opentrons 8.7.0a0__py3-none-any.whl → 8.7.0a2__py3-none-any.whl

opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py

@@ -39,6 +39,12 @@ 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):
@@ -90,6 +96,13 @@ 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
@@ -97,7 +110,10 @@ 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
+                target_temperature,
+                volume=target_volume,
+                hold_time_seconds=hold_time,
+                ramp_rate=target_ramp_rate,
             )
 
         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 {labware_id}"
+                f"Touch tip not allowed on labware {self._state_view.labware.get_display_name(labware_id)}"
             )
 
         if self._state_view.labware.is_tiprack(labware_id):

opentrons/protocol_engine/commands/unsafe/unsafe_place_labware.py

@@ -14,12 +14,11 @@ 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
@@ -100,22 +99,6 @@ 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
@@ -139,7 +122,7 @@ class UnsafePlaceLabwareImplementation(
         await ot3api.update_axis_position_estimations([Axis.X, Axis.Y])
 
         # Place the labware down
-        await self._start_movement(ot3api, definition, location, drop_offset)
+        await self._start_movement(ot3api, definition, location)
 
         return SuccessData(public=UnsafePlaceLabwareResult())
 
@@ -148,7 +131,6 @@ class UnsafePlaceLabwareImplementation(
         ot3api: OT3HardwareControlAPI,
         labware_definition: LabwareDefinition,
         location: OnDeckLabwareLocation,
-        drop_offset: Optional[Point],
     ) -> None:
         gripper_homed_position = await ot3api.gantry_position(
             mount=OT3Mount.GRIPPER,
@@ -156,13 +138,15 @@ class UnsafePlaceLabwareImplementation(
         )
 
         to_labware_center = self._state_view.geometry.get_labware_grip_point(
-            labware_definition=labware_definition, location=location
+            labware_definition=labware_definition,
+            location=location,
+            move_type=GripperMoveType.DROP_LABWARE,
+            user_additional_offset=None,
         )
 
         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/commands/wait_for_tasks.py

@@ -0,0 +1,98 @@
+"""WaitForTasks 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, ProtocolCommandFailedError
+from ..errors.exceptions import TaskFailedError
+
+if TYPE_CHECKING:
+    from ..execution import TaskHandler, RunControlHandler
+    from ..state.state import StateView
+
+
+WaitForTasksCommandType = Literal["waitForTasks"]
+
+
+class WaitForTasksParams(BaseModel):
+    """Payload required to annotate execution with a WaitForTasks."""
+
+    task_ids: list[str] = Field(
+        ...,
+        description="The list of task ids to wait for.",
+    )
+
+
+class WaitForTasksResult(BaseModel):
+    """Result data from the execution of a WaitForTasks command."""
+
+    task_ids: list[str] = Field(
+        ...,
+        description="The list of completed task ids.",
+    )
+
+
+class WaitForTasksImplementation(
+    AbstractCommandImpl[WaitForTasksParams, SuccessData[WaitForTasksResult]]
+):
+    """WaitForTasks command implementation."""
+
+    def __init__(
+        self,
+        task_handler: TaskHandler,
+        run_control: RunControlHandler,
+        state_view: StateView,
+        **kwargs: object,
+    ) -> None:
+        self._task_handler = task_handler
+        self._run_control = run_control
+        self._state_view = state_view
+
+    async def execute(
+        self, params: WaitForTasksParams
+    ) -> SuccessData[WaitForTasksResult]:
+        """Checks for existance of task id and then asynchronously waits for the valid, specified tasks to finish."""
+        # Raises the exception if we don't have a valid task id.
+        for task_id in params.task_ids:
+            _ = self._state_view.tasks.get(task_id)
+
+        await self._run_control.wait_for_tasks(params.task_ids)
+
+        failed_tasks = self._state_view.tasks.get_failed_tasks(params.task_ids)
+        if failed_tasks:
+            raise TaskFailedError(
+                message=f"{len(failed_tasks)} tasks failed.",
+                details={"failed_task_ids": failed_tasks},
+                wrapping=[
+                    ProtocolCommandFailedError(
+                        original_error=self._state_view.tasks.get_finished(
+                            task_id
+                        ).error
+                    )
+                    for task_id in failed_tasks
+                ],
+            )
+        return SuccessData(public=WaitForTasksResult(task_ids=params.task_ids))
+
+
+class WaitForTasks(
+    BaseCommand[WaitForTasksParams, WaitForTasksResult, ErrorOccurrence]
+):
+    """WaitForTasks command model."""
+
+    commandType: WaitForTasksCommandType = "waitForTasks"
+    params: WaitForTasksParams
+    result: Optional[WaitForTasksResult] = None
+
+    _ImplementationCls: Type[WaitForTasksImplementation] = WaitForTasksImplementation
+
+
+class WaitForTasksCreate(BaseCommandCreate[WaitForTasksParams]):
+    """WaitForTasks command request model."""
+
+    commandType: WaitForTasksCommandType = "waitForTasks"
+    params: WaitForTasksParams
+
+    _CommandCls: Type[WaitForTasks] = WaitForTasks

opentrons/protocol_engine/errors/__init__.py

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

opentrons/protocol_engine/errors/exceptions.py

@@ -413,6 +413,36 @@ 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."""
 
@@ -825,6 +855,19 @@ 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."""
 
@@ -1306,3 +1349,15 @@ 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

@@ -21,6 +21,7 @@ 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.
@@ -46,5 +47,6 @@ __all__ = [
     "DoorWatcher",
     "RailLightsHandler",
     "StatusBarHandler",
+    "TaskHandler",
     "FileProvider",
 ]

opentrons/protocol_engine/execution/command_executor.py

@@ -35,6 +35,7 @@ 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__)
@@ -85,6 +86,7 @@ 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:
@@ -106,6 +108,7 @@ 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.
@@ -131,6 +134,7 @@ 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()
@@ -214,3 +218,7 @@ 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

@@ -17,6 +17,7 @@ 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(
@@ -76,7 +77,9 @@ 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(
@@ -93,6 +96,7 @@ 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

@@ -31,6 +31,7 @@ from ..types import (
     OnLabwareLocation,
     LabwareLocation,
     OnDeckLabwareLocation,
+    GripperMoveType,
 )
 
 if TYPE_CHECKING:
@@ -141,10 +142,16 @@ 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
+            labware_definition=labware_definition,
+            location=current_location,
+            move_type=GripperMoveType.PICK_UP_LABWARE,
+            user_additional_offset=user_pick_up_offset,
         )
         to_labware_center = self._state_store.geometry.get_labware_grip_point(
-            labware_definition=labware_definition, location=new_location
+            labware_definition=labware_definition,
+            location=new_location,
+            move_type=GripperMoveType.DROP_LABWARE,
+            user_additional_offset=user_drop_offset,
         )
 
         if use_virtual_gripper:
@@ -193,20 +200,10 @@ 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

@@ -83,6 +83,7 @@ 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(
@@ -143,6 +144,7 @@ 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

@@ -51,6 +51,7 @@ 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."""
@@ -65,7 +66,10 @@ 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

@@ -31,3 +31,11 @@ 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
+            )
+        )

opentrons/protocol_engine/execution/task_handler.py

@@ -0,0 +1,157 @@
+"""Task handling."""
+
+from __future__ import annotations
+import logging
+from typing import Protocol, AsyncIterator
+from ..state.state import StateStore
+from ..resources import ModelUtils, ConcurrencyProvider
+from ..types import Task
+import asyncio
+import contextlib
+from ..actions import ActionDispatcher, FinishTaskAction, StartTaskAction
+from ..errors import ErrorOccurrence
+from opentrons_shared_data.errors.exceptions import EnumeratedError, PythonException
+
+log = logging.getLogger(__name__)
+
+
+class TaskFunction(Protocol):
+    """The function run inside a task protocol."""
+
+    async def __call__(self, task_handler: TaskHandler) -> None:
+        """The function called inside a task."""
+        ...
+
+
+class TaskHandler:
+    """Implementation logic for fast concurrency."""
+
+    _state_store: StateStore
+    _model_utils: ModelUtils
+    _concurrency_provider: ConcurrencyProvider
+
+    def __init__(
+        self,
+        state_store: StateStore,
+        action_dispatcher: ActionDispatcher,
+        model_utils: ModelUtils | None = None,
+        concurrency_provider: ConcurrencyProvider | None = None,
+    ) -> None:
+        """Initialize a TaskHandler instance."""
+        self._state_store = state_store
+        self._model_utils = model_utils or ModelUtils()
+        self._concurrency_provider = concurrency_provider or ConcurrencyProvider()
+        self._action_dispatcher = action_dispatcher
+
+    async def create_task(
+        self, task_function: TaskFunction, id: str | None = None
+    ) -> Task:
+        """Create a task and immediately schedules it."""
+        task_id = self._model_utils.ensure_id(id)
+        asyncio_task = asyncio.create_task(
+            task_function(task_handler=self), name=f"engine-task-{task_id}"
+        )
+
+        def _done_callback(task: asyncio.Task[None]) -> None:
+            try:
+                maybe_exception = task.exception()
+            except asyncio.CancelledError as e:
+                maybe_exception = e
+            if isinstance(maybe_exception, EnumeratedError):
+                occurence: ErrorOccurrence | None = ErrorOccurrence.from_failed(
+                    id=self._model_utils.generate_id(),
+                    createdAt=self._model_utils.get_timestamp(),
+                    error=maybe_exception,
+                )
+            elif isinstance(maybe_exception, BaseException):
+                occurence = ErrorOccurrence.from_failed(
+                    id=self._model_utils.generate_id(),
+                    createdAt=self._model_utils.get_timestamp(),
+                    error=PythonException(maybe_exception),
+                )
+            else:
+                occurence = None
+            try:
+                self._action_dispatcher.dispatch(
+                    FinishTaskAction(
+                        task_id=task_id,
+                        finished_at=self._model_utils.get_timestamp(),
+                        error=occurence,
+                    ),
+                )
+            except BaseException:
+                log.exception("Exception in task finish dispatch.")
+
+        asyncio_task.add_done_callback(_done_callback)
+        task = Task(
+            id=task_id,
+            createdAt=self._model_utils.get_timestamp(),
+            asyncioTask=asyncio_task,
+        )
+        self._action_dispatcher.dispatch(StartTaskAction(task))
+        return task
+
+    @staticmethod
+    def _empty_queue(
+        queue: "asyncio.Queue[asyncio.Task[None]]", this_task: asyncio.Task[None]
+    ) -> None:
+        """Empties the queue."""
+        try:
+            while True:
+                task = queue.get_nowait()
+                if task is this_task:
+                    break
+        except asyncio.QueueEmpty:
+            pass
+
+    @contextlib.asynccontextmanager
+    async def synchronize_cancel_latest(self, group_id: str) -> AsyncIterator[None]:
+        """Cancel current task."""
+        lock = self._concurrency_provider.lock_for_group(group_id)
+        if lock.locked():
+            raise asyncio.CancelledError()
+        async with lock:
+            yield
+
+    @contextlib.asynccontextmanager
+    async def synchronize_cancel_previous(self, group_id: str) -> AsyncIterator[None]:
+        """Cancel previous run."""
+        queue = self._concurrency_provider.queue_for_group(group_id)
+        while not queue.empty():
+            task = queue.get_nowait()
+            task.cancel()
+        this_task = asyncio.current_task()
+        assert this_task is not None
+        queue.put_nowait(this_task)
+        try:
+            yield
+        except asyncio.CancelledError:
+            raise
+        except BaseException:
+            self._empty_queue(queue, this_task)
+            raise
+        else:
+            self._empty_queue(queue, this_task)
+
+    @contextlib.asynccontextmanager
+    async def synchronize_sequential(self, group_id: str) -> AsyncIterator[None]:
+        """Run tasks one after the other."""
+        lock = self._concurrency_provider.lock_for_group(group_id)
+        async with lock:
+            yield
+
+    @contextlib.asynccontextmanager
+    async def synchronize_concurrent(self, group_id: str) -> AsyncIterator[None]:
+        """Run a list of tasks at the same time."""
+        yield
+
+    def cancel_all(self, message: str | None = None) -> None:
+        """Cancel all asyncio tasks immediately.
+
+        Do not call this more than once synchronously because
+        that could lead to tasks cancelling more than once.
+        It can be called if there are no current tasks. In that case
+        nothing will happen.
+        """
+        for task in self._state_store.tasks.get_all_current():
+            task.asyncioTask.cancel(msg=message)