opentrons 8.7.0a7__py3-none-any.whl → 8.8.0a7__py3-none-any.whl

opentrons/legacy_commands/module_commands.py

@@ -89,6 +89,24 @@ def thermocycler_set_block_temp(
     }
 
 
+def thermocycler_start_set_block_temp(
+    temperature: float,
+) -> command_types.ThermocyclerStartSetBlockTempCommand:
+    temp = round(float(temperature), utils.TC_GCODE_ROUNDING_PRECISION)
+    text = f"Starting to set Thermocycler well block temperature to {temp} °C"
+    # TODO: BC 2019-09-05 this time resolving logic is partially duplicated
+    # in the thermocycler api class definition, with this command logger
+    # implementation, there isn't a great way to avoid this, but it should
+    # be consolidated as soon as an alternative to the publisher is settled on.
+    return {
+        "name": command_types.THERMOCYCLER_START_SET_BLOCK_TEMP,
+        "payload": {
+            "temperature": temperature,
+            "text": text,
+        },
+    }
+
+
 def thermocycler_execute_profile(
     steps: List[ThermocyclerStep], repetitions: int
 ) -> command_types.ThermocyclerExecuteProfileCommand:
@@ -133,6 +151,17 @@ def thermocycler_set_lid_temperature(
     return {"name": command_types.THERMOCYCLER_SET_LID_TEMP, "payload": {"text": text}}
 
 
+def thermocycler_start_set_lid_temperature(
+    temperature: float,
+) -> command_types.ThermocyclerStartSetLidTempCommand:
+    temp = round(float(temperature), utils.TC_GCODE_ROUNDING_PRECISION)
+    text = f"Starting to set Thermocycler lid temperature to {temp} °C"
+    return {
+        "name": command_types.THERMOCYCLER_START_SET_LID_TEMP,
+        "payload": {"text": text},
+    }
+
+
 def thermocycler_deactivate_lid() -> command_types.ThermocyclerDeactivateLidCommand:
     text = "Deactivating Thermocycler lid heating"
     return {

opentrons/legacy_commands/protocol_commands.py

@@ -1,5 +1,5 @@
 from datetime import timedelta
-from typing import Optional
+from typing import Optional, Tuple
 from . import types as command_types
 from opentrons.protocol_api.tasks import Task
 
@@ -55,6 +55,38 @@ def move_labware(text: str) -> command_types.MoveLabwareCommand:
     }
 
 
+def capture_image(
+    resolution: Optional[Tuple[int, int]],
+    zoom: Optional[float],
+    contrast: Optional[float],
+    brightness: Optional[float],
+    saturation: Optional[float],
+) -> command_types.CaptureImageCommand:
+    text = "Capturing an image"
+    if resolution:
+        text += f" with resolution {resolution[0]}x{resolution[1]}"
+    if zoom:
+        text += f" zoom of {zoom}X"
+    if contrast:
+        text += f" contrast of {contrast}%"
+    if brightness:
+        text += f" brightness of {brightness}%"
+    if saturation:
+        text += f" saturation of {saturation}%"
+    text += "."
+    return {
+        "name": command_types.CAPTURE_IMAGE,
+        "payload": {
+            "text": text,
+            "resolution": resolution,
+            "zoom": zoom,
+            "contrast": contrast,
+            "brightness": brightness,
+            "saturation": saturation,
+        },
+    }
+
+
 def wait_for_tasks(tasks: list[Task]) -> command_types.WaitForTasksCommand:
     task_ids = [task.created_at.strftime("%Y-%m-%d %H:%M:%S") for task in tasks]
     msg = f"Waiting for tasks that started at: {task_ids}."

opentrons/legacy_commands/types.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from typing_extensions import Literal, Final, TypedDict
-from typing import Optional, List, Sequence, TYPE_CHECKING, Union
+from typing import Optional, List, Sequence, TYPE_CHECKING, Union, Tuple
 from opentrons.hardware_control.modules import ThermocyclerStep
 
 if TYPE_CHECKING:
@@ -25,6 +25,7 @@ PAUSE: Final = "command.PAUSE"
 RESUME: Final = "command.RESUME"
 COMMENT: Final = "command.COMMENT"
 MOVE_LABWARE: Final = "command.MOVE_LABWARE"
+CAPTURE_IMAGE: Final = "command.CAPTURE_IMAGE"
 
 # Pipette #
 
@@ -81,6 +82,7 @@ TEMPDECK_AWAIT_TEMP: Final = "command.TEMPDECK_AWAIT_TEMP"
 THERMOCYCLER_OPEN: Final = "command.THERMOCYCLER_OPEN"
 THERMOCYCLER_CLOSE: Final = "command.THERMOCYCLER_CLOSE"
 THERMOCYCLER_SET_BLOCK_TEMP: Final = "command.THERMOCYCLER_SET_BLOCK_TEMP"
+THERMOCYCLER_START_SET_BLOCK_TEMP: Final = "command.THERMOCYCLER_START_SET_BLOCK_TEMP"
 THERMOCYCLER_EXECUTE_PROFILE: Final = "command.THERMOCYCLER_EXECUTE_PROFILE"
 THERMOCYCLER_START_EXECUTE_PROFILE: Final = "command.THERMOCYCLER_START_EXECUTE_PROFILE"
 THERMOCYCLER_DEACTIVATE: Final = "command.THERMOCYCLER_DEACTIVATE"
@@ -88,6 +90,7 @@ THERMOCYCLER_WAIT_FOR_HOLD: Final = "command.THERMOCYCLER_WAIT_FOR_HOLD"
 THERMOCYCLER_WAIT_FOR_TEMP: Final = "command.THERMOCYCLER_WAIT_FOR_TEMP"
 THERMOCYCLER_WAIT_FOR_LID_TEMP: Final = "command.THERMOCYCLER_WAIT_FOR_LID_TEMP"
 THERMOCYCLER_SET_LID_TEMP: Final = "command.THERMOCYCLER_SET_LID_TEMP"
+THERMOCYCLER_START_SET_LID_TEMP: Final = "command.THERMOCYCLER_START_SET_LID_TEMP"
 THERMOCYCLER_DEACTIVATE_LID: Final = "command.THERMOCYCLER_DEACTIVATE_LID"
 THERMOCYCLER_DEACTIVATE_BLOCK: Final = "command.THERMOCYCLER_DEACTIVATE_BLOCK"
 
@@ -314,6 +317,15 @@ class ThermocyclerSetBlockTempCommand(TypedDict):
     payload: ThermocyclerSetBlockTempCommandPayload
 
 
+class ThermocyclerStartSetBlockTempCommandPayload(TextOnlyPayload):
+    temperature: float
+
+
+class ThermocyclerStartSetBlockTempCommand(TypedDict):
+    name: Literal["command.THERMOCYCLER_START_SET_BLOCK_TEMP"]
+    payload: ThermocyclerStartSetBlockTempCommandPayload
+
+
 class ThermocyclerExecuteProfileCommandPayload(TextOnlyPayload):
     steps: List[ThermocyclerStep]
 
@@ -359,6 +371,15 @@ class ThermocyclerSetLidTempCommand(TypedDict):
     payload: ThermocyclerSetLidTempCommandPayload
 
 
+class ThermocyclerStartSetLidTempCommandPayload(TextOnlyPayload):
+    pass
+
+
+class ThermocyclerStartSetLidTempCommand(TypedDict):
+    name: Literal["command.THERMOCYCLER_START_SET_LID_TEMP"]
+    payload: ThermocyclerStartSetLidTempCommandPayload
+
+
 class ThermocyclerDeactivateLidCommandPayload(TextOnlyPayload):
     pass
 
@@ -445,6 +466,7 @@ class AspirateDispenseCommandPayload(TextOnlyPayload, SingleInstrumentPayload):
     location: Location
     volume: float
     rate: float
+    end_location: Optional[Location]
 
 
 class AspirateCommand(TypedDict):
@@ -520,6 +542,21 @@ class MixCommand(TypedDict):
     payload: MixCommandPayload
 
 
+class DynamicMixCommandPayload(TextOnlyPayload, SingleInstrumentPayload):
+    aspirate_start_location: Location
+    dispense_start_location: Location
+    aspirate_end_location: Union[None, Location]
+    dispense_end_location: Union[None, Location]
+    volume: float
+    repetitions: int
+    movement_delay: float
+
+
+class DynamicMixCommand(TypedDict):
+    name: Literal["command.MIX"]
+    payload: DynamicMixCommandPayload
+
+
 class BlowOutCommandPayload(TextOnlyPayload, SingleInstrumentPayload):
     location: Optional[Location]
 
@@ -615,6 +652,14 @@ class MoveLabwareCommandPayload(TextOnlyPayload):
     pass
 
 
+class CaptureImageCommandPayload(TextOnlyPayload):
+    resolution: Optional[Tuple[int, int]]
+    zoom: Optional[float]
+    contrast: Optional[float]
+    brightness: Optional[float]
+    saturation: Optional[float]
+
+
 class LiquidClassCommandPayload(TextOnlyPayload, SingleInstrumentPayload):
     liquid_class: LiquidClass
     volume: float
@@ -670,6 +715,11 @@ class MoveLabwareCommand(TypedDict):
     payload: MoveLabwareCommandPayload
 
 
+class CaptureImageCommand(TypedDict):
+    name: Literal["command.CAPTURE_IMAGE"]
+    payload: CaptureImageCommandPayload
+
+
 class SealCommand(TypedDict):
     name: Literal["command.SEAL"]
     payload: SealCommandPayload
@@ -769,6 +819,7 @@ Command = Union[
     BlowOutCommand,
     BlowOutInDisposalLocationCommand,
     MixCommand,
+    DynamicMixCommand,
     TransferCommand,
     DistributeCommand,
     ConsolidateCommand,
@@ -790,11 +841,13 @@ Command = Union[
     ThermocyclerDeactivateBlockCommand,
     ThermocyclerDeactivateLidCommand,
     ThermocyclerSetLidTempCommand,
+    ThermocyclerStartSetLidTempCommand,
     ThermocyclerWaitForTempCommand,
     ThermocyclerWaitForHoldCommand,
     ThermocyclerExecuteProfileCommand,
     ThermocyclerStartExecuteProfileCommand,
     ThermocyclerSetBlockTempCommand,
+    ThermocyclerStartSetBlockTempCommand,
     ThermocyclerOpenCommand,
     TempdeckDeactivateCommand,
     TempdeckAwaitTempCommand,
@@ -817,6 +870,7 @@ Command = Union[
     PressurizeCommand,
     ConfigureForVolumeCommand,
     ConfigureNozzleLayoutCommand,
+    CaptureImageCommand,
     # Robot commands
     RobotMoveToCommand,
     RobotMoveAxisToCommand,
@@ -853,6 +907,7 @@ CommandPayload = Union[
     ThermocyclerWaitForHoldCommandPayload,
     ThermocyclerWaitForTempCommandPayload,
     ThermocyclerSetLidTempCommandPayload,
+    ThermocyclerStartSetLidTempCommandPayload,
     ThermocyclerDeactivateLidCommandPayload,
     ThermocyclerDeactivateBlockCommandPayload,
     ThermocyclerDeactivateCommandPayload,
@@ -867,6 +922,7 @@ CommandPayload = Union[
     BlowOutCommandPayload,
     BlowOutInDisposalLocationCommandPayload,
     MixCommandPayload,
+    DynamicMixCommandPayload,
     TransferCommandPayload,
     DistributeCommandPayload,
     ConsolidateCommandPayload,
@@ -876,6 +932,7 @@ CommandPayload = Union[
     ThermocyclerExecuteProfileCommandPayload,
     ThermocyclerStartExecuteProfileCommandPayload,
     ThermocyclerSetBlockTempCommandPayload,
+    ThermocyclerStartSetBlockTempCommandPayload,
     TempdeckAwaitTempCommandPayload,
     TempdeckSetTempCommandPayload,
     PauseCommandPayload,
@@ -889,6 +946,7 @@ CommandPayload = Union[
     PressurizeCommandPayload,
     ConfigureForVolumePayload,
     ConfigureNozzleLayoutPayload,
+    CaptureImageCommandPayload,
     # Robot payloads
     RobotMoveToCommandPayload,
     RobotMoveAxisRelativeCommandPayload,
@@ -959,6 +1017,10 @@ class MixMessage(CommandMessageFields, MixCommand):
     pass
 
 
+class DynamicMixMessage(CommandMessageFields, DynamicMixCommand):
+    pass
+
+
 class TransferMessage(CommandMessageFields, TransferCommand):
     pass
 
@@ -1071,6 +1133,18 @@ class ThermocyclerSetLidTempMessage(
     pass
 
 
+class ThermocyclerStartSetLidTempMessage(
+    CommandMessageFields, ThermocyclerStartSetLidTempCommand
+):
+    pass
+
+
+class ThermocyclerStartSetBlockTempMessage(
+    CommandMessageFields, ThermocyclerStartSetBlockTempCommand
+):
+    pass
+
+
 class ThermocyclerWaitForTempMessage(
     CommandMessageFields, ThermocyclerWaitForTempCommand
 ):

opentrons/protocol_api/_transfer_liquid_validation.py

@@ -24,9 +24,10 @@ class TransferInfo:
     tip_policy: TransferTipPolicyV2
     tip_racks: List[Labware]
     trash_location: Union[Location, TrashBin, WasteChute]
+    tips: Optional[List[Well]]
 
 
-def verify_and_normalize_transfer_args(
+def verify_and_normalize_transfer_args(  # noqa: C901
     source: Union[Well, Sequence[Well], Sequence[Sequence[Well]]],
     dest: Union[Well, Sequence[Well], Sequence[Sequence[Well]], TrashBin, WasteChute],
     tip_policy: TransferTipPolicyV2Type,
@@ -36,6 +37,7 @@ def verify_and_normalize_transfer_args(
     group_wells_for_multi_channel: bool,
     current_volume: float,
     trash_location: Union[Location, Well, Labware, TrashBin, WasteChute],
+    tips: Optional[Union[Sequence[Well], Sequence[Sequence[Well]]]],
 ) -> TransferInfo:
     flat_sources_list = validation.ensure_valid_flat_wells_list_for_transfer_v2(source)
     if not isinstance(dest, (TrashBin, WasteChute)):
@@ -57,8 +59,20 @@ def verify_and_normalize_transfer_args(
             reject_adapter=True,
         )
 
+    valid_tips: Optional[List[Well]] = None
+    if tips:
+        flat_tips_list = validation.ensure_valid_flat_wells_list_for_transfer_v2(tips)
+        if group_wells_for_multi_channel and nozzle_map.tip_count > 1:
+            valid_tips = tx_liquid_utils.group_wells_for_multi_channel_transfer(
+                flat_tips_list, nozzle_map, "tip"
+            )
+        else:
+            valid_tips = flat_tips_list
+
     valid_new_tip = validation.ensure_new_tip_policy(tip_policy)
-    if valid_new_tip == TransferTipPolicyV2.NEVER:
+    if valid_tips is not None:
+        valid_tip_racks = [tip.parent for tip in valid_tips]
+    elif valid_new_tip == TransferTipPolicyV2.NEVER:
         if last_tip_well is None:
             raise RuntimeError(
                 "Pipette has no tip attached to perform transfer."
@@ -92,6 +106,7 @@ def verify_and_normalize_transfer_args(
         tip_policy=valid_new_tip,
         tip_racks=valid_tip_racks,
         trash_location=valid_trash_location,
+        tips=valid_tips,
     )
 
 

opentrons/protocol_api/_types.py

@@ -11,9 +11,11 @@ class OffDeckType(enum.Enum):
     """
 
     OFF_DECK = "off-deck"
+    WASTE_CHUTE = "waste-chute"
 
 
 OFF_DECK: Final = OffDeckType.OFF_DECK
+WASTE_CHUTE: Final = OffDeckType.WASTE_CHUTE
 
 # Set __doc__ manually as a workaround. When this docstring is written the normal way, right after
 # the constant definition, Sphinx has trouble picking it up.

opentrons/protocol_api/core/engine/_default_labware_versions.py

@@ -140,6 +140,7 @@ DEFAULT_LABWARE_VERSIONS: DefaultLabwareVersions = {
         "opentrons_24_tuberack_nest_0.5ml_screwcap": 4,
         "opentrons_6_tuberack_nest_50ml_conical": 3,
         "opentrons_96_aluminumblock_generic_pcr_strip_200ul": 4,
+        "opentrons_tough_universal_lid": 2,
         "usascientific_12_reservoir_22ml": 4,
         "usascientific_96_wellplate_2.4ml_deep": 4,
     },

opentrons/protocol_api/core/engine/deck_conflict.py

@@ -26,6 +26,7 @@ from opentrons.protocol_engine import (
     OnLabwareLocation,
     AddressableAreaLocation,
     InStackerHopperLocation,
+    WASTE_CHUTE_LOCATION,
     OFF_DECK_LOCATION,
     SYSTEM_LOCATION,
 )
@@ -241,7 +242,6 @@ def _map_labware(
     Tuple[Union[DeckSlotName, StagingSlotName], wrapped_deck_conflict.DeckItem]
 ]:
     location_from_engine = engine_state.labware.get_location(labware_id=labware_id)
-
     if isinstance(location_from_engine, AddressableAreaLocation):
         # This will be guaranteed to be either deck slot name or staging slot name
         slot: Union[DeckSlotName, StagingSlotName]
@@ -299,10 +299,12 @@ def _map_labware(
         location_from_engine == OFF_DECK_LOCATION
         or location_from_engine == SYSTEM_LOCATION
         or isinstance(location_from_engine, InStackerHopperLocation)
+        or location_from_engine == WASTE_CHUTE_LOCATION
     ):
         # This labware is off-deck. Exclude it from conflict checking.
         # todo(mm, 2023-02-23): Move this logic into wrapped_deck_conflict.
         return None
+    return None
 
 
 def _map_module(