opentrons 8.7.0a2__py3-none-any.whl → 8.7.0a4__py3-none-any.whl

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, TipRackWellState
+from ..types import DropTipWellLocation
 from .pipetting_common import (
     PipetteIdMixin,
     TipPhysicallyAttachedError,
@@ -140,25 +140,6 @@ 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,
@@ -171,7 +152,12 @@ class DropTipImplementation(AbstractCommandImpl[DropTipParams, _ExecuteReturn]):
             return move_result
 
         scrape_type = TipScrapeType.NONE
-        if params.scrape_tips and is_tip_rack:
+        if (
+            params.scrape_tips
+            and self._state_view.geometry._labware.get_definition(
+                labware_id
+            ).parameters.isTiprack
+        ):
             if int("".join(filter(str.isdigit, well_name))) <= 6:
                 scrape_type = TipScrapeType.RIGHT_ONE_COL
             else:
@@ -208,10 +194,6 @@ 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:
@@ -219,16 +201,10 @@ 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/movement_common.py

@@ -152,7 +152,6 @@ 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:
@@ -166,7 +165,6 @@ 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, TipRackWellState
+from ..types import PickUpTipWellLocation, LabwareWellId
 from .pipetting_common import (
     PipetteIdMixin,
 )
@@ -121,14 +121,10 @@ class PickUpTipImplementation(AbstractCommandImpl[PickUpTipParams, _ExecuteRetur
         labware_id = params.labwareId
         well_name = params.wellName
 
-        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
-                ),
-            )
+        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),
         )
 
         well_location = self._state_view.geometry.convert_pick_up_tip_well_location(
@@ -164,20 +160,16 @@ class PickUpTipImplementation(AbstractCommandImpl[PickUpTipParams, _ExecuteRetur
                     ),
                 )
                 .set_fluid_empty(pipette_id=pipette_id, clean_tip=True)
-                .update_tip_rack_well_state(
-                    tip_state=TipRackWellState.EMPTY,
-                    labware_id=labware_id,
-                    well_names=tips_to_mark_as_empty,
+                .mark_tips_as_used(
+                    labware_id=labware_id, well_names=tips_to_mark_as_used
                 )
             )
             state_update = (
                 update_types.StateUpdate.reduce(
                     update_types.StateUpdate(), move_result.state_update
                 )
-                .update_tip_rack_well_state(
-                    tip_state=TipRackWellState.EMPTY,
-                    labware_id=labware_id,
-                    well_names=tips_to_mark_as_empty,
+                .mark_tips_as_used(
+                    labware_id=labware_id, well_names=tips_to_mark_as_used
                 )
                 .set_fluid_unknown(pipette_id=pipette_id)
             )
@@ -205,10 +197,8 @@ class PickUpTipImplementation(AbstractCommandImpl[PickUpTipParams, _ExecuteRetur
                         labware_id=labware_id, well_name=well_name
                     ),
                 )
-                .update_tip_rack_well_state(
-                    tip_state=TipRackWellState.EMPTY,
-                    labware_id=labware_id,
-                    well_names=tips_to_mark_as_empty,
+                .mark_tips_as_used(
+                    labware_id=labware_id, well_names=tips_to_mark_as_used
                 )
                 .set_fluid_empty(pipette_id=pipette_id, clean_tip=True)
                 .set_pipette_ready_to_aspirate(

opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py

@@ -33,11 +33,6 @@ 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):
@@ -73,7 +68,6 @@ 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

@@ -30,11 +30,6 @@ 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):
@@ -86,9 +81,6 @@ 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

@@ -39,12 +39,6 @@ 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,
-    )
 
 
 class SetTargetBlockTemperatureResult(BaseModel):
@@ -96,13 +90,6 @@ 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
@@ -110,10 +97,7 @@ class SetTargetBlockTemperatureImpl(
 
         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,
+                target_temperature, volume=target_volume, hold_time_seconds=hold_time
             )
 
         return SuccessData(

opentrons/protocol_engine/commands/touch_tip.py

@@ -114,7 +114,7 @@ class TouchTipImplementation(
 
         if self._state_view.labware.get_has_quirk(labware_id, "touchTipDisabled"):
             raise TouchTipDisabledError(
-                f"Touch tip not allowed on labware {self._state_view.labware.get_display_name(labware_id)}"
+                f"Touch tip not allowed on labware {labware_id}"
             )
 
         if self._state_view.labware.is_tiprack(labware_id):

opentrons/protocol_engine/commands/unsafe/unsafe_place_labware.py

@@ -14,11 +14,12 @@ from opentrons.protocol_engine.errors.exceptions import (
     CannotPerformGripperAction,
     GripperNotAttachedError,
 )
+from opentrons.types import Point
+
 from ...types import (
     DeckSlotLocation,
     ModuleModel,
     OnDeckLabwareLocation,
-    GripperMoveType,
 )
 from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData
 from ...errors.error_occurrence import ErrorOccurrence
@@ -99,6 +100,22 @@ class UnsafePlaceLabwareImplementation(
             LabwareUri(params.labwareURI)
         )
 
+        # todo(mm, 2024-11-06): This is only correct in the special case of an
+        # absorbance reader lid. Its definition currently puts the offsets for *itself*
+        # in the property that's normally meant for offsets for its *children.*
+        final_offsets = self._state_view.labware.get_child_gripper_offsets(
+            labware_definition=definition, slot_name=None
+        )
+        drop_offset = (
+            Point(
+                final_offsets.dropOffset.x,
+                final_offsets.dropOffset.y,
+                final_offsets.dropOffset.z,
+            )
+            if final_offsets
+            else None
+        )
+
         if isinstance(params.location, DeckSlotLocation):
             self._state_view.addressable_areas.raise_if_area_not_in_deck_configuration(
                 params.location.slotName.id
@@ -122,7 +139,7 @@ class UnsafePlaceLabwareImplementation(
         await ot3api.update_axis_position_estimations([Axis.X, Axis.Y])
 
         # Place the labware down
-        await self._start_movement(ot3api, definition, location)
+        await self._start_movement(ot3api, definition, location, drop_offset)
 
         return SuccessData(public=UnsafePlaceLabwareResult())
 
@@ -131,6 +148,7 @@ class UnsafePlaceLabwareImplementation(
         ot3api: OT3HardwareControlAPI,
         labware_definition: LabwareDefinition,
         location: OnDeckLabwareLocation,
+        drop_offset: Optional[Point],
     ) -> None:
         gripper_homed_position = await ot3api.gantry_position(
             mount=OT3Mount.GRIPPER,
@@ -138,15 +156,13 @@ class UnsafePlaceLabwareImplementation(
         )
 
         to_labware_center = self._state_view.geometry.get_labware_grip_point(
-            labware_definition=labware_definition,
-            location=location,
-            move_type=GripperMoveType.DROP_LABWARE,
-            user_additional_offset=None,
+            labware_definition=labware_definition, location=location
         )
 
         movement_waypoints = get_gripper_labware_placement_waypoints(
             to_labware_center=to_labware_center,
             gripper_home_z=gripper_homed_position.z,
+            drop_offset=drop_offset,
         )
 
         # start movement

opentrons/protocol_engine/errors/__init__.py

@@ -57,7 +57,6 @@ from .exceptions import (
     InvalidTargetSpeedError,
     InvalidTargetTemperatureError,
     InvalidBlockVolumeError,
-    InvalidRampRateError,
     InvalidHoldTimeError,
     InvalidWavelengthError,
     CannotPerformModuleAction,
@@ -91,7 +90,6 @@ from .exceptions import (
     FlexStackerLabwarePoolNotYetDefinedError,
     FlexStackerNotLogicallyEmptyError,
     InvalidLabwarePositionError,
-    InvalidModuleOrientation,
 )
 
 from .error_occurrence import ErrorOccurrence, ProtocolCommandFailedError
@@ -153,7 +151,6 @@ __all__ = [
     "NoTargetTemperatureSetError",
     "InvalidTargetTemperatureError",
     "InvalidTargetSpeedError",
-    "InvalidRampRateError",
     "InvalidBlockVolumeError",
     "InvalidHoldTimeError",
     "InvalidLiquidError",
@@ -177,7 +174,6 @@ __all__ = [
     "FlexStackerLabwarePoolNotYetDefinedError",
     "FlexStackerNotLogicallyEmptyError",
     "InvalidLabwarePositionError",
-    "InvalidModuleOrientation",
     # error occurrence models
     "ErrorOccurrence",
     "CommandNotAllowedError",

opentrons/protocol_engine/errors/exceptions.py

@@ -413,36 +413,6 @@ class WellDoesNotExistError(ProtocolEngineError):
         super().__init__(ErrorCodes.GENERAL_ERROR, message, details, wrapping)
 
 
-class NoTaskFoundError(ProtocolEngineError):
-    """Raised when referencing a task that does not exist.
-
-    This error could be raised if a protocol references a task before it
-    has been created.
-    """
-
-    def __init__(
-        self,
-        message: Optional[str] = None,
-        details: Optional[Dict[str, Any]] = None,
-        wrapping: Optional[Sequence[EnumeratedError]] = None,
-    ) -> None:
-        """Build a NoTaskFoundError."""
-        super().__init__(ErrorCodes.GENERAL_ERROR, message, details, wrapping)
-
-
-class TaskFailedError(ProtocolEngineError):
-    """Raised when waiting on a task that failed."""
-
-    def __init__(
-        self,
-        message: Optional[str] = None,
-        details: Optional[Dict[str, Any]] = None,
-        wrapping: Optional[Sequence[EnumeratedError]] = None,
-    ) -> None:
-        """Build a TaskFailedError."""
-        super().__init__(ErrorCodes.GENERAL_ERROR, message, details, wrapping)
-
-
 class PipetteNotLoadedError(ProtocolEngineError):
     """Raised when referencing a pipette that has not been loaded."""
 
@@ -855,19 +825,6 @@ class InvalidTargetTemperatureError(ProtocolEngineError):
         super().__init__(ErrorCodes.GENERAL_ERROR, message, details, wrapping)
 
 
-class InvalidRampRateError(ProtocolEngineError):
-    """Raised when attempting to set an invalid ramp rate."""
-
-    def __init__(
-        self,
-        message: Optional[str] = None,
-        details: Optional[Dict[str, Any]] = None,
-        wrapping: Optional[Sequence[EnumeratedError]] = None,
-    ) -> None:
-        """Build a InvalidRampRateError."""
-        super().__init__(ErrorCodes.GENERAL_ERROR, message, details, wrapping)
-
-
 class InvalidBlockVolumeError(ProtocolEngineError):
     """Raised when attempting to set an invalid block max volume."""
 
@@ -1349,15 +1306,3 @@ class InvalidLabwarePositionError(ProtocolEngineError):
         wrapping: Optional[Sequence[EnumeratedError]] = None,
     ) -> None:
         super().__init__(ErrorCodes.GENERAL_ERROR, message, details, wrapping)
-
-
-class InvalidModuleOrientation(ProtocolEngineError):
-    """Raised when a module orientation is invalid for a slot id."""
-
-    def __init__(
-        self,
-        message: Optional[str] = None,
-        details: Optional[dict[str, Any]] = None,
-        wrapping: Optional[Sequence[EnumeratedError]] = None,
-    ) -> None:
-        super().__init__(ErrorCodes.GENERAL_ERROR, message, details, wrapping)

opentrons/protocol_engine/execution/__init__.py

@@ -21,7 +21,6 @@ from .run_control import RunControlHandler
 from .hardware_stopper import HardwareStopper
 from .door_watcher import DoorWatcher
 from .status_bar import StatusBarHandler
-from .task_handler import TaskHandler
 from ..resources.file_provider import FileProvider
 
 # .thermocycler_movement_flagger omitted from package's public interface.
@@ -47,6 +46,5 @@ __all__ = [
     "DoorWatcher",
     "RailLightsHandler",
     "StatusBarHandler",
-    "TaskHandler",
     "FileProvider",
 ]

opentrons/protocol_engine/execution/command_executor.py

@@ -35,7 +35,6 @@ from .tip_handler import TipHandler
 from .run_control import RunControlHandler
 from .rail_lights import RailLightsHandler
 from .status_bar import StatusBarHandler
-from .task_handler import TaskHandler
 
 
 log = getLogger(__name__)
@@ -86,7 +85,6 @@ class CommandExecutor:
         run_control: RunControlHandler,
         rail_lights: RailLightsHandler,
         status_bar: StatusBarHandler,
-        task_handler: TaskHandler,
         model_utils: Optional[ModelUtils] = None,
         command_note_tracker_provider: Optional[CommandNoteTrackerProvider] = None,
     ) -> None:
@@ -108,7 +106,6 @@ class CommandExecutor:
         self._command_note_tracker_provider = (
             command_note_tracker_provider or _NoteTracker
         )
-        self._task_handler = task_handler
 
     async def execute(self, command_id: str) -> None:
         """Run a given command's execution procedure.
@@ -134,7 +131,6 @@ class CommandExecutor:
             model_utils=self._model_utils,
             status_bar=self._status_bar,
             command_note_adder=note_tracker,
-            task_handler=self._task_handler,
         )
 
         started_at = self._model_utils.get_timestamp()
@@ -218,7 +214,3 @@ class CommandExecutor:
                         type=error_recovery_type,
                     )
                 )
-
-    def cancel_tasks(self, message: str | None = None) -> None:
-        """Cancel all concurrent tasks."""
-        self._task_handler.cancel_all(message=message)

opentrons/protocol_engine/execution/create_queue_worker.py

@@ -17,7 +17,6 @@ from .run_control import RunControlHandler
 from .command_executor import CommandExecutor
 from .queue_worker import QueueWorker
 from .status_bar import StatusBarHandler
-from .task_handler import TaskHandler
 
 
 def create_queue_worker(
@@ -77,9 +76,7 @@ def create_queue_worker(
     rail_lights_handler = RailLightsHandler(
         hardware_api=hardware_api,
     )
-    task_handler = TaskHandler(
-        state_store=state_store, action_dispatcher=action_dispatcher
-    )
+
     status_bar_handler = StatusBarHandler(hardware_api=hardware_api)
 
     command_executor = CommandExecutor(
@@ -96,7 +93,6 @@ def create_queue_worker(
         run_control=run_control_handler,
         rail_lights=rail_lights_handler,
         status_bar=status_bar_handler,
-        task_handler=task_handler,
     )
 
     return QueueWorker(

opentrons/protocol_engine/execution/labware_movement.py

@@ -31,7 +31,6 @@ from ..types import (
     OnLabwareLocation,
     LabwareLocation,
     OnDeckLabwareLocation,
-    GripperMoveType,
 )
 
 if TYPE_CHECKING:
@@ -142,16 +141,10 @@ class LabwareMovementHandler:
             labware_definition = self._state_store.labware.get_definition(labware_id)
 
         from_labware_center = self._state_store.geometry.get_labware_grip_point(
-            labware_definition=labware_definition,
-            location=current_location,
-            move_type=GripperMoveType.PICK_UP_LABWARE,
-            user_additional_offset=user_pick_up_offset,
+            labware_definition=labware_definition, location=current_location
         )
         to_labware_center = self._state_store.geometry.get_labware_grip_point(
-            labware_definition=labware_definition,
-            location=new_location,
-            move_type=GripperMoveType.DROP_LABWARE,
-            user_additional_offset=user_drop_offset,
+            labware_definition=labware_definition, location=new_location
         )
 
         if use_virtual_gripper:
@@ -200,10 +193,20 @@ class LabwareMovementHandler:
         async with self._thermocycler_plate_lifter.lift_plate_for_labware_movement(
             labware_location=current_location
         ):
+            final_offsets = (
+                self._state_store.geometry.get_final_labware_movement_offset_vectors(
+                    from_location=current_location,
+                    to_location=new_location,
+                    additional_pick_up_offset=user_pick_up_offset,
+                    additional_drop_offset=user_drop_offset,
+                    current_labware=labware_definition,
+                )
+            )
             movement_waypoints = get_gripper_labware_movement_waypoints(
                 from_labware_center=from_labware_center,
                 to_labware_center=to_labware_center,
                 gripper_home_z=gripper_homed_position.z,
+                offset_data=final_offsets,
                 post_drop_slide_offset=post_drop_slide_offset,
                 gripper_home_z_offset=gripper_z_offset,
             )

opentrons/protocol_engine/execution/movement.py

@@ -83,7 +83,6 @@ class MovementHandler:
         minimum_z_height: Optional[float] = None,
         speed: Optional[float] = None,
         operation_volume: Optional[float] = None,
-        offset_pipette_for_reservoir_subwells: bool = False,
     ) -> Point:
         """Move to a specific well."""
         self._state_store.geometry.raise_if_labware_inaccessible_by_pipette(
@@ -144,7 +143,6 @@ class MovementHandler:
             force_direct=force_direct,
             minimum_z_height=minimum_z_height,
             operation_volume=operation_volume,
-            offset_pipette_for_reservoir_subwells=offset_pipette_for_reservoir_subwells,
         )
 
         speed = self._state_store.pipettes.get_movement_speed(

opentrons/protocol_engine/execution/queue_worker.py

@@ -51,7 +51,6 @@ class QueueWorker:
         """
         if self._worker_task:
             self._worker_task.cancel()
-            self._command_executor.cancel_tasks("Engine cancelled")
 
     async def join(self) -> None:
         """Wait for the worker to finish, propagating any errors."""
@@ -66,10 +65,7 @@ class QueueWorker:
                 pass
             except Exception as e:
                 log.error("Unhandled exception in QueueWorker job", exc_info=e)
-                self._command_executor.cancel_tasks("Engine failed")
                 raise e
-            else:
-                self._command_executor.cancel_tasks("Engine commands complete")
 
     async def _run_commands(self) -> None:
         async for command_id in self._command_generator():

opentrons/protocol_engine/execution/run_control.py

@@ -31,11 +31,3 @@ class RunControlHandler:
         """Delay protocol execution for a duration."""
         if not self._state_store.config.ignore_pause:
             await asyncio.sleep(seconds)
-
-    async def wait_for_tasks(self, tasks: list[str]) -> None:
-        """Wait for concurrent tasks to complete."""
-        await self._state_store.wait_for(
-            condition=lambda: self._state_store.tasks.all_tasks_finished_or_any_task_failed(
-                task_ids=tasks
-            )
-        )