Merge branch 'edge' into EXEC-281-volume-tracking

.github/workflows/app-test-build-deploy.yaml

@@ -148,7 +148,7 @@ jobs:
           yarn config set cache-folder ${{ github.workspace }}/.yarn-cache
           make setup-js
       - name: 'test native(er) packages'
-        run: make test-js-internal tests="${{}matrix.shell}/src" cov_opts="--coverage=true"
+        run: make test-js-internal tests="${{matrix.shell}}/src" cov_opts="--coverage=true"
       - name: 'Upload coverage report'
         uses: 'codecov/codecov-action@v3'
         with:

api-client/src/runs/types.ts

@@ -112,7 +112,7 @@ export interface GetRunsParams {
 }
 
 export interface Runs {
-  data: RunData[]
+  data: readonly RunData[]
   links: RunsLinks
 }
 
@@ -125,12 +125,15 @@ export const RUN_ACTION_TYPE_PAUSE: 'pause' = 'pause'
 export const RUN_ACTION_TYPE_STOP: 'stop' = 'stop'
 export const RUN_ACTION_TYPE_RESUME_FROM_RECOVERY: 'resume-from-recovery' =
   'resume-from-recovery'
+export const RUN_ACTION_TYPE_RESUME_FROM_RECOVERY_ASSUMING_FALSE_POSITIVE: 'resume-from-recovery-assuming-false-positive' =
+  'resume-from-recovery-assuming-false-positive'
 
 export type RunActionType =
   | typeof RUN_ACTION_TYPE_PLAY
   | typeof RUN_ACTION_TYPE_PAUSE
   | typeof RUN_ACTION_TYPE_STOP
   | typeof RUN_ACTION_TYPE_RESUME_FROM_RECOVERY
+  | typeof RUN_ACTION_TYPE_RESUME_FROM_RECOVERY_ASSUMING_FALSE_POSITIVE
 
 export interface RunAction {
   id: string
@@ -172,7 +175,11 @@ export type RunError = RunCommandError
  * Error Policy
  */
 
-export type IfMatchType = 'ignoreAndContinue' | 'failRun' | 'waitForRecovery'
+export type IfMatchType =
+  | 'assumeFalsePositiveAndContinue'
+  | 'ignoreAndContinue'
+  | 'failRun'
+  | 'waitForRecovery'
 
 export interface ErrorRecoveryPolicy {
   policyRules: Array<{

api/src/opentrons/hardware_control/api.py

@@ -1189,11 +1189,6 @@ async def tip_pickup_moves(
 
         await self.retract(mount, spec.retract_target)
 
-    def cache_tip(self, mount: top_types.Mount, tip_length: float) -> None:
-        instrument = self.get_pipette(mount)
-        instrument.add_tip(tip_length=tip_length)
-        instrument.set_current_volume(0)
-
     async def pick_up_tip(
         self,
         mount: top_types.Mount,

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

@@ -430,6 +430,14 @@ def add_tip(self, mount: MountType, tip_length: float) -> None:
                 f"attach tip called while tip already attached to {instr}"
             )
 
+    def cache_tip(self, mount: MountType, tip_length: float) -> None:
+        instrument = self.get_pipette(mount)
+        if instrument.has_tip:
+            # instrument.add_tip() would raise an AssertionError if we tried to overwrite an existing tip.
+            instrument.remove_tip()
+        instrument.add_tip(tip_length=tip_length)
+        instrument.set_current_volume(0)
+
     def remove_tip(self, mount: MountType) -> None:
         instr = self._attached_instruments[mount]
         attached = self.attached_instruments

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

@@ -440,6 +440,14 @@ def add_tip(self, mount: OT3Mount, tip_length: float) -> None:
                 "attach tip called while tip already attached to {instr}"
             )
 
+    def cache_tip(self, mount: OT3Mount, tip_length: float) -> None:
+        instrument = self.get_pipette(mount)
+        if instrument.has_tip:
+            # instrument.add_tip() would raise an AssertionError if we tried to overwrite an existing tip.
+            instrument.remove_tip()
+        instrument.add_tip(tip_length=tip_length)
+        instrument.set_current_volume(0)
+
     def remove_tip(self, mount: OT3Mount) -> None:
         instr = self._attached_instruments[mount]
         attached = self.attached_instruments

api/src/opentrons/hardware_control/ot3api.py

@@ -2236,15 +2236,6 @@ async def _tip_motor_action(
             )
             await self.home_gear_motors()
 
-    def cache_tip(
-        self, mount: Union[top_types.Mount, OT3Mount], tip_length: float
-    ) -> None:
-        realmount = OT3Mount.from_mount(mount)
-        instrument = self._pipette_handler.get_pipette(realmount)
-
-        instrument.add_tip(tip_length=tip_length)
-        instrument.set_current_volume(0)
-
     async def pick_up_tip(
         self,
         mount: Union[top_types.Mount, OT3Mount],
@@ -2613,6 +2604,11 @@ def add_tip(
     ) -> None:
         self._pipette_handler.add_tip(OT3Mount.from_mount(mount), tip_length)
 
+    def cache_tip(
+        self, mount: Union[top_types.Mount, OT3Mount], tip_length: float
+    ) -> None:
+        self._pipette_handler.cache_tip(OT3Mount.from_mount(mount), tip_length)
+
     def remove_tip(self, mount: Union[top_types.Mount, OT3Mount]) -> None:
         self._pipette_handler.remove_tip(OT3Mount.from_mount(mount))
 

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

@@ -142,17 +142,24 @@ def get_instrument_max_height(
         """
         ...
 
-    # 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.
+    # todo(mm, 2024-10-17): Consider deleting this in favor of cache_tip()
+    # 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.
 
+        If a tip is already attached, this no-ops.
+
         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.
         """
         ...
 
     def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
+        """Inform the hardware that a tip is now attached to a pipette.
+
+        This is like `add_tip()`, except that if a tip is already attached,
+        this replaces it instead of no-opping.
+        """
         ...
 
     def remove_tip(self, mount: MountArgType) -> None:

api/src/opentrons/protocol_engine/commands/move_labware.py

@@ -186,6 +186,10 @@ async def execute(self, params: MoveLabwareParams) -> _ExecuteReturn:  # noqa: C
                 top_labware_definition=current_labware_definition,
                 bottom_labware_id=available_new_location.labwareId,
             )
+            if params.labwareId == available_new_location.labwareId:
+                raise LabwareMovementNotAllowedError(
+                    "Cannot move a labware onto itself."
+                )
 
         # Allow propagation of ModuleNotLoadedError.
         new_offset_id = self._equipment.find_applicable_labware_offset_id(

api/src/opentrons/protocol_engine/execution/hardware_stopper.py

@@ -78,7 +78,9 @@ async def _drop_tip(self) -> None:
                 try:
                     if self._state_store.labware.get_fixed_trash_id() == FIXED_TRASH_ID:
                         # OT-2 and Flex 2.15 protocols will default to the Fixed Trash Labware
-                        await self._tip_handler.add_tip(pipette_id=pipette_id, tip=tip)
+                        await self._tip_handler.cache_tip(
+                            pipette_id=pipette_id, tip=tip
+                        )
                         await self._movement_handler.move_to_well(
                             pipette_id=pipette_id,
                             labware_id=FIXED_TRASH_ID,
@@ -90,7 +92,9 @@ async def _drop_tip(self) -> None:
                         )
                     elif self._state_store.config.robot_type == "OT-2 Standard":
                         # API 2.16 and above OT2 protocols use addressable areas
-                        await self._tip_handler.add_tip(pipette_id=pipette_id, tip=tip)
+                        await self._tip_handler.cache_tip(
+                            pipette_id=pipette_id, tip=tip
+                        )
                         await self._movement_handler.move_to_addressable_area(
                             pipette_id=pipette_id,
                             addressable_area_name="fixedTrash",

api/src/opentrons/protocol_engine/execution/tip_handler.py

@@ -83,7 +83,7 @@ async def drop_tip(self, pipette_id: str, home_after: Optional[bool]) -> None:
             TipAttachedError
         """
 
-    async def add_tip(self, pipette_id: str, tip: TipGeometry) -> None:
+    async def cache_tip(self, pipette_id: str, tip: TipGeometry) -> None:
         """Tell the Hardware API that a tip is attached."""
 
     async def get_tip_presence(self, pipette_id: str) -> TipPresenceStatus:
@@ -234,31 +234,23 @@ async def pick_up_tip(
             labware_definition=self._state_view.labware.get_definition(labware_id),
             nominal_fallback=nominal_tip_geometry.length,
         )
+        tip_geometry = TipGeometry(
+            length=actual_tip_length,
+            diameter=nominal_tip_geometry.diameter,
+            volume=nominal_tip_geometry.volume,
+        )
 
         await self._hardware_api.tip_pickup_moves(
             mount=hw_mount, presses=None, increment=None
         )
         # Allow TipNotAttachedError to propagate.
         await self.verify_tip_presence(pipette_id, TipPresenceStatus.PRESENT)
 
-        self._hardware_api.cache_tip(hw_mount, actual_tip_length)
-        await self._hardware_api.prepare_for_aspirate(hw_mount)
-
-        self._hardware_api.set_current_tiprack_diameter(
-            mount=hw_mount,
-            tiprack_diameter=nominal_tip_geometry.diameter,
-        )
+        await self.cache_tip(pipette_id, tip_geometry)
 
-        self._hardware_api.set_working_volume(
-            mount=hw_mount,
-            tip_volume=nominal_tip_geometry.volume,
-        )
+        await self._hardware_api.prepare_for_aspirate(hw_mount)
 
-        return TipGeometry(
-            length=actual_tip_length,
-            diameter=nominal_tip_geometry.diameter,
-            volume=nominal_tip_geometry.volume,
-        )
+        return tip_geometry
 
     async def drop_tip(self, pipette_id: str, home_after: Optional[bool]) -> None:
         """See documentation on abstract base class."""
@@ -279,11 +271,11 @@ async def drop_tip(self, pipette_id: str, home_after: Optional[bool]) -> None:
         self._hardware_api.remove_tip(hw_mount)
         self._hardware_api.set_current_tiprack_diameter(hw_mount, 0)
 
-    async def add_tip(self, pipette_id: str, tip: TipGeometry) -> None:
+    async def cache_tip(self, pipette_id: str, tip: TipGeometry) -> None:
         """See documentation on abstract base class."""
         hw_mount = self._state_view.pipettes.get_mount(pipette_id).to_hw_mount()
 
-        self._hardware_api.add_tip(mount=hw_mount, tip_length=tip.length)
+        self._hardware_api.cache_tip(mount=hw_mount, tip_length=tip.length)
 
         self._hardware_api.set_current_tiprack_diameter(
             mount=hw_mount,
@@ -422,12 +414,12 @@ async def drop_tip(
             expected_has_tip=True,
         )
 
-    async def add_tip(self, pipette_id: str, tip: TipGeometry) -> None:
+    async def cache_tip(self, pipette_id: str, tip: TipGeometry) -> None:
         """Add a tip using a virtual pipette.
 
         This should not be called when using virtual pipettes.
         """
-        assert False, "TipHandler.add_tip should not be used with virtual pipettes"
+        assert False, "TipHandler.cache_tip should not be used with virtual pipettes"
 
     async def verify_tip_presence(
         self,

api/src/opentrons/util/logging_config.py

@@ -5,7 +5,11 @@
 
 from opentrons.config import CONFIG, ARCHITECTURE, SystemArchitecture
 
-from opentrons_hardware.sensors import SENSOR_LOG_NAME
+if ARCHITECTURE is SystemArchitecture.BUILDROOT:
+    from opentrons_hardware.sensors import SENSOR_LOG_NAME
+else:
+    # we don't use the sensor log on ot2 or host
+    SENSOR_LOG_NAME = "unused"
 
 
 def _host_config(level_value: int) -> Dict[str, Any]:

api/tests/opentrons/protocol_engine/commands/test_move_labware.py

@@ -803,3 +803,38 @@ async def test_move_labware_raises_when_moving_fixed_trash_labware(
         match="Cannot move fixed trash labware 'My cool labware'.",
     ):
         await subject.execute(data)
+
+
+async def test_labware_raises_when_moved_onto_itself(
+    decoy: Decoy,
+    subject: MoveLabwareImplementation,
+    state_view: StateView,
+) -> None:
+    """It should raise when the OnLabwareLocation has the same labware ID as the labware being moved."""
+    data = MoveLabwareParams(
+        labwareId="the-same-labware-id",
+        newLocation=OnLabwareLocation(labwareId="a-cool-labware-id"),
+        strategy=LabwareMovementStrategy.MANUAL_MOVE_WITH_PAUSE,
+    )
+
+    decoy.when(state_view.labware.get(labware_id="the-same-labware-id")).then_return(
+        LoadedLabware(
+            id="the-same-labware-id",
+            loadName="load-name",
+            definitionUri="opentrons-test/load-name/1",
+            location=DeckSlotLocation(slotName=DeckSlotName.SLOT_4),
+            offsetId=None,
+        )
+    )
+
+    decoy.when(
+        state_view.geometry.ensure_location_not_occupied(
+            location=OnLabwareLocation(labwareId="a-cool-labware-id"),
+        )
+    ).then_return(OnLabwareLocation(labwareId="the-same-labware-id"))
+
+    with pytest.raises(
+        errors.LabwareMovementNotAllowedError,
+        match="Cannot move a labware onto itself.",
+    ):
+        await subject.execute(data)

api/tests/opentrons/protocol_engine/execution/test_hardware_stopper.py

@@ -158,7 +158,7 @@ async def test_hardware_stopping_sequence_no_tip_drop(
     decoy.verify(await hardware_api.stop(home_after=False), times=1)
 
     decoy.verify(
-        await mock_tip_handler.add_tip(
+        await mock_tip_handler.cache_tip(
             pipette_id="pipette-id",
             tip=TipGeometry(length=1.0, volume=2.0, diameter=3.0),
         ),
@@ -181,7 +181,7 @@ async def test_hardware_stopping_sequence_no_pipette(
     )
 
     decoy.when(
-        await mock_tip_handler.add_tip(
+        await mock_tip_handler.cache_tip(
             pipette_id="pipette-id",
             tip=TipGeometry(length=1.0, volume=2.0, diameter=3.0),
         ),
@@ -271,7 +271,7 @@ async def test_hardware_stopping_sequence_with_fixed_trash(
         await movement.home(
             axes=[MotorAxis.X, MotorAxis.Y, MotorAxis.LEFT_Z, MotorAxis.RIGHT_Z]
         ),
-        await mock_tip_handler.add_tip(
+        await mock_tip_handler.cache_tip(
             pipette_id="pipette-id",
             tip=TipGeometry(length=1.0, volume=2.0, diameter=3.0),
         ),
@@ -320,7 +320,7 @@ async def test_hardware_stopping_sequence_with_OT2_addressable_area(
         await movement.home(
             axes=[MotorAxis.X, MotorAxis.Y, MotorAxis.LEFT_Z, MotorAxis.RIGHT_Z]
         ),
-        await mock_tip_handler.add_tip(
+        await mock_tip_handler.cache_tip(
             pipette_id="pipette-id",
             tip=TipGeometry(length=1.0, volume=2.0, diameter=3.0),
         ),

api/tests/opentrons/protocol_engine/execution/test_tip_handler.py

@@ -289,10 +289,10 @@ async def test_add_tip(
         MountType.LEFT
     )
 
-    await subject.add_tip(pipette_id="pipette-id", tip=tip)
+    await subject.cache_tip(pipette_id="pipette-id", tip=tip)
 
     decoy.verify(
-        mock_hardware_api.add_tip(mount=Mount.LEFT, tip_length=50),
+        mock_hardware_api.cache_tip(mount=Mount.LEFT, tip_length=50),
         mock_hardware_api.set_current_tiprack_diameter(
             mount=Mount.LEFT,
             tiprack_diameter=5,