opentrons 8.4.0a6__tar.gz → 8.4.0a7__tar.gz

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.4.0a6
+Version: 8.4.0a7
 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==8.4.0a6
+Requires-Dist: opentrons-shared-data==8.4.0a7
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -35,9 +35,9 @@ Requires-Dist: pyusb==1.2.1
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.4.0a6; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.4.0a7; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.4.0a6; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.4.0a7; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_api/core/engine/well.py

@@ -3,7 +3,7 @@ from typing import Optional, Union
 
 from opentrons_shared_data.labware.constants import WELL_NAME_PATTERN
 
-from opentrons.types import Point
+from opentrons.types import Point, Mount, MountType
 
 from opentrons.protocol_engine import WellLocation, WellOrigin, WellOffset
 from opentrons.protocol_engine import commands as cmd
@@ -13,6 +13,7 @@ from opentrons.protocol_engine.types.liquid_level_detection import (
     SimulatedProbeResult,
     LiquidTrackingType,
 )
+from opentrons.protocol_engine.errors import PipetteNotAttachedError
 
 from . import point_calculations
 from . import stringify
@@ -181,15 +182,25 @@ class WellCore(AbstractWellCore):
 
     def estimate_liquid_height_after_pipetting(
         self,
+        mount: Mount | str,
         operation_volume: float,
     ) -> LiquidTrackingType:
         """Return an estimate of liquid height after pipetting without raising an error."""
         labware_id = self.labware_id
         well_name = self._name
+        if isinstance(mount, Mount):
+            mount_type = MountType.from_hw_mount(mount)
+        else:
+            mount_type = MountType(mount)
+        pipette_from_mount = self._engine_client.state.pipettes.get_by_mount(mount_type)
+        if pipette_from_mount is None:
+            raise PipetteNotAttachedError(f"No pipette present on mount {mount}")
+        pipette_id = pipette_from_mount.id
         starting_liquid_height = self.current_liquid_height()
         projected_final_height = self._engine_client.state.geometry.get_well_height_after_liquid_handling_no_error(
             labware_id=labware_id,
             well_name=well_name,
+            pipette_id=pipette_id,
             initial_height=starting_liquid_height,
             volume=operation_volume,
         )

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_api/core/legacy/legacy_well_core.py

@@ -5,7 +5,7 @@ from opentrons_shared_data.labware.constants import WELL_NAME_PATTERN
 
 from opentrons.protocols.api_support.util import APIVersionError
 
-from opentrons.types import Point
+from opentrons.types import Point, Mount
 
 from opentrons.protocol_engine.types.liquid_level_detection import (
     SimulatedProbeResult,
@@ -129,6 +129,7 @@ class LegacyWellCore(AbstractWellCore):
 
     def estimate_liquid_height_after_pipetting(
         self,
+        mount: Mount | str,
         operation_volume: float,
     ) -> LiquidTrackingType:
         """Estimate what the liquid height will be after pipetting, without raising an error."""

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_api/core/well.py

@@ -3,7 +3,7 @@
 from abc import ABC, abstractmethod
 from typing import TypeVar, Optional, Union
 
-from opentrons.types import Point
+from opentrons.types import Point, Mount
 from opentrons.protocol_engine.types import LiquidTrackingType
 
 from .._liquid import Liquid
@@ -91,6 +91,7 @@ class AbstractWellCore(ABC):
     @abstractmethod
     def estimate_liquid_height_after_pipetting(
         self,
+        mount: Mount | str,
         operation_volume: float,
     ) -> LiquidTrackingType:
         """Estimate what the liquid height will be after pipetting, without raising an error."""

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_api/instrument_context.py

@@ -1528,6 +1528,9 @@ class InstrumentContext(publisher.CommandPublisher):
     ) -> InstrumentContext:
         """Move a particular type of liquid from one well or group of wells to another.
 
+        ..
+            This is intended for Opentrons internal use only and is not a guaranteed API.
+
         :param liquid_class: The type of liquid to move. You must specify the liquid class,
             even if you have used :py:meth:`.Labware.load_liquid` to indicate what liquid the
             source contains.
@@ -1553,7 +1556,7 @@ class InstrumentContext(publisher.CommandPublisher):
         :param return_tip: Whether to drop used tips in their original locations
             in the tip rack, instead of the trash.
 
-            :meta private:
+        :meta private:
         """
         if volume == 0.0:
             _log.info(
@@ -1635,6 +1638,9 @@ class InstrumentContext(publisher.CommandPublisher):
         """
         Distribute a particular type of liquid from one well to a group of wells.
 
+        ..
+            This is intended for Opentrons internal use only and is not a guaranteed API.
+
         :param liquid_class: The type of liquid to move. You must specify the liquid class,
             even if you have used :py:meth:`.Labware.load_liquid` to indicate what liquid the
             source contains.
@@ -1657,7 +1663,7 @@ class InstrumentContext(publisher.CommandPublisher):
         :param return_tip: Whether to drop used tips in their original locations
             in the tip rack, instead of the trash.
 
-            :meta private:
+        :meta private:
         """
         if volume == 0.0:
             _log.info(
@@ -1748,6 +1754,9 @@ class InstrumentContext(publisher.CommandPublisher):
         """
         Consolidate a particular type of liquid from a group of wells to one well.
 
+        ..
+            This is intended for Opentrons internal use only and is not a guaranteed API.
+
         :param liquid_class: The type of liquid to move. You must specify the liquid class,
             even if you have used :py:meth:`.Labware.load_liquid` to indicate what liquid the
             source contains.
@@ -1770,7 +1779,7 @@ class InstrumentContext(publisher.CommandPublisher):
         :param return_tip: Whether to drop used tips in their original locations
             in the tip rack, instead of the trash.
 
-            :meta private:
+        :meta private:
         """
         if volume == 0.0:
             _log.info(
@@ -1944,19 +1953,19 @@ class InstrumentContext(publisher.CommandPublisher):
 
         return self
 
-    @requires_version(2, 22)
+    @requires_version(2, 23)
     def resin_tip_seal(
         self,
         location: Union[labware.Well, labware.Labware],
     ) -> InstrumentContext:
         """Seal resin tips onto the pipette.
 
-        The location provided should contain resin tips. Sealing the
-        tip will perform a `pick up` action but there will be no tip tracking
-        associated with the pipette.
+        The location provided should contain resin tips. The pipette will attach itself
+        to the resin tips but does not check any tip presence sensors. Before the pipette
+        seals to the tips, the plunger will rise to the top of its working range so that
+        it can perform a :py:func:`resin_tip_dispense` immediately.
 
         :param location: A location containing resin tips, must be a Labware or a Well.
-
         :type location: :py:class:`~.types.Location`
         """
         if isinstance(location, labware.Labware):
@@ -1976,7 +1985,7 @@ class InstrumentContext(publisher.CommandPublisher):
             )
         return self
 
-    @requires_version(2, 22)
+    @requires_version(2, 23)
     def resin_tip_unseal(
         self,
         location: Union[labware.Well, labware.Labware],
@@ -2014,31 +2023,62 @@ class InstrumentContext(publisher.CommandPublisher):
 
         return self
 
-    @requires_version(2, 22)
+    @requires_version(2, 23)
     def resin_tip_dispense(
         self,
         location: types.Location,
         volume: Optional[float] = None,
         rate: Optional[float] = None,
     ) -> InstrumentContext:
-        """Dispense a volume from resin tips into a labware.
+        """Push liquid out of resin tips that are currently sealed to a pipette.
+
+        The volume and rate parameters for this function control the motion of the plunger
+        to create a desired pressure profile inside the pipette chamber. Unlike a regular
+        dispense action, the volume and rate do not correspond to liquid volume or flow rate
+        dispensed from the resin tips. Select your values for volume and flow rate based on
+        experimentation with the resin tips to create a pressure profile.
+
+        The common way to use this function is as follows:
+
+        #. Seal resin tips to the pipette using :py:meth:`InstrumentContext.resin_tip_seal`.
 
-        The location provided should contain resin tips labware as well as a
-        receptical for dispensed liquid. Dispensing from tip will perform a
-        `dispense` action of the specified volume at a desired flow rate.
+        #. Use :py:meth:`InstrumentContext.resin_tip_dispense` to displace an experimentally
+           derived volume at an experimentally derived rate to create an experimentally derived
+           target pressure inside the pipette.
 
-        :param location: A location containing resin tips.
+        #. Use :py:meth:`ProtocolContext.delay` to wait an experimentally derived amount of
+           time for the pressure inside the pipette to push liquid into and through the resin tip
+           and out the other side.
+
+        #. As liquid passes through the resin tip, the pressure inside the pipette will
+           fall. If not all liquid has been dispensed from the resin tip, repeat steps 2
+           and 3.
+
+        #. Unseal resin tips from the pipette using :py:meth:`InstrumentContext.resin_tip_unseal`.
+
+        Flex pipette pressure sensors will raise an overpressure when a differential pressure
+        inside the pipette chamber above sensor limits is detected. You may need to disable the
+        pressure sensor to create the required pressure profile.
+
+        .. warning::
+            Building excessive pressure inside the pipette chamber (significantly above the sensor
+            limit) with the pressure sensors disabled can damage the pipette.
+
+
+        :param location: Tells the robot where to dispense.
         :type location: :py:class:`~.types.Location`
 
-        :param volume: Will default to maximum, recommended to use the default.
-                       The volume, in µL, that the pipette will prepare to handle.
+        :param volume: The volume that the plunger should displace, in µL. Does not directly relate
+                       to the volume of liquid that will be dispensed.
         :type volume: float
 
-        :param rate: Will default to 10.0, recommended to use the default. How quickly
-                     a pipette dispenses liquid. The speed in µL/s is calculated as
-                     ``rate`` multiplied by :py:attr:`flow_rate.dispense<flow_rate>`.
-        :type rate: float
+        :param rate: How quickly the plunger moves to displace the commanded volume. The plunger speed
+                     in µL/s is calculated as ``rate`` multiplied by
+                     :py:attr:`flow_rate.dispense<flow_rate>`. This rate does not directly relate to
+                     the flow rate of liquid out of the resin tip.
 
+                     The default value of ``10.0`` is recommended.
+        :type rate: float
         """
         well: Optional[labware.Well] = None
         last_location = self._get_last_location_by_api_version()
@@ -2658,7 +2698,8 @@ class InstrumentContext(publisher.CommandPublisher):
         """
         self._raise_if_pressure_not_supported_by_pipette()
         loc = well.top()
-        return self._core.liquid_probe_without_recovery(well._core, loc)
+        self._core.liquid_probe_with_recovery(well._core, loc)
+        return well.current_liquid_height()
 
     def _raise_if_configuration_not_supported_by_pipette(
         self, style: NozzleLayout

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_api/labware.py

@@ -39,6 +39,7 @@ from opentrons.types import (
     Point,
     NozzleMapInterface,
     MeniscusTrackingTarget,
+    Mount,
 )
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocols.api_support.util import (
@@ -348,6 +349,7 @@ class Well:
     @requires_version(2, 21)
     def estimate_liquid_height_after_pipetting(
         self,
+        mount: Mount | str,
         operation_volume: float,
     ) -> LiquidTrackingType:
         """Check the height of the liquid within a well.
@@ -360,7 +362,7 @@ class Well:
         """
 
         projected_final_height = self._core.estimate_liquid_height_after_pipetting(
-            operation_volume=operation_volume,
+            operation_volume=operation_volume, mount=mount
         )
         return projected_final_height
 

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_api/protocol_context.py

@@ -1363,6 +1363,8 @@ class ProtocolContext(CommandPublisher):
     ) -> LiquidClass:
         """
         Define a liquid class for use in the protocol.
+        ..
+            This is intended for Opentrons internal use only and is not a guaranteed API.
 
         :meta private:
         """

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_engine/execution/pipetting.py

@@ -199,6 +199,7 @@ class HardwarePipettingHandler(PipettingHandler):
             labware_id=labware_id,
             well_name=well_name,
             operation_volume=volume * -1,
+            pipette_id=pipette_id,
         )
         if isinstance(aspirate_z_distance, SimulatedProbeResult):
             raise InvalidLiquidHeightFound(
@@ -234,6 +235,7 @@ class HardwarePipettingHandler(PipettingHandler):
             labware_id=labware_id,
             well_name=well_name,
             operation_volume=volume,
+            pipette_id=pipette_id,
         )
         if isinstance(dispense_z_distance, SimulatedProbeResult):
             raise InvalidLiquidHeightFound(

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_engine/state/geometry.py

@@ -520,6 +520,7 @@ class GeometryView:
                 well_location=well_location,
                 well_depth=well_depth,
                 operation_volume=operation_volume,
+                pipette_id=pipette_id,
             )
             if not isinstance(offset_adjustment, SimulatedProbeResult):
                 offset = offset.model_copy(update={"z": offset.z + offset_adjustment})
@@ -1844,6 +1845,7 @@ class GeometryView:
         self,
         labware_id: str,
         well_name: str,
+        pipette_id: str,
         operation_volume: float,
     ) -> float:
         """Get the change in height from a liquid handling operation."""
@@ -1853,6 +1855,7 @@ class GeometryView:
         final_height = self.get_well_height_after_liquid_handling(
             labware_id=labware_id,
             well_name=well_name,
+            pipette_id=pipette_id,
             initial_height=initial_handling_height,
             volume=operation_volume,
         )
@@ -1873,6 +1876,7 @@ class GeometryView:
         well_name: str,
         well_location: WellLocationType,
         well_depth: float,
+        pipette_id: Optional[str] = None,
         operation_volume: Optional[float] = None,
     ) -> LiquidTrackingType:
         """Return a z-axis distance that accounts for well handling height and operation volume.
@@ -1906,9 +1910,14 @@ class GeometryView:
                 volume = well_location.volumeOffset
 
         if volume:
+            if pipette_id is None:
+                raise ValueError(
+                    "cannot get liquid handling offset without pipette id."
+                )
             liquid_height_after = self.get_well_height_after_liquid_handling(
                 labware_id=labware_id,
                 well_name=well_name,
+                pipette_id=pipette_id,
                 initial_height=initial_handling_height,
                 volume=volume,
             )
@@ -2030,6 +2039,7 @@ class GeometryView:
         self,
         labware_id: str,
         well_name: str,
+        pipette_id: str,
         initial_height: LiquidTrackingType,
         volume: float,
     ) -> LiquidTrackingType:
@@ -2044,7 +2054,14 @@ class GeometryView:
             initial_volume = find_volume_at_well_height(
                 target_height=initial_height, well_geometry=well_geometry
             )
-            final_volume = initial_volume + volume
+            final_volume = initial_volume + (
+                volume
+                * self.get_nozzles_per_well(
+                    labware_id=labware_id,
+                    target_well_name=well_name,
+                    pipette_id=pipette_id,
+                )
+            )
             return find_height_at_well_volume(
                 target_volume=final_volume, well_geometry=well_geometry
             )
@@ -2058,6 +2075,7 @@ class GeometryView:
         self,
         labware_id: str,
         well_name: str,
+        pipette_id: str,
         initial_height: LiquidTrackingType,
         volume: float,
     ) -> LiquidTrackingType:
@@ -2073,7 +2091,14 @@ class GeometryView:
             initial_volume = find_volume_at_well_height(
                 target_height=initial_height, well_geometry=well_geometry
             )
-            final_volume = initial_volume + volume
+            final_volume = initial_volume + (
+                volume
+                * self.get_nozzles_per_well(
+                    labware_id=labware_id,
+                    target_well_name=well_name,
+                    pipette_id=pipette_id,
+                )
+            )
             well_volume = find_height_at_well_volume(
                 target_volume=final_volume,
                 well_geometry=well_geometry,

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_engine/types/__init__.py

@@ -135,6 +135,7 @@ from .liquid_level_detection import (
     WellInfoSummary,
     WellLiquidInfo,
     LiquidTrackingType,
+    SimulatedProbeResult,
 )
 from .liquid_handling import FlowRates
 from .labware_movement import LabwareMovementStrategy, LabwareMovementOffsetData
@@ -280,6 +281,7 @@ __all__ = [
     "WellInfoSummary",
     "WellLiquidInfo",
     "LiquidTrackingType",
+    "SimulatedProbeResult",
     # Liquid handling
     "FlowRates",
     # Labware movement

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons/protocol_engine/types/liquid_level_detection.py

@@ -1,9 +1,10 @@
 """Protocol Engine types to do with liquid level detection."""
+
 from __future__ import annotations
 from dataclasses import dataclass
 from datetime import datetime
-from typing import Optional, List
-from pydantic import BaseModel, model_serializer, field_validator
+from typing import Optional, List, Any
+from pydantic import BaseModel, model_serializer, model_validator
 
 
 class SimulatedProbeResult(BaseModel):
@@ -17,6 +18,14 @@ class SimulatedProbeResult(BaseModel):
         """Serialize instances of this class as a string."""
         return "SimulatedProbeResult"
 
+    @model_validator(mode="before")
+    @classmethod
+    def validate_model(cls, data: object) -> Any:
+        """Handle deserializing from a simulated probe result."""
+        if isinstance(data, str) and data == "SimulatedProbeResult":
+            return {}
+        return data
+
     def __add__(
         self, other: float | SimulatedProbeResult
     ) -> float | SimulatedProbeResult:
@@ -75,7 +84,9 @@ class SimulatedProbeResult(BaseModel):
         self.operations_after_probe.append(volume)
 
 
-LiquidTrackingType = SimulatedProbeResult | float
+# Work around https://github.com/pydantic/pydantic/issues/6830 - do not change the order of
+# this union
+LiquidTrackingType = float | SimulatedProbeResult
 
 
 class LoadedVolumeInfo(BaseModel):
@@ -104,23 +115,6 @@ class ProbedVolumeInfo(BaseModel):
 class WellInfoSummary(BaseModel):
     """Payload for a well's liquid info in StateSummary."""
 
-    # TODO(cm): 3/21/25: refactor SimulatedLiquidProbe in a way that
-    # doesn't require models like this one that are just using it to
-    # need a custom validator
-    @field_validator("probed_height", "probed_volume", mode="before")
-    @classmethod
-    def validate_simulated_probe_result(
-        cls, input_val: object
-    ) -> LiquidTrackingType | None:
-        """Return the appropriate input to WellInfoSummary from json data."""
-        if input_val is None:
-            return None
-        if isinstance(input_val, LiquidTrackingType):
-            return input_val
-        if isinstance(input_val, str) and input_val == "SimulatedProbeResult":
-            return SimulatedProbeResult()
-        raise ValueError(f"Invalid input value {input_val} to WellInfoSummary")
-
     labware_id: str
     well_name: str
     loaded_volume: Optional[float] = None

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.4.0a6
+Version: 8.4.0a7
 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==8.4.0a6
+Requires-Dist: opentrons-shared-data==8.4.0a7
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -35,9 +35,9 @@ Requires-Dist: pyusb==1.2.1
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.4.0a6; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.4.0a7; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.4.0a6; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.4.0a7; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.4.0a6 → opentrons-8.4.0a7}/src/opentrons.egg-info/requires.txt

@@ -1,4 +1,4 @@
-opentrons-shared-data==8.4.0a6
+opentrons-shared-data==8.4.0a7
 aionotify==0.3.1
 anyio<4.0.0,>=3.6.1
 jsonschema<4.18.0,>=3.0.1
@@ -15,7 +15,7 @@ packaging>=21.0
 importlib-metadata>=1.0
 
 [flex-hardware]
-opentrons-hardware[FLEX]==8.4.0a6
+opentrons-hardware[FLEX]==8.4.0a7
 
 [ot2-hardware]
-opentrons-hardware==8.4.0a6
+opentrons-hardware==8.4.0a7