Merge branch 'edge' into local-code-snapshots

api/src/opentrons/cli/analyze.py

@@ -332,6 +332,7 @@ async def _do_analyze(
                 liquids=[],
                 wells=[],
                 hasEverEnteredErrorRecovery=False,
+                files=[],
             ),
             parameters=[],
         )

api/src/opentrons/execute.py

@@ -546,6 +546,7 @@ def _create_live_context_pe(
             hardware_api=hardware_api_wrapped,
             config=_get_protocol_engine_config(),
             deck_configuration=entrypoint_util.get_deck_configuration(),
+            file_provider=None,
             error_recovery_policy=error_recovery_policy.never_recover,
             drop_tips_after_run=False,
             post_run_hardware_state=PostRunHardwareState.STAY_ENGAGED_IN_PLACE,

api/src/opentrons/hardware_control/api.py

@@ -1241,10 +1241,10 @@ async def pick_up_tip(
         if prep_after:
             await self.prepare_for_aspirate(mount)
 
-    async def drop_tip(self, mount: top_types.Mount, home_after: bool = True) -> None:
-        """Drop tip at the current location."""
-
-        spec, _remove = self.plan_check_drop_tip(mount, home_after)
+    async def tip_drop_moves(
+        self, mount: top_types.Mount, home_after: bool = True
+    ) -> None:
+        spec, _ = self.plan_check_drop_tip(mount, home_after)
 
         for move in spec.drop_moves:
             self._backend.set_active_current(move.current)
@@ -1272,7 +1272,20 @@ async def drop_tip(self, mount: top_types.Mount, home_after: bool = True) -> Non
             await self.move_rel(mount, shake[0], speed=shake[1])
 
         self._backend.set_active_current(spec.ending_current)
-        _remove()
+
+    async def drop_tip(self, mount: top_types.Mount, home_after: bool = True) -> None:
+        """Drop tip at the current location."""
+        await self.tip_drop_moves(mount, home_after)
+
+        # todo(mm, 2024-10-17): Ideally, callers would be able to replicate the behavior
+        # of this method via self.drop_tip_moves() plus other public methods. This
+        # currently prevents that: there is no public equivalent for
+        # instrument.set_current_volume().
+        instrument = self.get_pipette(mount)
+        instrument.set_current_volume(0)
+
+        self.set_current_tiprack_diameter(mount, 0.0)
+        self.remove_tip(mount)
 
     async def create_simulating_module(
         self,

api/src/opentrons/hardware_control/instruments/ot2/pipette_handler.py

@@ -415,7 +415,7 @@ async def reset_nozzle_configuration(self, mount: MountType) -> None:
         if instr:
             instr.reset_nozzle_configuration()
 
-    async def add_tip(self, mount: MountType, tip_length: float) -> None:
+    def add_tip(self, mount: MountType, tip_length: float) -> None:
         instr = self._attached_instruments[mount]
         attached = self.attached_instruments
         instr_dict = attached[mount]
@@ -430,7 +430,7 @@ async def add_tip(self, mount: MountType, tip_length: float) -> None:
                 f"attach tip called while tip already attached to {instr}"
             )
 
-    async def remove_tip(self, mount: MountType) -> None:
+    def remove_tip(self, mount: MountType) -> None:
         instr = self._attached_instruments[mount]
         attached = self.attached_instruments
         instr_dict = attached[mount]
@@ -929,6 +929,8 @@ def plan_check_drop_tip(
     ) -> Tuple[DropTipSpec, Callable[[], None]]:
         ...
 
+    # todo(mm, 2024-10-17): The returned _remove_tips() callable is not used by anything
+    # anymore. Delete it.
     def plan_check_drop_tip(  # type: ignore[no-untyped-def]
         self,
         mount,

api/src/opentrons/hardware_control/instruments/ot3/pipette_handler.py

@@ -425,7 +425,7 @@ async def reset_nozzle_configuration(self, mount: OT3Mount) -> None:
         if instr:
             instr.reset_nozzle_configuration()
 
-    async def add_tip(self, mount: OT3Mount, tip_length: float) -> None:
+    def add_tip(self, mount: OT3Mount, tip_length: float) -> None:
         instr = self._attached_instruments[mount]
         attached = self.attached_instruments
         instr_dict = attached[mount]
@@ -440,7 +440,7 @@ async def add_tip(self, mount: OT3Mount, tip_length: float) -> None:
                 "attach tip called while tip already attached to {instr}"
             )
 
-    async def remove_tip(self, mount: OT3Mount) -> None:
+    def remove_tip(self, mount: OT3Mount) -> None:
         instr = self._attached_instruments[mount]
         attached = self.attached_instruments
         instr_dict = attached[mount]

api/src/opentrons/hardware_control/ot3_calibration.py

@@ -819,13 +819,13 @@ async def find_pipette_offset(
     try:
         if reset_instrument_offset:
             await hcapi.reset_instrument_offset(mount)
-        await hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
+        hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
         offset = await _calibrate_mount(
             hcapi, mount, slot, method, raise_verify_error, probe=probe
         )
         return offset
     finally:
-        await hcapi.remove_tip(mount)
+        hcapi.remove_tip(mount)
 
 
 async def calibrate_pipette(
@@ -877,7 +877,7 @@ async def calibrate_module(
         if mount == OT3Mount.GRIPPER:
             hcapi.add_gripper_probe(GripperProbe.FRONT)
         else:
-            await hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
+            hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
 
         LOG.info(
             f"Starting module calibration for {module_id} at {nominal_position} using {mount}"
@@ -903,7 +903,7 @@ async def calibrate_module(
             hcapi.remove_gripper_probe()
             await hcapi.ungrip()
         else:
-            await hcapi.remove_tip(mount)
+            hcapi.remove_tip(mount)
 
 
 async def calibrate_belts(
@@ -927,15 +927,15 @@ async def calibrate_belts(
         raise RuntimeError("Must use pipette mount, not gripper")
     try:
         hcapi.reset_deck_calibration()
-        await hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
+        hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
         belt_attitude, alignment_details = await _determine_transform_matrix(
             hcapi, mount
         )
         save_robot_belt_attitude(belt_attitude, pipette_id)
         return belt_attitude, alignment_details
     finally:
         hcapi.load_deck_calibration()
-        await hcapi.remove_tip(mount)
+        hcapi.remove_tip(mount)
 
 
 def apply_machine_transform(

api/src/opentrons/hardware_control/ot3api.py

@@ -2289,17 +2289,10 @@ def set_working_volume(
         )
         instrument.working_volume = tip_volume
 
-    async def drop_tip(
+    async def tip_drop_moves(
         self, mount: Union[top_types.Mount, OT3Mount], home_after: bool = False
     ) -> None:
-        """Drop tip at the current location."""
         realmount = OT3Mount.from_mount(mount)
-        instrument = self._pipette_handler.get_pipette(realmount)
-
-        def _remove_tips() -> None:
-            instrument.set_current_volume(0)
-            instrument.current_tiprack_diameter = 0.0
-            instrument.remove_tip()
 
         await self._move_to_plunger_bottom(realmount, rate=1.0, check_current_vol=False)
 
@@ -2326,11 +2319,27 @@ def _remove_tips() -> None:
         if home_after:
             await self._home([Axis.by_mount(mount)])
 
-        _remove_tips()
-        # call this in case we're simulating
+        # call this in case we're simulating:
         if isinstance(self._backend, OT3Simulator):
             self._backend._update_tip_state(realmount, False)
 
+    async def drop_tip(
+        self, mount: Union[top_types.Mount, OT3Mount], home_after: bool = False
+    ) -> None:
+        """Drop tip at the current location."""
+        await self.tip_drop_moves(mount=mount, home_after=home_after)
+
+        # todo(mm, 2024-10-17): Ideally, callers would be able to replicate the behavior
+        # of this method via self.drop_tip_moves() plus other public methods. This
+        # currently prevents that: there is no public equivalent for
+        # instrument.set_current_volume().
+        realmount = OT3Mount.from_mount(mount)
+        instrument = self._pipette_handler.get_pipette(realmount)
+        instrument.set_current_volume(0)
+
+        self.set_current_tiprack_diameter(mount, 0.0)
+        self.remove_tip(mount)
+
     async def clean_up(self) -> None:
         """Get the API ready to stop cleanly."""
         await self._backend.clean_up()
@@ -2598,13 +2607,13 @@ async def update_nozzle_configuration_for_mount(
                 starting_nozzle,
             )
 
-    async def add_tip(
+    def add_tip(
         self, mount: Union[top_types.Mount, OT3Mount], tip_length: float
     ) -> None:
-        await self._pipette_handler.add_tip(OT3Mount.from_mount(mount), tip_length)
+        self._pipette_handler.add_tip(OT3Mount.from_mount(mount), tip_length)
 
-    async def remove_tip(self, mount: Union[top_types.Mount, OT3Mount]) -> None:
-        await self._pipette_handler.remove_tip(OT3Mount.from_mount(mount))
+    def remove_tip(self, mount: Union[top_types.Mount, OT3Mount]) -> None:
+        self._pipette_handler.remove_tip(OT3Mount.from_mount(mount))
 
     def add_gripper_probe(self, probe: GripperProbe) -> None:
         self._gripper_handler.add_probe(probe)

api/src/opentrons/hardware_control/protocols/__init__.py

@@ -58,9 +58,6 @@ class HardwareControlInterface(
     def get_robot_type(self) -> Type[OT2RobotType]:
         return OT2RobotType
 
-    def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
-        ...
-
 
 class FlexHardwareControlInterface(
     PositionEstimator,
@@ -87,12 +84,9 @@ class FlexHardwareControlInterface(
     def get_robot_type(self) -> Type[FlexRobotType]:
         return FlexRobotType
 
-    def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
-        ...
-
 
 __all__ = [
-    "HardwareControlAPI",
+    "HardwareControlInterface",
     "FlexHardwareControlInterface",
     "Simulatable",
     "Stoppable",

api/src/opentrons/hardware_control/protocols/instrument_configurer.py

@@ -142,15 +142,20 @@ def get_instrument_max_height(
         """
         ...
 
-    async def add_tip(self, mount: MountArgType, tip_length: float) -> None:
+    # todo(mm, 2024-10-17): Consider deleting this in favor of cache_tip(), which is
+    # the same except for `assert`s, if we can do so without breaking anything.
+    def add_tip(self, mount: MountArgType, tip_length: float) -> None:
         """Inform the hardware that a tip is now attached to a pipette.
 
         This changes the critical point of the pipette to make sure that
         the end of the tip is what moves around, and allows liquid handling.
         """
         ...
 
-    async def remove_tip(self, mount: MountArgType) -> None:
+    def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
+        ...
+
+    def remove_tip(self, mount: MountArgType) -> None:
         """Inform the hardware that a tip is no longer attached to a pipette.
 
         This changes the critical point of the system to the end of the

api/src/opentrons/hardware_control/protocols/liquid_handler.py

@@ -164,6 +164,11 @@ async def pick_up_tip(
         """
         ...
 
+    async def tip_drop_moves(
+        self, mount: MountArgType, home_after: bool = True
+    ) -> None:
+        ...
+
     async def drop_tip(
         self,
         mount: MountArgType,

api/src/opentrons/protocol_api/core/engine/module_core.py

@@ -586,11 +586,20 @@ def initialize(
         )
         self._initialized_value = wavelengths
 
-    def read(self) -> Optional[Dict[int, Dict[str, float]]]:
-        """Initiate a read on the Absorbance Reader, and return the results. During Analysis, this will return None."""
+    def read(self, filename: Optional[str]) -> 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)
+                cmd.absorbance_reader.ReadAbsorbanceParams(
+                    moduleId=self.module_id, fileName=filename
+                )
             )
         if not self._engine_client.state.config.use_virtual_modules:
             read_result = (
@@ -603,7 +612,17 @@ def read(self) -> Optional[Dict[int, Dict[str, float]]]:
             raise CannotPerformModuleAction(
                 "Absorbance Reader failed to return expected read result."
             )
-        return None
+
+        # 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,

api/src/opentrons/protocol_api/core/module.py

@@ -365,7 +365,7 @@ def initialize(
         """Initialize the Absorbance Reader by taking zero reading."""
 
     @abstractmethod
-    def read(self) -> Optional[Dict[int, Dict[str, float]]]:
+    def read(self, filename: Optional[str]) -> Dict[int, Dict[str, float]]:
         """Get an absorbance reading from the Absorbance Reader."""
 
     @abstractmethod

api/src/opentrons/protocol_api/module_contexts.py

@@ -1035,6 +1035,17 @@ def initialize(
         )
 
     @requires_version(2, 21)
-    def read(self) -> Optional[Dict[int, Dict[str, float]]]:
-        """Initiate read on the Absorbance Reader. Returns a dictionary of wavelengths to dictionary of values ordered by well name."""
-        return self._core.read()
+    def read(self, export_filename: Optional[str]) -> Dict[int, Dict[str, float]]:
+        """Initiate read on the Absorbance Reader.
+
+        Returns a dictionary of wavelengths to dictionary of values ordered by well name.
+
+        :param export_filename: Optional, if a filename is provided a CSV file will be saved
+             as a result of the read action containing measurement data. The filename will
+             be modified to include the wavelength used during measurement. If multiple
+             measurements are taken, then a file will be generated for each wavelength provided.
+
+        Example: If `export_filename="my_data"` and wavelengths 450 and 531 are used during
+        measurement, the output files will be "my_data_450.csv" and "my_data_531.csv".
+        """
+        return self._core.read(filename=export_filename)