNextTipCommandType,
 )
 
+from .set_tip_state import (
+    SetTipState,
+    SetTipStateCreate,
+    SetTipStateParams,
+    SetTipStateResult,
+    SetTipStateCommandType,
+)
+
 from .liquid_probe import (
     LiquidProbe,
     LiquidProbeParams,
@@ -454,6 +478,8 @@ Command = Annotated[
         PrepareToAspirate,
         WaitForResume,
         WaitForDuration,
+        WaitForTasks,
+        CreateTimer,
         PickUpTip,
         SavePosition,
         SetRailLights,
@@ -462,6 +488,7 @@ Command = Annotated[
         VerifyTipPresence,
         GetTipPresence,
         GetNextTip,
+        SetTipState,
         LiquidProbe,
         TryLiquidProbe,
         SealPipetteToTip,
@@ -471,6 +498,7 @@ Command = Annotated[
         heater_shaker.SetTargetTemperature,
         heater_shaker.DeactivateHeater,
         heater_shaker.SetAndWaitForShakeSpeed,
+        heater_shaker.SetShakeSpeed,
         heater_shaker.DeactivateShaker,
         heater_shaker.OpenLabwareLatch,
         heater_shaker.CloseLabwareLatch,
@@ -488,6 +516,7 @@ Command = Annotated[
         thermocycler.OpenLid,
         thermocycler.CloseLid,
         thermocycler.RunProfile,
+        thermocycler.StartRunExtendedProfile,
         thermocycler.RunExtendedProfile,
         absorbance_reader.CloseLid,
         absorbance_reader.OpenLid,
@@ -557,6 +586,8 @@ CommandParams = Union[
     PrepareToAspirateParams,
     WaitForResumeParams,
     WaitForDurationParams,
+    WaitForTasksParams,
+    CreateTimerParams,
     PickUpTipParams,
     SavePositionParams,
     SetRailLightsParams,
@@ -565,6 +596,7 @@ CommandParams = Union[
     VerifyTipPresenceParams,
     GetTipPresenceParams,
     GetNextTipParams,
+    SetTipStateParams,
     LiquidProbeParams,
     TryLiquidProbeParams,
     SealPipetteToTipParams,
@@ -574,6 +606,7 @@ CommandParams = Union[
     heater_shaker.SetTargetTemperatureParams,
     heater_shaker.DeactivateHeaterParams,
     heater_shaker.SetAndWaitForShakeSpeedParams,
+    heater_shaker.SetShakeSpeedParams,
     heater_shaker.DeactivateShakerParams,
     heater_shaker.OpenLabwareLatchParams,
     heater_shaker.CloseLabwareLatchParams,
@@ -591,6 +624,7 @@ CommandParams = Union[
     thermocycler.OpenLidParams,
     thermocycler.CloseLidParams,
     thermocycler.RunProfileParams,
+    thermocycler.StartRunExtendedProfileParams,
     thermocycler.RunExtendedProfileParams,
     absorbance_reader.CloseLidParams,
     absorbance_reader.OpenLidParams,
@@ -658,6 +692,8 @@ CommandType = Union[
     PrepareToAspirateCommandType,
     WaitForResumeCommandType,
     WaitForDurationCommandType,
+    WaitForTasksCommandType,
+    CreateTimerCommandType,
     PickUpTipCommandType,
     SavePositionCommandType,
     SetRailLightsCommandType,
@@ -666,6 +702,7 @@ CommandType = Union[
     VerifyTipPresenceCommandType,
     GetTipPresenceCommandType,
     GetNextTipCommandType,
+    SetTipStateCommandType,
     LiquidProbeCommandType,
     TryLiquidProbeCommandType,
     SealPipetteToTipCommandType,
@@ -675,6 +712,7 @@ CommandType = Union[
     heater_shaker.SetTargetTemperatureCommandType,
     heater_shaker.DeactivateHeaterCommandType,
     heater_shaker.SetAndWaitForShakeSpeedCommandType,
+    heater_shaker.SetShakeSpeedCommandType,
     heater_shaker.DeactivateShakerCommandType,
     heater_shaker.OpenLabwareLatchCommandType,
     heater_shaker.CloseLabwareLatchCommandType,
@@ -692,6 +730,7 @@ CommandType = Union[
     thermocycler.OpenLidCommandType,
     thermocycler.CloseLidCommandType,
     thermocycler.RunProfileCommandType,
+    thermocycler.StartRunExtendedProfileCommandType,
     thermocycler.RunExtendedProfileCommandType,
     absorbance_reader.CloseLidCommandType,
     absorbance_reader.OpenLidCommandType,
@@ -760,6 +799,8 @@ CommandCreate = Annotated[
         PrepareToAspirateCreate,
         WaitForResumeCreate,
         WaitForDurationCreate,
+        WaitForTasksCreate,
+        CreateTimerCreate,
         PickUpTipCreate,
         SavePositionCreate,
         SetRailLightsCreate,
@@ -768,6 +809,7 @@ CommandCreate = Annotated[
         VerifyTipPresenceCreate,
         GetTipPresenceCreate,
         GetNextTipCreate,
+        SetTipStateCreate,
         LiquidProbeCreate,
         TryLiquidProbeCreate,
         SealPipetteToTipCreate,
@@ -777,6 +819,7 @@ CommandCreate = Annotated[
         heater_shaker.SetTargetTemperatureCreate,
         heater_shaker.DeactivateHeaterCreate,
         heater_shaker.SetAndWaitForShakeSpeedCreate,
+        heater_shaker.SetShakeSpeedCreate,
         heater_shaker.DeactivateShakerCreate,
         heater_shaker.OpenLabwareLatchCreate,
         heater_shaker.CloseLabwareLatchCreate,
@@ -794,6 +837,7 @@ CommandCreate = Annotated[
         thermocycler.OpenLidCreate,
         thermocycler.CloseLidCreate,
         thermocycler.RunProfileCreate,
+        thermocycler.StartRunExtendedProfileCreate,
         thermocycler.RunExtendedProfileCreate,
         absorbance_reader.CloseLidCreate,
         absorbance_reader.OpenLidCreate,
@@ -870,6 +914,8 @@ CommandResult = Union[
     PrepareToAspirateResult,
     WaitForResumeResult,
     WaitForDurationResult,
+    WaitForTasksResult,
+    CreateTimerResult,
     PickUpTipResult,
     SavePositionResult,
     SetRailLightsResult,
@@ -878,6 +924,7 @@ CommandResult = Union[
     VerifyTipPresenceResult,
     GetTipPresenceResult,
     GetNextTipResult,
+    SetTipStateResult,
     LiquidProbeResult,
     TryLiquidProbeResult,
     SealPipetteToTipResult,
@@ -887,6 +934,7 @@ CommandResult = Union[
     heater_shaker.SetTargetTemperatureResult,
     heater_shaker.DeactivateHeaterResult,
     heater_shaker.SetAndWaitForShakeSpeedResult,
+    heater_shaker.SetShakeSpeedResult,
     heater_shaker.DeactivateShakerResult,
     heater_shaker.OpenLabwareLatchResult,
     heater_shaker.CloseLabwareLatchResult,
@@ -904,6 +952,7 @@ CommandResult = Union[
     thermocycler.OpenLidResult,
     thermocycler.CloseLidResult,
     thermocycler.RunProfileResult,
+    thermocycler.StartRunExtendedProfileResult,
     thermocycler.RunExtendedProfileResult,
     absorbance_reader.CloseLidResult,
     absorbance_reader.OpenLidResult,

opentrons/protocol_engine/commands/create_timer.py

@@ -0,0 +1,83 @@
+"""CreateTimer command request, result, and implementation models."""
+
+from __future__ import annotations
+from pydantic import BaseModel, Field
+from typing import Optional, Type, TYPE_CHECKING
+from typing_extensions import Literal
+
+from .command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData
+from ..errors.error_occurrence import ErrorOccurrence
+
+if TYPE_CHECKING:
+    from ..execution import TaskHandler, RunControlHandler
+
+
+CreateTimerCommandType = Literal["createTimer"]
+
+
+class CreateTimerParams(BaseModel):
+    """Payload required to annotate execution with a CreateTimer."""
+
+    time: float = Field(
+        ...,
+        description="The time before the timer should elapse in seconds. This is the minimum time before the timer elapses; it may in practice take longer than this.",
+    )
+    task_id: str | None = Field(
+        None,
+        description="The id of the timer task",
+    )
+
+
+class CreateTimerResult(BaseModel):
+    """Result data from the execution of a CreateTimer command."""
+
+    task_id: str = Field(..., description="The id of the timer task")
+    time: float = Field(..., description="The same time as the parameter.")
+
+
+class CreateTimerImplementation(
+    AbstractCommandImpl[CreateTimerParams, SuccessData[CreateTimerResult]]
+):
+    """CreateTimer command implementation."""
+
+    def __init__(
+        self,
+        task_handler: TaskHandler,
+        run_control: RunControlHandler,
+        **kwargs: object,
+    ) -> None:
+        self._task_handler = task_handler
+        self._run_control = run_control
+
+    async def execute(
+        self, params: CreateTimerParams
+    ) -> SuccessData[CreateTimerResult]:
+        """No operation taken other than capturing message in command."""
+
+        async def timer(task_handler: TaskHandler) -> None:
+            async with task_handler.synchronize_concurrent("createTimer"):
+                await self._run_control.wait_for_duration(params.time)
+
+        task = await self._task_handler.create_task(timer, params.task_id)
+        return SuccessData(
+            public=CreateTimerResult(task_id=task.id, time=params.time),
+        )
+
+
+class CreateTimer(BaseCommand[CreateTimerParams, CreateTimerResult, ErrorOccurrence]):
+    """CreateTimer command model."""
+
+    commandType: CreateTimerCommandType = "createTimer"
+    params: CreateTimerParams
+    result: Optional[CreateTimerResult] = None
+
+    _ImplementationCls: Type[CreateTimerImplementation] = CreateTimerImplementation
+
+
+class CreateTimerCreate(BaseCommandCreate[CreateTimerParams]):
+    """CreateTimer command request model."""
+
+    commandType: CreateTimerCommandType = "createTimer"
+    params: CreateTimerParams
+
+    _CommandCls: Type[CreateTimer] = CreateTimer

opentrons/protocol_engine/commands/dispense.py

@@ -101,6 +101,7 @@ class DispenseImplementation(AbstractCommandImpl[DispenseParams, _ExecuteReturn]
             well_name=well_name,
             well_location=well_location,
             operation_volume=volume,
+            offset_pipette_for_reservoir_subwells=False,
         )
         if isinstance(move_result, DefinedErrorData):
             return move_result

opentrons/protocol_engine/commands/drop_tip.py

@@ -12,7 +12,7 @@ from opentrons.protocol_engine.errors.exceptions import TipAttachedError
 from opentrons.protocol_engine.resources.model_utils import ModelUtils
 
 from ..state.update_types import StateUpdate
-from ..types import DropTipWellLocation
+from ..types import DropTipWellLocation, TipRackWellState
 from .pipetting_common import (
     PipetteIdMixin,
     TipPhysicallyAttachedError,
@@ -140,6 +140,25 @@ class DropTipImplementation(AbstractCommandImpl[DropTipParams, _ExecuteReturn]):
             partially_configured=is_partially_configured,
         )
 
+        is_tip_rack = self._state_view.labware.get_definition(
+            labware_id
+        ).parameters.isTiprack
+
+        # It's possible that we are dropping tips into a labware trash for pre API v2.14 OT-2 protocols
+        # (or something else unexpected), so if it is not a tip rack mark no wells as used
+        if is_tip_rack:
+            tips_to_mark_as_used = (
+                self._state_view.tips.compute_tips_to_mark_as_used_or_empty(
+                    labware_id=labware_id,
+                    well_name=well_name,
+                    nozzle_map=self._state_view.pipettes.get_nozzle_configuration(
+                        pipette_id
+                    ),
+                )
+            )
+        else:
+            tips_to_mark_as_used = []
+
         move_result = await move_to_well(
             movement=self._movement_handler,
             model_utils=self._model_utils,
@@ -152,12 +171,7 @@ class DropTipImplementation(AbstractCommandImpl[DropTipParams, _ExecuteReturn]):
             return move_result
 
         scrape_type = TipScrapeType.NONE
-        if (
-            params.scrape_tips
-            and self._state_view.geometry._labware.get_definition(
-                labware_id
-            ).parameters.isTiprack
-        ):
+        if params.scrape_tips and is_tip_rack:
             if int("".join(filter(str.isdigit, well_name))) <= 6:
                 scrape_type = TipScrapeType.RIGHT_ONE_COL
             else:
@@ -194,6 +208,10 @@ class DropTipImplementation(AbstractCommandImpl[DropTipParams, _ExecuteReturn]):
                     pipette_id=params.pipetteId,
                     tip_geometry=None,
                     tip_source=None,
+                ).update_tip_rack_well_state(
+                    tip_state=TipRackWellState.USED,
+                    labware_id=labware_id,
+                    well_names=tips_to_mark_as_used,
                 ),
             )
         else:
@@ -201,10 +219,16 @@ class DropTipImplementation(AbstractCommandImpl[DropTipParams, _ExecuteReturn]):
                 public=DropTipResult(position=move_result.public.position),
                 state_update=move_result.state_update.set_fluid_unknown(
                     pipette_id=pipette_id
-                ).update_pipette_tip_state(
+                )
+                .update_pipette_tip_state(
                     pipette_id=params.pipetteId,
                     tip_geometry=None,
                     tip_source=None,
+                )
+                .update_tip_rack_well_state(
+                    tip_state=TipRackWellState.USED,
+                    labware_id=labware_id,
+                    well_names=tips_to_mark_as_used,
                 ),
             )
 

opentrons/protocol_engine/commands/heater_shaker/__init__.py

@@ -32,6 +32,14 @@ from .set_and_wait_for_shake_speed import (
     SetAndWaitForShakeSpeedCommandType,
 )
 
+from .set_shake_speed import (
+    SetShakeSpeed,
+    SetShakeSpeedCreate,
+    SetShakeSpeedParams,
+    SetShakeSpeedResult,
+    SetShakeSpeedCommandType,
+)
+
 from .deactivate_shaker import (
     DeactivateShaker,
     DeactivateShakerCreate,
@@ -81,6 +89,12 @@ __all__ = [
     "SetAndWaitForShakeSpeedParams",
     "SetAndWaitForShakeSpeedResult",
     "SetAndWaitForShakeSpeedCommandType",
+    # heaterShaker/setShakeSpeed
+    "SetShakeSpeed",
+    "SetShakeSpeedCreate",
+    "SetShakeSpeedParams",
+    "SetShakeSpeedResult",
+    "SetShakeSpeedCommandType",
     # heaterShaker/deactivateShaker
     "DeactivateShaker",
     "DeactivateShakerCreate",

opentrons/protocol_engine/commands/heater_shaker/common.py

@@ -0,0 +1,20 @@
+"""Common heatershaker base models."""
+from opentrons.protocol_engine.state.module_substates.heater_shaker_module_substate import (
+    HeaterShakerModuleSubState,
+)
+
+
+async def get_heatershaker_ready_to_shake(
+    hs_module_substate: HeaterShakerModuleSubState,
+    rpm: float,
+) -> int:
+    """Check heatershaker state to confirm if it is ready to shake.
+
+    This includes
+    - Checking latch closure
+    - Validating target speed
+    """
+    hs_module_substate.raise_if_labware_latch_not_closed()
+    # Verify speed from hs module view
+    validated_speed = hs_module_substate.validate_target_speed(rpm)
+    return validated_speed

opentrons/protocol_engine/commands/heater_shaker/set_and_wait_for_shake_speed.py

@@ -8,6 +8,8 @@ from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, Succe
 from ...errors.error_occurrence import ErrorOccurrence
 from ...state import update_types
 
+from .common import get_heatershaker_ready_to_shake
+
 if TYPE_CHECKING:
     from opentrons.protocol_engine.state.state import StateView
     from opentrons.protocol_engine.execution import EquipmentHandler, MovementHandler
@@ -64,10 +66,9 @@ class SetAndWaitForShakeSpeedImpl(
             module_id=params.moduleId
         )
 
-        hs_module_substate.raise_if_labware_latch_not_closed()
-
-        # Verify speed from hs module view
-        validated_speed = hs_module_substate.validate_target_speed(params.rpm)
+        validated_speed = await get_heatershaker_ready_to_shake(
+            hs_module_substate, params.rpm
+        )
 
         pipette_should_retract = (
             self._state_view.motion.check_pipette_blocking_hs_shaker(