opentrons 8.0.0a6__tar.gz → 8.0.0a8__tar.gz

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.0.0a6
+Version: 8.0.0a8
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Author: Opentrons
 Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 License-File: ../LICENSE
-Requires-Dist: opentrons-shared-data==8.0.0a6
+Requires-Dist: opentrons-shared-data==8.0.0a8
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -33,9 +33,9 @@ Requires-Dist: click<9,>=8.0.0
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.0.0a6; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.0.0a8; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.0.0a6; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.0.0a8; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons/hardware_control/ot3api.py

@@ -2683,6 +2683,15 @@ class OT3API(
         self._pipette_handler.ready_for_tip_action(
             instrument, HardwareAction.LIQUID_PROBE, checked_mount
         )
+        # default to using all available sensors
+        if probe:
+            checked_probe = probe
+        else:
+            checked_probe = (
+                InstrumentProbeType.BOTH
+                if instrument.channels > 1
+                else InstrumentProbeType.PRIMARY
+            )
 
         if not probe_settings:
             probe_settings = deepcopy(self.config.liquid_sense)
@@ -2756,7 +2765,7 @@ class OT3API(
                 height = await self._liquid_probe_pass(
                     checked_mount,
                     probe_settings,
-                    probe if probe else InstrumentProbeType.PRIMARY,
+                    checked_probe,
                     p_pass_travel + p_impulse_mm,
                 )
                 # if we made it here without an error we found the liquid

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons/protocol_api/core/engine/deck_conflict.py

@@ -16,6 +16,7 @@ from typing import (
 from opentrons_shared_data.errors.exceptions import MotionPlanningFailureError
 from opentrons_shared_data.module import FLEX_TC_LID_COLLISION_ZONE
 
+from opentrons.hardware_control import CriticalPoint
 from opentrons.hardware_control.modules.types import ModuleType
 from opentrons.motion_planning import deck_conflict as wrapped_deck_conflict
 from opentrons.motion_planning import adjacent_slots_getters
@@ -228,9 +229,13 @@ def check_safe_for_pipette_movement(
     )
     primary_nozzle = engine_state.pipettes.get_primary_nozzle(pipette_id)
 
+    destination_cp = _get_critical_point_to_use(engine_state, labware_id)
+
     pipette_bounds_at_well_location = (
         engine_state.pipettes.get_pipette_bounds_at_specified_move_to_position(
-            pipette_id=pipette_id, destination_position=well_location_point
+            pipette_id=pipette_id,
+            destination_position=well_location_point,
+            critical_point=destination_cp,
         )
     )
     if not _is_within_pipette_extents(
@@ -284,6 +289,21 @@ def check_safe_for_pipette_movement(
             )
 
 
+def _get_critical_point_to_use(
+    engine_state: StateView, labware_id: str
+) -> Optional[CriticalPoint]:
+    """Return the critical point to use when accessing the given labware."""
+    # TODO (spp, 2024-09-17): looks like Y_CENTER of column is the same as its XY_CENTER.
+    #   I'm using this if-else ladder to be consistent with what we do in
+    #   `MotionPlanning.get_movement_waypoints_to_well()`.
+    #   We should probably use only XY_CENTER in both places.
+    if engine_state.labware.get_should_center_column_on_target_well(labware_id):
+        return CriticalPoint.Y_CENTER
+    elif engine_state.labware.get_should_center_pipette_on_target_well(labware_id):
+        return CriticalPoint.XY_CENTER
+    return None
+
+
 def _slot_has_potential_colliding_object(
     engine_state: StateView,
     pipette_bounds: Tuple[Point, Point, Point, Point],

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons/protocol_api/instrument_context.py

@@ -266,6 +266,7 @@ class InstrumentContext(publisher.CommandPublisher):
             and well is not None
             and self.liquid_presence_detection
             and self._96_tip_config_valid()
+            and self._core.get_current_volume() == 0
         ):
             self.require_liquid_presence(well=well)
 

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons/protocol_engine/commands/liquid_probe.py

@@ -2,7 +2,11 @@
 
 from __future__ import annotations
 from typing import TYPE_CHECKING, Optional, Type, Union
-from opentrons.protocol_engine.errors.exceptions import MustHomeError, TipNotEmptyError
+from opentrons.protocol_engine.errors.exceptions import (
+    MustHomeError,
+    PipetteNotReadyToAspirateError,
+    TipNotEmptyError,
+)
 from opentrons.types import MountType
 from opentrons_shared_data.errors.exceptions import (
     PipetteLiquidNotFoundError,
@@ -32,6 +36,7 @@ from ..errors.error_occurrence import ErrorOccurrence
 if TYPE_CHECKING:
     from ..execution import MovementHandler, PipettingHandler
     from ..resources import ModelUtils
+    from ..state import StateView
 
 
 LiquidProbeCommandType = Literal["liquidProbe"]
@@ -92,11 +97,13 @@ class LiquidProbeImplementation(
 
     def __init__(
         self,
+        state_view: StateView,
         movement: MovementHandler,
         pipetting: PipettingHandler,
         model_utils: ModelUtils,
         **kwargs: object,
     ) -> None:
+        self._state_view = state_view
         self._movement = movement
         self._pipetting = pipetting
         self._model_utils = model_utils
@@ -112,6 +119,8 @@ class LiquidProbeImplementation(
                 the pipette.
             TipNotEmptyError: as an undefined error, if the tip starts with liquid
                 in it.
+            PipetteNotReadyToAspirateError: as an undefined error, if the plunger is not
+                in a safe position to do the liquid probe.
             MustHomeError: as an undefined error, if the plunger is not in a valid
                 position.
         """
@@ -119,13 +128,21 @@ class LiquidProbeImplementation(
         labware_id = params.labwareId
         well_name = params.wellName
 
-        # _validate_tip_attached in pipetting.py is a private method so we're using
-        # get_is_ready_to_aspirate as an indirect way to throw a TipNotAttachedError if appropriate
-        self._pipetting.get_is_ready_to_aspirate(pipette_id=pipette_id)
-
-        if self._pipetting.get_is_empty(pipette_id=pipette_id) is False:
+        # May raise TipNotAttachedError.
+        aspirated_volume = self._state_view.pipettes.get_aspirated_volume(pipette_id)
+
+        if aspirated_volume is None:
+            # Theoretically, we could avoid raising an error by automatically preparing
+            # to aspirate above the well like AspirateImplementation does. However, the
+            # only way for this to happen is if someone tries to do a liquid probe with
+            # a tip that's previously held liquid, which they should avoid anyway.
+            raise PipetteNotReadyToAspirateError(
+                "The pipette cannot probe liquid because of a previous blow out."
+                " The plunger must be reset while the tip is somewhere away from liquid."
+            )
+        elif aspirated_volume != 0:
             raise TipNotEmptyError(
-                message="This operation requires a tip with no liquid in it."
+                message="The pipette cannot probe for liquid when the tip has liquid in it."
             )
 
         if await self._movement.check_for_valid_position(mount=MountType.LEFT) is False:
@@ -182,11 +199,13 @@ class TryLiquidProbeImplementation(
 
     def __init__(
         self,
+        state_view: StateView,
         movement: MovementHandler,
         pipetting: PipettingHandler,
         model_utils: ModelUtils,
         **kwargs: object,
     ) -> None:
+        self._state_view = state_view
         self._movement = movement
         self._pipetting = pipetting
         self._model_utils = model_utils
@@ -203,6 +222,7 @@ class TryLiquidProbeImplementation(
         # Otherwise, we return the result or propagate the exception unchanged.
 
         original_impl = LiquidProbeImplementation(
+            state_view=self._state_view,
             movement=self._movement,
             pipetting=self._pipetting,
             model_utils=self._model_utils,

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons/protocol_engine/execution/pipetting.py

@@ -29,9 +29,6 @@ _VOLUME_ROUNDING_ERROR_TOLERANCE = 1e-9
 class PipettingHandler(TypingProtocol):
     """Liquid handling commands."""
 
-    def get_is_empty(self, pipette_id: str) -> bool:
-        """Get whether a pipette has an aspirated volume equal to 0."""
-
     def get_is_ready_to_aspirate(self, pipette_id: str) -> bool:
         """Get whether a pipette is ready to aspirate."""
 
@@ -81,10 +78,6 @@ class HardwarePipettingHandler(PipettingHandler):
         self._state_view = state_view
         self._hardware_api = hardware_api
 
-    def get_is_empty(self, pipette_id: str) -> bool:
-        """Get whether a pipette has an aspirated volume equal to 0."""
-        return self._state_view.pipettes.get_aspirated_volume(pipette_id) == 0
-
     def get_is_ready_to_aspirate(self, pipette_id: str) -> bool:
         """Get whether a pipette is ready to aspirate."""
         hw_pipette = self._state_view.pipettes.get_hardware_pipette(
@@ -236,10 +229,6 @@ class VirtualPipettingHandler(PipettingHandler):
         """Initialize a PipettingHandler instance."""
         self._state_view = state_view
 
-    def get_is_empty(self, pipette_id: str) -> bool:
-        """Get whether a pipette has an aspirated volume equal to 0."""
-        return self._state_view.pipettes.get_aspirated_volume(pipette_id) == 0
-
     def get_is_ready_to_aspirate(self, pipette_id: str) -> bool:
         """Get whether a pipette is ready to aspirate."""
         return self._state_view.pipettes.get_aspirated_volume(pipette_id) is not None

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons/protocol_engine/execution/tip_handler.py

@@ -20,6 +20,8 @@ from ..errors import (
     ProtocolEngineError,
 )
 
+from opentrons.hardware_control.nozzle_manager import NozzleConfigurationType
+
 
 PRIMARY_NOZZLE_TO_ENDING_NOZZLE_MAP = {
     "A1": {"COLUMN": "H1", "ROW": "A12"},
@@ -300,6 +302,30 @@ class HardwareTipHandler(TipHandler):
         This function will raise an exception if the specified tip presence status
         isn't matched.
         """
+        nozzle_configuration = (
+            self._state_view.pipettes.state.nozzle_configuration_by_id[pipette_id]
+        )
+
+        # Configuration metrics by which tip presence checking is ignored
+        unsupported_pipette_types = [8, 96]
+        unsupported_layout_types = [
+            NozzleConfigurationType.SINGLE,
+            NozzleConfigurationType.COLUMN,
+        ]
+        # NOTE: (09-20-2024) Current on multi-channel pipettes, utilizing less than 4 nozzles risks false positives on the tip presence sensor
+        supported_partial_nozzle_minimum = 4
+
+        if (
+            nozzle_configuration is not None
+            and self._state_view.pipettes.get_channels(pipette_id)
+            in unsupported_pipette_types
+            and nozzle_configuration.configuration in unsupported_layout_types
+            and len(nozzle_configuration.map_store) < supported_partial_nozzle_minimum
+        ):
+            # Tip presence sensing is not supported for single tip pick up on the 96ch Flex Pipette, nor with single and some partial layous of the 8ch Flex Pipette.
+            # This is due in part to a press distance tolerance which creates a risk case for false positives. In the case of single tip, the mechanical tolerance
+            # for presses with 100% success is below the minimum average achieved press distance for a given multi channel pipette in that configuration.
+            return
         try:
             ot3api = ensure_ot3_hardware(hardware_api=self._hardware_api)
             hw_mount = self._state_view.pipettes.get_mount(pipette_id).to_hw_mount()

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons/protocol_engine/state/pipettes.py

@@ -7,6 +7,7 @@ from typing_extensions import assert_type
 from opentrons_shared_data.pipette import pipette_definition
 from opentrons.config.defaults_ot2 import Z_RETRACT_DISTANCE
 from opentrons.hardware_control.dev_types import PipetteDict
+from opentrons.hardware_control import CriticalPoint
 from opentrons.hardware_control.nozzle_manager import (
     NozzleConfigurationType,
     NozzleMap,
@@ -610,7 +611,7 @@ class PipetteView(HasState[PipetteState]):
 
         Returns:
             The volume the pipette has aspirated.
-            None, after blow-out and the plunger is in an unsafe position or drop-tip and there is no tip attached.
+            None, after blow-out and the plunger is in an unsafe position.
 
         Raises:
             PipetteNotLoadedError: pipette ID does not exist.
@@ -795,17 +796,27 @@ class PipetteView(HasState[PipetteState]):
         nozzle_map = self._state.nozzle_configuration_by_id.get(pipette_id)
         return nozzle_map.starting_nozzle if nozzle_map else None
 
-    def get_primary_nozzle_offset(self, pipette_id: str) -> Point:
-        """Get the pipette's current primary nozzle's offset."""
+    def _get_critical_point_offset_without_tip(
+        self, pipette_id: str, critical_point: Optional[CriticalPoint]
+    ) -> Point:
+        """Get the offset of the specified critical point from pipette's mount position."""
         nozzle_map = self._state.nozzle_configuration_by_id.get(pipette_id)
-        if nozzle_map:
-            primary_nozzle_offset = nozzle_map.starting_nozzle_offset
-        else:
-            # When not in partial configuration, back-left nozzle is the primary
-            primary_nozzle_offset = self.get_config(
-                pipette_id
-            ).bounding_nozzle_offsets.back_left_offset
-        return primary_nozzle_offset
+        # Nozzle map is unavailable only when there's no pipette loaded
+        # so this is merely for satisfying the type checker
+        assert (
+            nozzle_map is not None
+        ), "Error getting critical point offset. Nozzle map not found."
+        match critical_point:
+            case CriticalPoint.INSTRUMENT_XY_CENTER:
+                return nozzle_map.instrument_xy_center_offset
+            case CriticalPoint.XY_CENTER:
+                return nozzle_map.xy_center_offset
+            case CriticalPoint.Y_CENTER:
+                return nozzle_map.y_center_offset
+            case CriticalPoint.FRONT_NOZZLE:
+                return nozzle_map.front_nozzle_offset
+            case _:
+                return nozzle_map.starting_nozzle_offset
 
     def get_pipette_bounding_nozzle_offsets(
         self, pipette_id: str
@@ -817,32 +828,46 @@ class PipetteView(HasState[PipetteState]):
         """Get the bounding box of the pipette."""
         return self.get_config(pipette_id).pipette_bounding_box_offsets
 
+    # TODO (spp, 2024-09-17): in order to find the position of pipette at destination,
+    #  this method repeats the same steps that waypoints builder does while finding
+    #  waypoints to move to. We should consolidate these steps into a shared entity
+    #  so that the deck conflict checker and movement plan builder always remain in sync.
     def get_pipette_bounds_at_specified_move_to_position(
         self,
         pipette_id: str,
         destination_position: Point,
+        critical_point: Optional[CriticalPoint],
     ) -> Tuple[Point, Point, Point, Point]:
-        """Get the pipette's bounding offsets when primary nozzle is at the given position."""
-        primary_nozzle_offset = self.get_primary_nozzle_offset(pipette_id)
+        """Get the pipette's bounding box position when critical point is at the destination position.
+
+        Returns a tuple of the pipette's bounding box position in deck coordinates as-
+            (back_left_bound, front_right_bound, back_right_bound, front_left_bound)
+        Bounding box of the pipette includes the pipette's outer casing as well as nozzles.
+        """
         tip = self.get_attached_tip(pipette_id)
-        # TODO update this for pipette robot stackup
-        # Primary nozzle position at destination, in deck coordinates
-        primary_nozzle_position = destination_position + Point(
+
+        # *Offset* of pipette's critical point w.r.t pipette mount
+        critical_point_offset = self._get_critical_point_offset_without_tip(
+            pipette_id, critical_point
+        )
+
+        # Position of the above critical point at destination, in deck coordinates
+        critical_point_position = destination_position + Point(
             x=0, y=0, z=tip.length if tip else 0
         )
 
-        # Get the pipette bounding box based on total nozzles
+        # Get the pipette bounding box coordinates
         pipette_bounds_offsets = self.get_config(
             pipette_id
         ).pipette_bounding_box_offsets
         pip_back_left_bound = (
-            primary_nozzle_position
-            - primary_nozzle_offset
+            critical_point_position
+            - critical_point_offset
             + pipette_bounds_offsets.back_left_corner
         )
         pip_front_right_bound = (
-            primary_nozzle_position
-            - primary_nozzle_offset
+            critical_point_position
+            - critical_point_offset
             + pipette_bounds_offsets.front_right_corner
         )
         pip_back_right_bound = Point(

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.0.0a6
+Version: 8.0.0a8
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Author: Opentrons
 Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 License-File: ../LICENSE
-Requires-Dist: opentrons-shared-data==8.0.0a6
+Requires-Dist: opentrons-shared-data==8.0.0a8
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -33,9 +33,9 @@ Requires-Dist: click<9,>=8.0.0
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.0.0a6; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.0.0a8; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.0.0a6; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.0.0a8; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.0.0a6 → opentrons-8.0.0a8}/src/opentrons.egg-info/requires.txt

@@ -1,4 +1,4 @@
-opentrons-shared-data==8.0.0a6
+opentrons-shared-data==8.0.0a8
 aionotify==0.3.1
 anyio<4.0.0,>=3.6.1
 jsonschema<4.18.0,>=3.0.1
@@ -13,7 +13,7 @@ packaging>=21.0
 importlib-metadata>=1.0
 
 [flex-hardware]
-opentrons-hardware[FLEX]==8.0.0a6
+opentrons-hardware[FLEX]==8.0.0a8
 
 [ot2-hardware]
-opentrons-hardware==8.0.0a6
+opentrons-hardware==8.0.0a8