opentrons 8.6.0__py3-none-any.whl

opentrons/protocol_api/core/engine/module_core.py

@@ -0,0 +1,1027 @@
+"""Protocol API module implementation logic."""
+
+from __future__ import annotations
+from dataclasses import dataclass
+from typing import Optional, List, Dict, Union, Sequence, TYPE_CHECKING, overload
+
+from opentrons_shared_data.errors.exceptions import CommandPreconditionViolated
+
+from opentrons.hardware_control import SynchronousAdapter, modules as hw_modules
+from opentrons.hardware_control.modules.types import (
+    ModuleModel,
+    TemperatureStatus,
+    MagneticStatus,
+    SpeedStatus,
+    module_model_from_string,
+)
+from opentrons.drivers.types import (
+    HeaterShakerLabwareLatchStatus,
+    ThermocyclerLidStatus,
+)
+
+from opentrons.protocol_engine import commands as cmd
+from opentrons.protocol_engine.types import (
+    ABSMeasureMode,
+    StackerFillEmptyStrategy,
+    StackerStoredLabwareGroup,
+    StackerLabwareMovementStrategy,
+)
+from opentrons.types import DeckSlotName
+from opentrons.protocol_engine.clients import SyncClient as ProtocolEngineClient
+from opentrons.protocol_engine.errors.exceptions import (
+    LabwareNotLoadedOnModuleError,
+    NoMagnetEngageHeightError,
+    CannotPerformModuleAction,
+    FlexStackerLabwarePoolNotYetDefinedError,
+)
+
+from opentrons.protocols.api_support.types import APIVersion, ThermocyclerStep
+
+from ... import validation
+from ..module import (
+    AbstractModuleCore,
+    AbstractTemperatureModuleCore,
+    AbstractMagneticModuleCore,
+    AbstractThermocyclerCore,
+    AbstractHeaterShakerCore,
+    AbstractMagneticBlockCore,
+    AbstractAbsorbanceReaderCore,
+    AbstractFlexStackerCore,
+)
+from .exceptions import InvalidMagnetEngageHeightError
+
+from .labware import LabwareCore
+from . import load_labware_params
+
+if TYPE_CHECKING:
+    from .protocol import ProtocolCore
+
+# Valid wavelength range for absorbance reader
+ABS_WAVELENGTH_MIN = 350
+ABS_WAVELENGTH_MAX = 1000
+
+
+class ModuleCore(AbstractModuleCore[LabwareCore]):
+    """Module core logic implementation for Python protocols.
+    Args:
+        module_id: ProtocolEngine ID of the loaded modules.
+    """
+
+    def __init__(
+        self,
+        module_id: str,
+        engine_client: ProtocolEngineClient,
+        api_version: APIVersion,
+        sync_module_hardware: SynchronousAdapter[hw_modules.AbstractModule],
+        protocol_core: ProtocolCore,
+    ) -> None:
+        self._module_id = module_id
+        self._engine_client = engine_client
+        self._api_version = api_version
+        self._sync_module_hardware = sync_module_hardware
+        self._protocol_core = protocol_core
+
+    @property
+    def api_version(self) -> APIVersion:
+        """Get the api version protocol module target."""
+        return self._api_version
+
+    @property
+    def module_id(self) -> str:
+        """The module's unique ProtocolEngine ID."""
+        return self._module_id
+
+    def get_model(self) -> ModuleModel:
+        """Get the module's model identifier."""
+        return module_model_from_string(
+            self._engine_client.state.modules.get_connected_model(self.module_id)
+        )
+
+    def get_serial_number(self) -> str:
+        """Get the module's unique hardware serial number."""
+        return self._engine_client.state.modules.get_serial_number(self.module_id)
+
+    def get_deck_slot(self) -> DeckSlotName:
+        """Get the module's deck slot."""
+        return self._engine_client.state.modules.get_location(self.module_id).slotName
+
+    def get_deck_slot_id(self) -> str:
+        slot_name = self.get_deck_slot()
+        return validation.internal_slot_to_public_string(
+            slot_name, robot_type=self._engine_client.state.config.robot_type
+        )
+
+    def get_display_name(self) -> str:
+        """Get the module's display name."""
+        return self._engine_client.state.modules.get_definition(
+            self.module_id
+        ).displayName
+
+
+class NonConnectedModuleCore(AbstractModuleCore[LabwareCore]):
+    """Not connected module core logic implementation for Python protocols.
+
+    Args:
+        module_id: ProtocolEngine ID of the loaded modules.
+    """
+
+    def __init__(
+        self,
+        module_id: str,
+        engine_client: ProtocolEngineClient,
+        api_version: APIVersion,
+        protocol_core: ProtocolCore,
+    ) -> None:
+        self._module_id = module_id
+        self._engine_client = engine_client
+        self._api_version = api_version
+        self._protocol_core = protocol_core
+
+    @property
+    def api_version(self) -> APIVersion:
+        """Get the api version protocol module target."""
+        return self._api_version
+
+    @property
+    def module_id(self) -> str:
+        """The module's unique ProtocolEngine ID."""
+        return self._module_id
+
+    def get_model(self) -> ModuleModel:
+        """Get the module's model identifier."""
+        return module_model_from_string(
+            self._engine_client.state.modules.get_connected_model(self.module_id)
+        )
+
+    def get_deck_slot(self) -> DeckSlotName:
+        """Get the module's deck slot."""
+        return self._engine_client.state.modules.get_location(self.module_id).slotName
+
+    def get_display_name(self) -> str:
+        """Get the module's display name."""
+        return self._engine_client.state.modules.get_definition(
+            self.module_id
+        ).displayName
+
+    def get_deck_slot_id(self) -> str:
+        slot_name = self.get_deck_slot()
+        return validation.internal_slot_to_public_string(
+            slot_name, robot_type=self._engine_client.state.config.robot_type
+        )
+
+
+class TemperatureModuleCore(ModuleCore, AbstractTemperatureModuleCore[LabwareCore]):
+    """Temperature Module core logic implementation for Python protocols."""
+
+    _sync_module_hardware: SynchronousAdapter[hw_modules.TempDeck]
+
+    def set_target_temperature(self, celsius: float) -> None:
+        """Set the Temperature Module's target temperature in °C."""
+        self._engine_client.execute_command(
+            cmd.temperature_module.SetTargetTemperatureParams(
+                moduleId=self.module_id, celsius=celsius
+            )
+        )
+
+    def wait_for_target_temperature(self, celsius: Optional[float] = None) -> None:
+        """Wait until the module's target temperature is reached.
+        Specifying a value for ``celsius`` that is different than
+        the module's current target temperature may behave unpredictably.
+        """
+        self._engine_client.execute_command(
+            cmd.temperature_module.WaitForTemperatureParams(
+                moduleId=self.module_id, celsius=celsius
+            )
+        )
+
+    def deactivate(self) -> None:
+        """Deactivate the Temperature Module."""
+        self._engine_client.execute_command(
+            cmd.temperature_module.DeactivateTemperatureParams(moduleId=self.module_id)
+        )
+
+    def get_current_temperature(self) -> float:
+        """Get the module's current temperature in °C."""
+        return self._sync_module_hardware.temperature  # type: ignore[no-any-return]
+
+    def get_target_temperature(self) -> Optional[float]:
+        """Get the module's target temperature in °C, if set."""
+        return self._sync_module_hardware.target  # type: ignore[no-any-return]
+
+    def get_status(self) -> TemperatureStatus:
+        """Get the module's current temperature status."""
+        return self._sync_module_hardware.status  # type: ignore[no-any-return]
+
+
+class MagneticModuleCore(ModuleCore, AbstractMagneticModuleCore[LabwareCore]):
+    """Magnetic Module control interface via a ProtocolEngine."""
+
+    _sync_module_hardware: SynchronousAdapter[hw_modules.MagDeck]
+
+    def engage(
+        self,
+        height_from_base: Optional[float] = None,
+        height_from_home: Optional[float] = None,
+    ) -> None:
+        """Raise the module's magnets.
+        Only one of `height_from_base` or `height_from_home` may be specified.
+        Args:
+            height_from_base: Distance from labware base to raise the magnets.
+            height_from_home: Distance from motor home position to raise the magnets.
+        """
+
+        # This core will only be used in apiLevels >=2.14, where
+        # MagneticModuleContext.engage(height=...) is no longer available.
+        # So these asserts should always pass.
+        assert (
+            height_from_home is None
+        ), "Expected engage height to be specified from base."
+        assert (
+            height_from_base is not None
+        ), "Expected engage height to be specified from base."
+
+        self._engine_client.execute_command(
+            cmd.magnetic_module.EngageParams(
+                moduleId=self._module_id, height=height_from_base
+            )
+        )
+
+    def engage_to_labware(
+        self, offset: float = 0, preserve_half_mm: bool = False
+    ) -> None:
+        """Raise the module's magnets up to its loaded labware.
+        Args:
+            offset: Offset from the labware's default engage height.
+            preserve_half_mm: For labware whose definitions
+                erroneously use half-mm for their defined default engage height,
+                use the value directly instead of converting it to real millimeters.
+        """
+        try:
+            default_height = (
+                self._engine_client.state.labware.get_default_magnet_height(
+                    module_id=self.module_id, offset=offset
+                )
+            )
+        except LabwareNotLoadedOnModuleError:
+            raise InvalidMagnetEngageHeightError(
+                "There is no labware loaded on this Magnetic Module,"
+                " so you must specify an engage height"
+                " with the `height_from_base` parameter."
+            )
+        except NoMagnetEngageHeightError:
+            raise InvalidMagnetEngageHeightError(
+                "The labware loaded on this Magnetic Module"
+                " does not have a default engage height,"
+                " so you must specify an engage height"
+                " with the `height_from_base` parameter."
+            )
+
+        self._engine_client.execute_command(
+            cmd.magnetic_module.EngageParams(
+                moduleId=self.module_id, height=default_height
+            )
+        )
+
+    def disengage(self) -> None:
+        """Lower the magnets back into the module."""
+        self._engine_client.execute_command(
+            cmd.magnetic_module.DisengageParams(moduleId=self.module_id)
+        )
+
+    def get_status(self) -> MagneticStatus:
+        """Get the module's current magnet status."""
+        return self._sync_module_hardware.status  # type: ignore[no-any-return]
+
+
+class ThermocyclerModuleCore(ModuleCore, AbstractThermocyclerCore[LabwareCore]):
+    """Core control interface for an attached Thermocycler Module."""
+
+    _sync_module_hardware: SynchronousAdapter[hw_modules.Thermocycler]
+    _repetitions: Optional[int] = None
+    _step_count: Optional[int] = None
+
+    def open_lid(self) -> ThermocyclerLidStatus:
+        """Open the Thermocycler's lid."""
+        self._engine_client.execute_command(
+            cmd.thermocycler.OpenLidParams(moduleId=self.module_id)
+        )
+        return ThermocyclerLidStatus.OPEN
+
+    def close_lid(self) -> ThermocyclerLidStatus:
+        """Close the Thermocycler's lid."""
+        self._engine_client.execute_command(
+            cmd.thermocycler.CloseLidParams(moduleId=self.module_id)
+        )
+        return ThermocyclerLidStatus.CLOSED
+
+    def set_target_block_temperature(
+        self,
+        celsius: float,
+        hold_time_seconds: Optional[float] = None,
+        block_max_volume: Optional[float] = None,
+    ) -> None:
+        """Set the target temperature for the well block, in °C."""
+        self._engine_client.execute_command(
+            cmd.thermocycler.SetTargetBlockTemperatureParams(
+                moduleId=self.module_id,
+                celsius=celsius,
+                blockMaxVolumeUl=block_max_volume,
+                holdTimeSeconds=hold_time_seconds,
+            )
+        )
+
+    def wait_for_block_temperature(self) -> None:
+        """Wait for target block temperature to be reached."""
+        self._engine_client.execute_command(
+            cmd.thermocycler.WaitForBlockTemperatureParams(moduleId=self.module_id)
+        )
+
+    def set_target_lid_temperature(self, celsius: float) -> None:
+        """Set the target temperature for the heated lid, in °C."""
+        self._engine_client.execute_command(
+            cmd.thermocycler.SetTargetLidTemperatureParams(
+                moduleId=self.module_id, celsius=celsius
+            )
+        )
+
+    def wait_for_lid_temperature(self) -> None:
+        """Wait for target lid temperature to be reached."""
+        self._engine_client.execute_command(
+            cmd.thermocycler.WaitForLidTemperatureParams(moduleId=self.module_id)
+        )
+
+    def _execute_profile_pre_221(
+        self,
+        steps: List[ThermocyclerStep],
+        repetitions: int,
+        block_max_volume: Optional[float],
+    ) -> None:
+        """Execute a thermocycler profile using thermocycler/runProfile and flattened steps."""
+        engine_steps = [
+            cmd.thermocycler.RunProfileStepParams(
+                celsius=step["temperature"],
+                holdSeconds=step["hold_time_seconds"],
+            )
+            for step in steps
+        ]
+        repeated_engine_steps = engine_steps * repetitions
+        self._engine_client.execute_command(
+            cmd.thermocycler.RunProfileParams(
+                moduleId=self.module_id,
+                profile=repeated_engine_steps,
+                blockMaxVolumeUl=block_max_volume,
+            )
+        )
+
+    def _execute_profile_post_221(
+        self,
+        steps: List[ThermocyclerStep],
+        repetitions: int,
+        block_max_volume: Optional[float],
+    ) -> None:
+        """Execute a thermocycler profile using thermocycler/runExtendedProfile."""
+        engine_steps: List[
+            Union[cmd.thermocycler.ProfileCycle, cmd.thermocycler.ProfileStep]
+        ] = [
+            cmd.thermocycler.ProfileCycle(
+                repetitions=repetitions,
+                steps=[
+                    cmd.thermocycler.ProfileStep(
+                        celsius=step["temperature"],
+                        holdSeconds=step["hold_time_seconds"],
+                    )
+                    for step in steps
+                ],
+            )
+        ]
+        self._engine_client.execute_command(
+            cmd.thermocycler.RunExtendedProfileParams(
+                moduleId=self.module_id,
+                profileElements=engine_steps,
+                blockMaxVolumeUl=block_max_volume,
+            )
+        )
+
+    def execute_profile(
+        self,
+        steps: List[ThermocyclerStep],
+        repetitions: int,
+        block_max_volume: Optional[float] = None,
+    ) -> None:
+        """Execute a Thermocycler Profile."""
+        self._repetitions = repetitions
+        self._step_count = len(steps)
+        if self.api_version >= APIVersion(2, 21):
+            return self._execute_profile_post_221(steps, repetitions, block_max_volume)
+        else:
+            return self._execute_profile_pre_221(steps, repetitions, block_max_volume)
+
+    def deactivate_lid(self) -> None:
+        """Turn off the heated lid."""
+        self._engine_client.execute_command(
+            cmd.thermocycler.DeactivateLidParams(moduleId=self.module_id)
+        )
+
+    def deactivate_block(self) -> None:
+        """Turn off the well block temperature controller"""
+        self._clear_cycle_counters()
+        self._engine_client.execute_command(
+            cmd.thermocycler.DeactivateBlockParams(moduleId=self.module_id)
+        )
+
+    def deactivate(self) -> None:
+        """Turn off the well block temperature controller, and heated lid"""
+        self.deactivate_block()
+        self.deactivate_lid()
+
+    def get_lid_position(self) -> Optional[ThermocyclerLidStatus]:
+        """Get the thermocycler's lid position."""
+        return self._sync_module_hardware.lid_status  # type: ignore[no-any-return]
+
+    def get_block_temperature_status(self) -> TemperatureStatus:
+        """Get the thermocycler's block temperature status."""
+        return self._sync_module_hardware.status  # type: ignore[no-any-return]
+
+    def get_lid_temperature_status(self) -> Optional[TemperatureStatus]:
+        """Get the thermocycler's lid temperature status."""
+        return self._sync_module_hardware.lid_temp_status  # type: ignore[no-any-return]
+
+    def get_block_temperature(self) -> Optional[float]:
+        """Get the thermocycler's current block temperature in °C."""
+        return self._sync_module_hardware.temperature  # type: ignore[no-any-return]
+
+    def get_block_target_temperature(self) -> Optional[float]:
+        """Get the thermocycler's target block temperature in °C."""
+        return self._sync_module_hardware.target  # type: ignore[no-any-return]
+
+    def get_lid_temperature(self) -> Optional[float]:
+        """Get the thermocycler's current lid temperature in °C."""
+        return self._sync_module_hardware.lid_temp  # type: ignore[no-any-return]
+
+    def get_lid_target_temperature(self) -> Optional[float]:
+        """Get the thermocycler's target lid temperature in °C."""
+        return self._sync_module_hardware.lid_target  # type: ignore[no-any-return]
+
+    def get_ramp_rate(self) -> Optional[float]:
+        """Get the thermocycler's current ramp rate in °C/sec."""
+        return self._sync_module_hardware.ramp_rate  # type: ignore[no-any-return]
+
+    def get_hold_time(self) -> Optional[float]:
+        """Get the remaining hold time in seconds."""
+        return self._sync_module_hardware.hold_time  # type: ignore[no-any-return]
+
+    def get_total_cycle_count(self) -> Optional[int]:
+        """Get number of repetitions for current set cycle."""
+        return self._repetitions
+
+    def get_current_cycle_index(self) -> Optional[int]:
+        """Get index of the current set cycle repetition."""
+        if self._repetitions is None:
+            return None
+        step_index = self._sync_module_hardware.current_step_index
+        # TODO(jbl 2022-10-31) this is intended to work even if execute profile is non-blocking, but it is blocking so
+        #   this is not guaranteed to be accurate
+        return (step_index - 1) // self._step_count + 1  # type: ignore[no-any-return]
+
+    def get_total_step_count(self) -> Optional[int]:
+        """Get number of steps within the current cycle."""
+        return self._step_count
+
+    def get_current_step_index(self) -> Optional[int]:
+        """Get the index of the current step within the current cycle."""
+        if self._step_count is None:
+            return None
+        step_index = self._sync_module_hardware.current_step_index
+        # TODO(jbl 2022-10-31) this is intended to work even if execute profile is non-blocking, but it is blocking so
+        #   this is not guaranteed to be accurate
+        return (step_index - 1) % self._step_count + 1  # type: ignore[no-any-return]
+
+    def _clear_cycle_counters(self) -> None:
+        """Clear core-tracked cycle counters."""
+        self._repetitions = None
+        self._step_count = None
+
+
+class HeaterShakerModuleCore(ModuleCore, AbstractHeaterShakerCore[LabwareCore]):
+    """Core control interface for an attached Heater-Shaker Module."""
+
+    _sync_module_hardware: SynchronousAdapter[hw_modules.HeaterShaker]
+
+    def set_target_temperature(self, celsius: float) -> None:
+        """Set the labware plate's target temperature in °C."""
+        self._engine_client.execute_command(
+            cmd.heater_shaker.SetTargetTemperatureParams(
+                moduleId=self.module_id, celsius=celsius
+            )
+        )
+
+    def wait_for_target_temperature(self) -> None:
+        """Wait for the labware plate's target temperature to be reached."""
+        self._engine_client.execute_command(
+            cmd.heater_shaker.WaitForTemperatureParams(moduleId=self.module_id)
+        )
+
+    def set_and_wait_for_shake_speed(self, rpm: int) -> None:
+        """Set the shaker's target shake speed and wait for it to spin up."""
+        self._engine_client.execute_command(
+            cmd.heater_shaker.SetAndWaitForShakeSpeedParams(
+                moduleId=self.module_id, rpm=rpm
+            )
+        )
+
+    def open_labware_latch(self) -> None:
+        """Open the labware latch."""
+        self._engine_client.execute_command(
+            cmd.heater_shaker.OpenLabwareLatchParams(moduleId=self.module_id)
+        )
+
+    def close_labware_latch(self) -> None:
+        """Close the labware latch."""
+        self._engine_client.execute_command(
+            cmd.heater_shaker.CloseLabwareLatchParams(moduleId=self.module_id)
+        )
+
+    def deactivate_shaker(self) -> None:
+        """Stop shaking."""
+        self._engine_client.execute_command(
+            cmd.heater_shaker.DeactivateShakerParams(moduleId=self.module_id)
+        )
+
+    def deactivate_heater(self) -> None:
+        """Stop heating."""
+        self._engine_client.execute_command(
+            cmd.heater_shaker.DeactivateHeaterParams(moduleId=self.module_id)
+        )
+
+    def get_current_temperature(self) -> float:
+        """Get the labware plate's current temperature in °C."""
+        return self._sync_module_hardware.temperature  # type: ignore[no-any-return]
+
+    def get_target_temperature(self) -> Optional[float]:
+        """Get the labware plate's target temperature in °C, if set."""
+        return self._sync_module_hardware.target_temperature  # type: ignore[no-any-return]
+
+    def get_current_speed(self) -> int:
+        """Get the shaker's current speed in RPM."""
+        return self._sync_module_hardware.speed  # type: ignore[no-any-return]
+
+    def get_target_speed(self) -> Optional[int]:
+        """Get the shaker's target speed in RPM, if set."""
+        return self._sync_module_hardware.target_speed  # type: ignore[no-any-return]
+
+    def get_temperature_status(self) -> TemperatureStatus:
+        """Get the module's heater status."""
+        return self._sync_module_hardware.temperature_status  # type: ignore[no-any-return]
+
+    def get_speed_status(self) -> SpeedStatus:
+        """Get the module's heater status."""
+        return self._sync_module_hardware.speed_status  # type: ignore[no-any-return]
+
+    def get_labware_latch_status(self) -> HeaterShakerLabwareLatchStatus:
+        """Get the module's labware latch status."""
+        return self._sync_module_hardware.labware_latch_status  # type: ignore[no-any-return]
+
+
+class MagneticBlockCore(NonConnectedModuleCore, AbstractMagneticBlockCore[LabwareCore]):
+    """Magnetic Block control interface via a ProtocolEngine."""
+
+
+class AbsorbanceReaderCore(ModuleCore, AbstractAbsorbanceReaderCore[LabwareCore]):
+    """Absorbance Reader core logic implementation for Python protocols."""
+
+    _sync_module_hardware: SynchronousAdapter[hw_modules.AbsorbanceReader]
+    _initialized_value: Optional[List[int]] = None
+    _ready_to_initialize: bool = False
+
+    def initialize(
+        self,
+        mode: ABSMeasureMode,
+        wavelengths: List[int],
+        reference_wavelength: Optional[int] = None,
+    ) -> None:
+        """Initialize the Absorbance Reader by taking zero reading."""
+        if not self._ready_to_initialize:
+            raise CannotPerformModuleAction(
+                "Cannot perform Initialize action on Absorbance Reader without calling `.close_lid()` first."
+            )
+
+        wavelength_len = len(wavelengths)
+        if mode == "single" and wavelength_len != 1:
+            raise ValueError(
+                f"Single mode can only be initialized with 1 wavelength"
+                f" {wavelength_len} wavelengths provided instead."
+            )
+
+        if mode == "multi" and (wavelength_len < 1 or wavelength_len > 6):
+            raise ValueError(
+                f"Multi mode can only be initialized with 1 - 6 wavelengths."
+                f" {wavelength_len} wavelengths provided instead."
+            )
+
+        if reference_wavelength is not None and (
+            reference_wavelength < ABS_WAVELENGTH_MIN
+            or reference_wavelength > ABS_WAVELENGTH_MAX
+        ):
+            raise ValueError(
+                f"Unsupported reference wavelength: ({reference_wavelength}) needs"
+                f" to between {ABS_WAVELENGTH_MIN} and {ABS_WAVELENGTH_MAX} nm."
+            )
+
+        for wavelength in wavelengths:
+            if (
+                not isinstance(wavelength, int)
+                or wavelength < ABS_WAVELENGTH_MIN
+                or wavelength > ABS_WAVELENGTH_MAX
+            ):
+                raise ValueError(
+                    f"Unsupported sample wavelength: ({wavelength}) needs"
+                    f" to between {ABS_WAVELENGTH_MIN} and {ABS_WAVELENGTH_MAX} nm."
+                )
+
+        self._engine_client.execute_command(
+            cmd.absorbance_reader.InitializeParams(
+                moduleId=self.module_id,
+                measureMode=mode,
+                sampleWavelengths=wavelengths,
+                referenceWavelength=reference_wavelength,
+            ),
+        )
+        self._initialized_value = wavelengths
+
+    def read(self, filename: Optional[str] = None) -> Dict[int, Dict[str, float]]:
+        """Initiate a read on the Absorbance Reader, and return the results. During Analysis, this will return a measurement of zero for all wells."""
+        wavelengths = self._engine_client.state.modules.get_absorbance_reader_substate(
+            self.module_id
+        ).configured_wavelengths
+        if wavelengths is None:
+            raise CannotPerformModuleAction(
+                "Cannot perform Read action on Absorbance Reader without calling `.initialize(...)` first."
+            )
+        if self._initialized_value:
+            self._engine_client.execute_command(
+                cmd.absorbance_reader.ReadAbsorbanceParams(
+                    moduleId=self.module_id, fileName=filename
+                )
+            )
+        if not self._engine_client.state.config.use_virtual_modules:
+            read_result = (
+                self._engine_client.state.modules.get_absorbance_reader_substate(
+                    self.module_id
+                ).data
+            )
+            if read_result is not None:
+                return read_result
+            raise CannotPerformModuleAction(
+                "Absorbance Reader failed to return expected read result."
+            )
+
+        # When using virtual modules, return all zeroes
+        virtual_asbsorbance_result: Dict[int, Dict[str, float]] = {}
+        for wavelength in wavelengths:
+            converted_values = (
+                self._engine_client.state.modules.convert_absorbance_reader_data_points(
+                    data=[0] * 96
+                )
+            )
+            virtual_asbsorbance_result[wavelength] = converted_values
+        return virtual_asbsorbance_result
+
+    def close_lid(
+        self,
+    ) -> None:
+        """Close the Absorbance Reader's lid."""
+        self._engine_client.execute_command(
+            cmd.absorbance_reader.CloseLidParams(
+                moduleId=self.module_id,
+            )
+        )
+        self._ready_to_initialize = True
+
+    def open_lid(self) -> None:
+        """Close the Absorbance Reader's lid."""
+        self._engine_client.execute_command(
+            cmd.absorbance_reader.OpenLidParams(
+                moduleId=self.module_id,
+            )
+        )
+
+    def is_lid_on(self) -> bool:
+        """Returns True if the Absorbance Reader's lid is currently on the Reader slot."""
+        abs_state = self._engine_client.state.modules.get_absorbance_reader_substate(
+            self.module_id
+        )
+        return abs_state.is_lid_on
+
+
+@dataclass
+class _CoreTrio:
+    primary: LabwareCore
+    adapter: LabwareCore | None
+    lid: LabwareCore | None
+
+
+class FlexStackerCore(ModuleCore, AbstractFlexStackerCore[LabwareCore]):
+    """Flex Stacker core logic implementation for Python protocols."""
+
+    _sync_module_hardware: SynchronousAdapter[hw_modules.FlexStacker]
+
+    def retrieve(self) -> LabwareCore:
+        """Retrieve a labware from the Flex Stacker's hopper.
+
+        Returns the primary labware.
+        """
+        self._engine_client.execute_command(
+            cmd.flex_stacker.RetrieveParams(
+                moduleId=self.module_id,
+            )
+        )
+        base = self._protocol_core.get_labware_on_module(self)
+        assert base, "Retrieve failed to provide a labware"
+        if base.is_adapter():
+            primary = self._protocol_core.get_labware_on_labware(base)
+            if primary:
+                return primary
+        return base
+
+    def store(self) -> None:
+        """Store a labware into Flex Stacker's hopper."""
+        self._engine_client.execute_command(
+            cmd.flex_stacker.StoreParams(
+                moduleId=self.module_id,
+                strategy=StackerLabwareMovementStrategy.AUTOMATIC,
+            )
+        )
+
+    def fill(self, count: int | None, message: str | None) -> None:
+        """Pause the protocol to add more labware to the Flex Stacker's hopper."""
+        self._engine_client.execute_command(
+            cmd.flex_stacker.FillParams(
+                moduleId=self.module_id,
+                strategy=StackerFillEmptyStrategy.MANUAL_WITH_PAUSE,
+                message=message,
+                count=count,
+            )
+        )
+
+    def _core_groups_from_primary_core(self, labware: LabwareCore) -> _CoreTrio:
+        possible_adapter = self._protocol_core.get_labware_location(labware)
+        return _CoreTrio(
+            primary=labware,
+            adapter=(
+                possible_adapter if isinstance(possible_adapter, LabwareCore) else None
+            ),
+            lid=self._protocol_core.get_labware_on_labware(labware),
+        )
+
+    def _group_from_core_group(
+        self, core_group: _CoreTrio
+    ) -> StackerStoredLabwareGroup:
+        return StackerStoredLabwareGroup(
+            primaryLabwareId=core_group.primary.labware_id,
+            adapterLabwareId=(
+                core_group.adapter.labware_id if core_group.adapter else None
+            ),
+            lidLabwareId=core_group.lid.labware_id if core_group.lid else None,
+        )
+
+    def _group_from_core(self, labware: LabwareCore) -> StackerStoredLabwareGroup:
+        return self._group_from_core_group(self._core_groups_from_primary_core(labware))
+
+    def fill_items(self, labware: Sequence[LabwareCore], message: str | None) -> None:
+        """Pause the protocol to fill with a specific set of labware."""
+        groups = [self._group_from_core(core) for core in labware]
+        self._engine_client.execute_command(
+            cmd.flex_stacker.FillParams(
+                moduleId=self._module_id,
+                strategy=StackerFillEmptyStrategy.MANUAL_WITH_PAUSE,
+                message=message,
+                labwareToStore=groups,
+                count=None,
+            )
+        )
+
+    def empty(self, message: str | None) -> None:
+        """Pause the protocol to remove labware from the Flex Stacker's hopper."""
+        self._engine_client.execute_command(
+            cmd.flex_stacker.EmptyParams(
+                moduleId=self.module_id,
+                strategy=StackerFillEmptyStrategy.MANUAL_WITH_PAUSE,
+                message=message,
+                count=0,
+            )
+        )
+
+    def get_max_storable_labware(self) -> int:
+        """Get the total number of configured labware the stacker can store."""
+        max_lw = self._engine_client.state.modules.stacker_max_pool_count(
+            self._module_id
+        )
+        if max_lw is None:
+            location = self._engine_client.state.modules.get_location(self._module_id)
+            raise FlexStackerLabwarePoolNotYetDefinedError(
+                message=f"The Flex Stacker in {location} has not been configured yet and cannot be filled."
+            )
+        return max_lw
+
+    def get_current_storable_labware(self) -> int:
+        """Get the amount of space currently available for labware."""
+        max_lw = self.get_max_storable_labware()
+        if max_lw is None:
+            location = self._engine_client.state.modules.get_location(self._module_id)
+            raise FlexStackerLabwarePoolNotYetDefinedError(
+                message=f"The Flex Stacker in {location} has not been configured yet and cannot be filled."
+            )
+        current = len(
+            self._engine_client.state.modules.stacker_contained_labware(self._module_id)
+        )
+        return max_lw - current
+
+    def _predict_storable_count(
+        self,
+        labwares: _CoreTrio,
+        overlap_offset: float | None = None,
+    ) -> int:
+        definitions = (
+            self._engine_client.state.labware.stacker_labware_pool_to_ordered_list(
+                labwares.primary.get_engine_definition(),
+                labwares.lid.get_engine_definition() if labwares.lid else None,
+                labwares.adapter.get_engine_definition() if labwares.adapter else None,
+            )
+        )
+        pool_height = self._engine_client.state.geometry.get_height_of_labware_stack(
+            definitions
+        )
+        pool_overlap = (
+            overlap_offset
+            if overlap_offset is not None
+            else self._engine_client.state.labware.get_stacker_labware_overlap_offset(
+                definitions
+            ).z
+        )
+        return self._engine_client.state.modules.stacker_max_pool_count_by_height(
+            self._module_id, pool_height, pool_overlap
+        )
+
+    def get_max_storable_labware_from_list(
+        self,
+        labware: Sequence[LabwareCore],
+        overlap_offset: float | None = None,
+    ) -> Sequence[LabwareCore]:
+        """Limit the passed list to how many labware can fit in a stacker."""
+        if not labware:
+            return labware
+        max_count: int
+        try:
+            # if the stacker has been configured, make sure the provided overlap
+            # offset, if any, matches the configured one
+            max_count = self.get_max_storable_labware()
+            if overlap_offset is not None:
+                self._engine_client.state.modules.validate_stacker_overlap_offset(
+                    self._module_id, overlap_offset
+                )
+        except FlexStackerLabwarePoolNotYetDefinedError:
+            max_count = self._predict_storable_count(
+                self._core_groups_from_primary_core(labware[0]), overlap_offset
+            )
+        return labware[:max_count]
+
+    def get_current_storable_labware_from_list(
+        self,
+        labware: Sequence[LabwareCore],
+    ) -> Sequence[LabwareCore]:
+        """Limit the passed list to how many labware can fit in the stacker right now."""
+        if not labware:
+            return labware
+        storable = self.get_current_storable_labware()
+        return labware[:storable]
+
+    def get_stored_labware(self) -> Sequence[LabwareCore]:
+        """Get the currently-stored primary labware from the stacker."""
+        stored_groups = self._engine_client.state.modules.stacker_contained_labware(
+            self._module_id
+        )
+        return [
+            self._protocol_core.add_or_get_labware_core(group.primaryLabwareId)
+            for group in stored_groups
+        ]
+
+    @overload
+    def _ssld_from_core(
+        self, core: LabwareCore
+    ) -> cmd.flex_stacker.StackerStoredLabwareDetails:
+        ...
+
+    @overload
+    def _ssld_from_core(self, core: None) -> None:
+        ...
+
+    def _ssld_from_core(
+        self, core: LabwareCore | None
+    ) -> cmd.flex_stacker.StackerStoredLabwareDetails | None:
+        if not core:
+            return None
+        definition = core.get_engine_definition()
+        return cmd.flex_stacker.StackerStoredLabwareDetails(
+            loadName=definition.parameters.loadName,
+            namespace=definition.namespace,
+            version=definition.version,
+        )
+
+    def set_stored_labware_items(
+        self,
+        labware: Sequence[LabwareCore],
+        stacking_offset_z: float | None,
+    ) -> None:
+        """Configure the stacker to contain a set of labware."""
+        core_groups = [self._core_groups_from_primary_core(core) for core in labware]
+        if len(core_groups) < 1:
+            raise CommandPreconditionViolated(
+                "At least one labware must be passed to set_stored_labware_items"
+            )
+        stacker_groups = [
+            self._group_from_core_group(core_group) for core_group in core_groups
+        ]
+
+        self._engine_client.execute_command(
+            cmd.flex_stacker.SetStoredLabwareParams(
+                moduleId=self.module_id,
+                initialCount=None,
+                initialStoredLabware=stacker_groups,
+                primaryLabware=self._ssld_from_core(core_groups[0].primary),
+                lidLabware=self._ssld_from_core(core_groups[0].lid),
+                adapterLabware=self._ssld_from_core(core_groups[0].adapter),
+                poolOverlapOverride=stacking_offset_z,
+            )
+        )
+
+    def set_stored_labware(
+        self,
+        main_load_name: str,
+        main_namespace: str | None,
+        main_version: int | None,
+        lid_load_name: str | None,
+        lid_namespace: str | None,
+        lid_version: int | None,
+        adapter_load_name: str | None,
+        adapter_namespace: str | None,
+        adapter_version: int | None,
+        count: int | None,
+        stacking_offset_z: float | None = None,
+    ) -> None:
+        """Configure the kind of labware that the stacker stores."""
+
+        custom_labware_params = (
+            self._engine_client.state.labware.find_custom_labware_load_params()
+        )
+
+        main_namespace, main_version = load_labware_params.resolve(
+            main_load_name,
+            main_namespace,
+            main_version,
+            custom_labware_params,
+            self._api_version,
+        )
+        main_labware = cmd.flex_stacker.StackerStoredLabwareDetails(
+            loadName=main_load_name, namespace=main_namespace, version=main_version
+        )
+
+        lid_labware: cmd.flex_stacker.StackerStoredLabwareDetails | None = None
+
+        if lid_load_name:
+            lid_namespace, lid_version = load_labware_params.resolve(
+                lid_load_name,
+                lid_namespace,
+                lid_version,
+                custom_labware_params,
+                self._api_version,
+            )
+            lid_labware = cmd.flex_stacker.StackerStoredLabwareDetails(
+                loadName=lid_load_name, namespace=lid_namespace, version=lid_version
+            )
+
+        adapter_labware: cmd.flex_stacker.StackerStoredLabwareDetails | None = None
+
+        if adapter_load_name:
+            adapter_namespace, adapter_version = load_labware_params.resolve(
+                adapter_load_name,
+                adapter_namespace,
+                adapter_version,
+                custom_labware_params,
+                self._api_version,
+            )
+            adapter_labware = cmd.flex_stacker.StackerStoredLabwareDetails(
+                loadName=adapter_load_name,
+                namespace=adapter_namespace,
+                version=adapter_version,
+            )
+
+        self._engine_client.execute_command(
+            cmd.flex_stacker.SetStoredLabwareParams(
+                moduleId=self.module_id,
+                initialCount=count,
+                primaryLabware=main_labware,
+                lidLabware=lid_labware,
+                adapterLabware=adapter_labware,
+                poolOverlapOverride=stacking_offset_z,
+            )
+        )