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

opentrons/protocol_engine/commands/heater_shaker/set_shake_speed.py

@@ -0,0 +1,136 @@
+"""Command models to set a shake speed for a Heater-Shaker Module."""
+from __future__ import annotations
+from typing import Optional, TYPE_CHECKING
+from typing_extensions import Literal, Type
+from pydantic import BaseModel, Field
+
+from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData
+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,
+        TaskHandler,
+    )
+
+SetShakeSpeedCommandType = Literal["heaterShaker/setShakeSpeed"]
+
+
+class SetShakeSpeedParams(BaseModel):
+    """Input parameters to set a shake speed for a Heater-Shaker Module."""
+
+    moduleId: str = Field(..., description="Unique ID of the Heater-Shaker Module.")
+    rpm: float = Field(..., description="Target speed in rotations per minute.")
+    taskId: str | None = Field(
+        None,
+        description="Id for the background task that manages the temperature",
+    )
+
+
+class SetShakeSpeedResult(BaseModel):
+    """Result data from setting and waiting for a Heater-Shaker's shake speed."""
+
+    pipetteRetracted: bool = Field(
+        ...,
+        description=(
+            "Whether this command automatically retracted the pipettes"
+            " before starting the shake, to avoid a potential collision."
+        ),
+    )
+    taskId: str = Field(
+        description="The task id for the setTargetTemperature task",
+    )
+
+
+class SetShakeSpeedImpl(
+    AbstractCommandImpl[SetShakeSpeedParams, SuccessData[SetShakeSpeedResult]]
+):
+    """Execution implementation of Heater-Shaker's set shake speed command."""
+
+    def __init__(
+        self,
+        state_view: StateView,
+        equipment: EquipmentHandler,
+        movement: MovementHandler,
+        task_handler: TaskHandler,
+        **unused_dependencies: object,
+    ) -> None:
+        self._state_view = state_view
+        self._equipment = equipment
+        self._movement = movement
+        self._task_handler = task_handler
+
+    async def execute(
+        self,
+        params: SetShakeSpeedParams,
+    ) -> SuccessData[SetShakeSpeedResult]:
+        """Set a Heater-Shaker's target shake speed."""
+        state_update = update_types.StateUpdate()
+
+        # Allow propagation of ModuleNotLoadedError and WrongModuleTypeError.
+        hs_module_substate = self._state_view.modules.get_heater_shaker_module_substate(
+            module_id=params.moduleId
+        )
+
+        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(
+                hs_module_substate.module_id
+            )
+        )
+        if pipette_should_retract:
+            # Move pipette away if it is close to the heater-shaker
+            # TODO(jbl 2022-07-28) replace home movement with a retract movement
+            await self._movement.home(
+                axes=self._state_view.motion.get_robot_mount_axes()
+            )
+            state_update.clear_all_pipette_locations()
+
+        # Allow propagation of ModuleNotAttachedError.
+        hs_hardware_module = self._equipment.get_module_hardware_api(
+            hs_module_substate.module_id
+        )
+
+        async def start_shake(task_handler: TaskHandler) -> None:
+            if hs_hardware_module is not None:
+                async with task_handler.synchronize_cancel_previous(
+                    hs_module_substate.module_id
+                ):
+                    await hs_hardware_module.set_speed(rpm=validated_speed)
+
+        task = await self._task_handler.create_task(
+            task_function=start_shake, id=params.taskId
+        )
+        return SuccessData(
+            public=SetShakeSpeedResult(
+                pipetteRetracted=pipette_should_retract, taskId=task.id
+            ),
+            state_update=state_update,
+        )
+
+
+class SetShakeSpeed(
+    BaseCommand[SetShakeSpeedParams, SetShakeSpeedResult, ErrorOccurrence]
+):
+    """A command to set a Heater-Shaker's shake speed."""
+
+    commandType: SetShakeSpeedCommandType = "heaterShaker/setShakeSpeed"
+    params: SetShakeSpeedParams
+    result: Optional[SetShakeSpeedResult] = None
+
+    _ImplementationCls: Type[SetShakeSpeedImpl] = SetShakeSpeedImpl
+
+
+class SetShakeSpeedCreate(BaseCommandCreate[SetShakeSpeedParams]):
+    """A request to create a Heater-Shaker's set shake speed command."""
+
+    commandType: SetShakeSpeedCommandType = "heaterShaker/setShakeSpeed"
+    params: SetShakeSpeedParams
+
+    _CommandCls: Type[SetShakeSpeed] = SetShakeSpeed

opentrons/protocol_engine/commands/heater_shaker/set_target_temperature.py

@@ -1,31 +1,47 @@
 """Command models to start heating a Heater-Shaker Module."""
 from __future__ import annotations
-from typing import Optional, TYPE_CHECKING
+from typing import Optional, TYPE_CHECKING, Any
 from typing_extensions import Literal, Type
 
 from pydantic import BaseModel, Field
+from pydantic.json_schema import SkipJsonSchema
 
 from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData
 from ...errors.error_occurrence import ErrorOccurrence
 
 if TYPE_CHECKING:
     from opentrons.protocol_engine.state.state import StateView
-    from opentrons.protocol_engine.execution import EquipmentHandler
+    from opentrons.protocol_engine.execution import EquipmentHandler, TaskHandler
 
 
 SetTargetTemperatureCommandType = Literal["heaterShaker/setTargetTemperature"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default", None)
+
+
 class SetTargetTemperatureParams(BaseModel):
     """Input parameters to set a Heater-Shaker's target temperature."""
 
     moduleId: str = Field(..., description="Unique ID of the Heater-Shaker Module.")
     celsius: float = Field(..., description="Target temperature in °C.")
+    taskId: str | SkipJsonSchema[None] = Field(
+        None,
+        description="Id for the background task that manages the temperature",
+        json_schema_extra=_remove_default,
+    )
 
 
 class SetTargetTemperatureResult(BaseModel):
     """Result data from setting a Heater-Shaker's target temperature."""
 
+    taskId: str | SkipJsonSchema[None] = Field(
+        None,
+        description="The task id for the setTargetTemperature task",
+        json_schema_extra=_remove_default,
+    )
+
 
 class SetTargetTemperatureImpl(
     AbstractCommandImpl[
@@ -38,10 +54,12 @@ class SetTargetTemperatureImpl(
         self,
         state_view: StateView,
         equipment: EquipmentHandler,
+        task_handler: TaskHandler,
         **unused_dependencies: object,
     ) -> None:
         self._state_view = state_view
         self._equipment = equipment
+        self._task_handler = task_handler
 
     async def execute(
         self,
@@ -61,11 +79,19 @@ class SetTargetTemperatureImpl(
             hs_module_substate.module_id
         )
 
-        if hs_hardware_module is not None:
-            await hs_hardware_module.start_set_temperature(validated_temp)
+        async def start_set_temperature(task_handler: TaskHandler) -> None:
+            if hs_hardware_module is not None:
+                async with task_handler.synchronize_cancel_previous(
+                    hs_module_substate.module_id
+                ):
+                    await hs_hardware_module.start_set_temperature(validated_temp)
+                    await hs_hardware_module.await_temperature(validated_temp)
 
+        task = await self._task_handler.create_task(
+            task_function=start_set_temperature, id=params.taskId
+        )
         return SuccessData(
-            public=SetTargetTemperatureResult(),
+            public=SetTargetTemperatureResult(taskId=task.id),
         )
 
 

opentrons/protocol_engine/commands/movement_common.py

@@ -152,6 +152,7 @@ async def move_to_well(
     minimum_z_height: Optional[float] = None,
     speed: Optional[float] = None,
     operation_volume: Optional[float] = None,
+    offset_pipette_for_reservoir_subwells: bool = False,
 ) -> MoveToWellOperationReturn:
     """Execute a move to well microoperation."""
     try:
@@ -165,6 +166,7 @@ async def move_to_well(
             minimum_z_height=minimum_z_height,
             speed=speed,
             operation_volume=operation_volume,
+            offset_pipette_for_reservoir_subwells=offset_pipette_for_reservoir_subwells,
         )
     except StallOrCollisionDetectedError as e:
         return DefinedErrorData(

opentrons/protocol_engine/commands/pick_up_tip.py

@@ -10,7 +10,7 @@ from typing_extensions import Literal
 from ..errors import ErrorOccurrence, PickUpTipTipNotAttachedError
 from ..resources import ModelUtils
 from ..state import update_types
-from ..types import PickUpTipWellLocation, LabwareWellId
+from ..types import PickUpTipWellLocation, LabwareWellId, TipRackWellState
 from .pipetting_common import (
     PipetteIdMixin,
 )
@@ -121,10 +121,14 @@ class PickUpTipImplementation(AbstractCommandImpl[PickUpTipParams, _ExecuteRetur
         labware_id = params.labwareId
         well_name = params.wellName
 
-        tips_to_mark_as_used = self._state_view.tips.compute_tips_to_mark_as_used(
-            labware_id=labware_id,
-            well_name=well_name,
-            nozzle_map=self._state_view.pipettes.get_nozzle_configuration(pipette_id),
+        tips_to_mark_as_empty = (
+            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
+                ),
+            )
         )
 
         well_location = self._state_view.geometry.convert_pick_up_tip_well_location(
@@ -160,16 +164,20 @@ class PickUpTipImplementation(AbstractCommandImpl[PickUpTipParams, _ExecuteRetur
                     ),
                 )
                 .set_fluid_empty(pipette_id=pipette_id, clean_tip=True)
-                .mark_tips_as_used(
-                    labware_id=labware_id, well_names=tips_to_mark_as_used
+                .update_tip_rack_well_state(
+                    tip_state=TipRackWellState.EMPTY,
+                    labware_id=labware_id,
+                    well_names=tips_to_mark_as_empty,
                 )
             )
             state_update = (
                 update_types.StateUpdate.reduce(
                     update_types.StateUpdate(), move_result.state_update
                 )
-                .mark_tips_as_used(
-                    labware_id=labware_id, well_names=tips_to_mark_as_used
+                .update_tip_rack_well_state(
+                    tip_state=TipRackWellState.EMPTY,
+                    labware_id=labware_id,
+                    well_names=tips_to_mark_as_empty,
                 )
                 .set_fluid_unknown(pipette_id=pipette_id)
             )
@@ -197,8 +205,10 @@ class PickUpTipImplementation(AbstractCommandImpl[PickUpTipParams, _ExecuteRetur
                         labware_id=labware_id, well_name=well_name
                     ),
                 )
-                .mark_tips_as_used(
-                    labware_id=labware_id, well_names=tips_to_mark_as_used
+                .update_tip_rack_well_state(
+                    tip_state=TipRackWellState.EMPTY,
+                    labware_id=labware_id,
+                    well_names=tips_to_mark_as_empty,
                 )
                 .set_fluid_empty(pipette_id=pipette_id, clean_tip=True)
                 .set_pipette_ready_to_aspirate(

opentrons/protocol_engine/commands/set_tip_state.py

@@ -0,0 +1,97 @@
+"""Set tip state command request, result, and implementation models."""
+
+from __future__ import annotations
+from pydantic import BaseModel, Field
+from typing import TYPE_CHECKING, Optional, Type, List
+from typing_extensions import Literal
+
+from ..errors.error_occurrence import ErrorOccurrence
+from ..state.update_types import StateUpdate
+from ..types import TipRackWellState
+
+
+from .command import (
+    AbstractCommandImpl,
+    BaseCommand,
+    BaseCommandCreate,
+    SuccessData,
+)
+
+if TYPE_CHECKING:
+    from ..state.state import StateView
+
+
+SetTipStateCommandType = Literal["setTipState"]
+
+
+class SetTipStateParams(BaseModel):
+    """Payload needed to set tip wells of a tip rack to the requested state."""
+
+    labwareId: str = Field(
+        ..., description="Identifier of tip rack labware to set tip wells in."
+    )
+    wellNames: List[str] = Field(
+        ..., description="Names of the well to set tip well state for."
+    )
+    tipWellState: TipRackWellState = Field(
+        ..., description="State to set tip wells to."
+    )
+
+
+class SetTipStateResult(BaseModel):
+    """Result data from the execution of a setTipState command."""
+
+    pass
+
+
+class SetTipStateImplementation(
+    AbstractCommandImpl[SetTipStateParams, SuccessData[SetTipStateResult]]
+):
+    """Set tip state command implementation."""
+
+    def __init__(
+        self,
+        state_view: StateView,
+        **kwargs: object,
+    ) -> None:
+        self._state_view = state_view
+
+    async def execute(
+        self, params: SetTipStateParams
+    ) -> SuccessData[SetTipStateResult]:
+        """Set the tip rack wells to the requested state."""
+        labware_id = params.labwareId
+        well_names = params.wellNames
+
+        self._state_view.labware.raise_if_not_tip_rack(labware_id=labware_id)
+        self._state_view.labware.raise_if_wells_are_invalid(
+            labware_id=labware_id, well_names=well_names
+        )
+
+        return SuccessData(
+            public=SetTipStateResult(),
+            state_update=StateUpdate().update_tip_rack_well_state(
+                tip_state=params.tipWellState,
+                labware_id=labware_id,
+                well_names=well_names,
+            ),
+        )
+
+
+class SetTipState(BaseCommand[SetTipStateParams, SetTipStateResult, ErrorOccurrence]):
+    """Set tip state command model."""
+
+    commandType: SetTipStateCommandType = "setTipState"
+    params: SetTipStateParams
+    result: Optional[SetTipStateResult] = None
+
+    _ImplementationCls: Type[SetTipStateImplementation] = SetTipStateImplementation
+
+
+class SetTipStateCreate(BaseCommandCreate[SetTipStateParams]):
+    """Set tip state command creation request model."""
+
+    commandType: SetTipStateCommandType = "setTipState"
+    params: SetTipStateParams
+
+    _CommandCls: Type[SetTipState] = SetTipState

opentrons/protocol_engine/commands/temperature_module/set_target_temperature.py

@@ -1,25 +1,35 @@
 """Command models to start heating a Temperature Module."""
 from __future__ import annotations
-from typing import Optional, TYPE_CHECKING
+from typing import Optional, TYPE_CHECKING, Any
 from typing_extensions import Literal, Type
 
 from pydantic import BaseModel, Field
+from pydantic.json_schema import SkipJsonSchema
 
 from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData
 from ...errors.error_occurrence import ErrorOccurrence
 
 if TYPE_CHECKING:
     from opentrons.protocol_engine.state.state import StateView
-    from opentrons.protocol_engine.execution import EquipmentHandler
+    from opentrons.protocol_engine.execution import EquipmentHandler, TaskHandler
 
 SetTargetTemperatureCommandType = Literal["temperatureModule/setTargetTemperature"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default", None)
+
+
 class SetTargetTemperatureParams(BaseModel):
     """Input parameters to set a Temperature Module's target temperature."""
 
     moduleId: str = Field(..., description="Unique ID of the Temperature Module.")
     celsius: float = Field(..., description="Target temperature in °C.")
+    taskId: str | SkipJsonSchema[None] = Field(
+        None,
+        description="Id for the background task that manages the temperature",
+        json_schema_extra=_remove_default,
+    )
 
 
 class SetTargetTemperatureResult(BaseModel):
@@ -30,6 +40,11 @@ class SetTargetTemperatureResult(BaseModel):
         description="The target temperature that was set after validation "
         "and type conversion (if any).",
     )
+    taskId: str | SkipJsonSchema[None] = Field(
+        None,
+        description="The task id for the setTargetTemperature task",
+        json_schema_extra=_remove_default,
+    )
 
 
 class SetTargetTemperatureImpl(
@@ -43,10 +58,12 @@ class SetTargetTemperatureImpl(
         self,
         state_view: StateView,
         equipment: EquipmentHandler,
+        task_handler: TaskHandler,
         **unused_dependencies: object,
     ) -> None:
         self._state_view = state_view
         self._equipment = equipment
+        self._task_handler = task_handler
 
     async def execute(
         self, params: SetTargetTemperatureParams
@@ -56,19 +73,33 @@ class SetTargetTemperatureImpl(
         module_substate = self._state_view.modules.get_temperature_module_substate(
             module_id=params.moduleId
         )
-
         # Verify temperature from temperature module view
         validated_temp = module_substate.validate_target_temperature(params.celsius)
-
         # Allow propagation of ModuleNotAttachedError.
         temp_hardware_module = self._equipment.get_module_hardware_api(
             module_substate.module_id
         )
 
-        if temp_hardware_module is not None:
-            await temp_hardware_module.start_set_temperature(celsius=validated_temp)
+        async def start_set_temperature(task_handler: TaskHandler) -> None:
+            if temp_hardware_module is not None:
+                async with task_handler.synchronize_cancel_previous(
+                    module_substate.module_id
+                ):
+                    await temp_hardware_module.start_set_temperature(
+                        celsius=validated_temp
+                    )
+                    await temp_hardware_module.await_temperature(
+                        awaiting_temperature=validated_temp
+                    )
+
+        task = await self._task_handler.create_task(
+            task_function=start_set_temperature, id=params.taskId
+        )
+
         return SuccessData(
-            public=SetTargetTemperatureResult(targetTemperature=validated_temp),
+            public=SetTargetTemperatureResult(
+                targetTemperature=validated_temp, taskId=task.id
+            ),
         )
 
 

opentrons/protocol_engine/commands/thermocycler/__init__.py

@@ -73,6 +73,15 @@ from .run_profile import (
     RunProfileCreate,
 )
 
+from .start_run_extended_profile import (
+    StartRunExtendedProfileCommandType,
+    StartRunExtendedProfileParams,
+    StartRunExtendedProfileStepParams,
+    StartRunExtendedProfileResult,
+    StartRunExtendedProfile,
+    StartRunExtendedProfileCreate,
+)
+
 from .run_extended_profile import (
     RunExtendedProfileCommandType,
     RunExtendedProfileParams,
@@ -140,6 +149,13 @@ __all__ = [
     "RunProfileResult",
     "RunProfile",
     "RunProfileCreate",
+    # Start run profile command models,
+    "StartRunExtendedProfileCommandType",
+    "StartRunExtendedProfileParams",
+    "StartRunExtendedProfileStepParams",
+    "StartRunExtendedProfileResult",
+    "StartRunExtendedProfile",
+    "StartRunExtendedProfileCreate",
     # Run extended profile command models.
     "RunExtendedProfileCommandType",
     "RunExtendedProfileParams",

opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py

@@ -33,6 +33,11 @@ class ProfileStep(BaseModel):
     holdSeconds: float = Field(
         ..., description="Time to hold target temperature in seconds."
     )
+    rampRate: float | SkipJsonSchema[None] = Field(
+        None,
+        description="How quickly to change temperature in °C/second.",
+        json_schema_extra=_remove_default,
+    )
 
 
 class ProfileCycle(BaseModel):
@@ -68,6 +73,7 @@ def _transform_profile_step(
     return ThermocyclerStep(
         temperature=thermocycler_state.validate_target_block_temperature(step.celsius),
         hold_time_seconds=step.holdSeconds,
+        ramp_rate=thermocycler_state.validate_ramp_rate(step.rampRate, step.celsius),
     )
 
 

opentrons/protocol_engine/commands/thermocycler/run_profile.py

@@ -30,6 +30,11 @@ class RunProfileStepParams(BaseModel):
     holdSeconds: float = Field(
         ..., description="Time to hold target temperature at in seconds."
     )
+    rampRate: float | SkipJsonSchema[None] = Field(
+        None,
+        description="How quickly to change temperature in °C/second.",
+        json_schema_extra=_remove_default,
+    )
 
 
 class RunProfileParams(BaseModel):
@@ -81,6 +86,9 @@ class RunProfileImpl(
                     profile_step.celsius
                 ),
                 hold_time_seconds=profile_step.holdSeconds,
+                ramp_rate=thermocycler_state.validate_ramp_rate(
+                    profile_step.rampRate, profile_step.celsius
+                ),
             )
             for profile_step in params.profile
         ]

opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py

@@ -11,7 +11,7 @@ from ...errors.error_occurrence import ErrorOccurrence
 
 if TYPE_CHECKING:
     from opentrons.protocol_engine.state.state import StateView
-    from opentrons.protocol_engine.execution import EquipmentHandler
+    from opentrons.protocol_engine.execution import EquipmentHandler, TaskHandler
 
 
 SetTargetBlockTemperatureCommandType = Literal["thermocycler/setTargetBlockTemperature"]
@@ -39,6 +39,17 @@ class SetTargetBlockTemperatureParams(BaseModel):
         " the given hold time has elapsed.",
         json_schema_extra=_remove_default,
     )
+    ramp_rate: float | SkipJsonSchema[None] = Field(
+        None,
+        description="The rate in C°/second to change temperature from the current target."
+        " If unspecified, the Thermocycler will change temperature at the fastest possible rate.",
+        json_schema_extra=_remove_default,
+    )
+    taskId: str | SkipJsonSchema[None] = Field(
+        None,
+        description="Id for the background task that manages the temperature.",
+        json_schema_extra=_remove_default,
+    )
 
 
 class SetTargetBlockTemperatureResult(BaseModel):
@@ -48,6 +59,11 @@ class SetTargetBlockTemperatureResult(BaseModel):
         ...,
         description="The target block temperature that was set after validation.",
     )
+    taskId: str | SkipJsonSchema[None] = Field(
+        None,
+        description="The task id for the setTargetBlockTemperature",
+        json_schema_extra=_remove_default,
+    )
 
 
 class SetTargetBlockTemperatureImpl(
@@ -62,10 +78,12 @@ class SetTargetBlockTemperatureImpl(
         self,
         state_view: StateView,
         equipment: EquipmentHandler,
+        task_handler: TaskHandler,
         **unused_dependencies: object,
     ) -> None:
         self._state_view = state_view
         self._equipment = equipment
+        self._task_handler = task_handler
 
     async def execute(
         self,
@@ -90,19 +108,35 @@ class SetTargetBlockTemperatureImpl(
             hold_time = thermocycler_state.validate_hold_time(params.holdTimeSeconds)
         else:
             hold_time = None
+        target_ramp_rate: Optional[float]
+        if params.ramp_rate is not None:
+            target_ramp_rate = thermocycler_state.validate_ramp_rate(
+                params.ramp_rate, target_temperature
+            )
+        else:
+            target_ramp_rate = None
 
         thermocycler_hardware = self._equipment.get_module_hardware_api(
             thermocycler_state.module_id
         )
 
-        if thermocycler_hardware is not None:
-            await thermocycler_hardware.set_target_block_temperature(
-                target_temperature, volume=target_volume, hold_time_seconds=hold_time
-            )
+        async def set_target_block_temperature(task_handler: TaskHandler) -> None:
+            if thermocycler_hardware is not None:
+                await thermocycler_hardware.set_target_block_temperature(
+                    target_temperature,
+                    volume=target_volume,
+                    hold_time_seconds=hold_time,
+                    ramp_rate=target_ramp_rate,
+                )
+                await thermocycler_hardware.wait_for_block_target()
+
+        task = await self._task_handler.create_task(
+            task_function=set_target_block_temperature, id=params.taskId
+        )
 
         return SuccessData(
             public=SetTargetBlockTemperatureResult(
-                targetBlockTemperature=target_temperature
+                targetBlockTemperature=target_temperature, taskId=task.id
             ),
         )