Merge branch 'edge' into PLAT-451-handle-estop-with-plate-reader

.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

@@ -113,7 +113,7 @@ export interface GetRunsParams {
 }
 
 export interface Runs {
-  data: RunData[]
+  data: readonly RunData[]
   links: RunsLinks
 }
 
@@ -128,12 +128,15 @@ 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
@@ -175,7 +178,11 @@ 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/docs/v2/new_examples.rst

@@ -383,7 +383,7 @@ Opentrons electronic pipettes can do some things that a human cannot do with a p
                     location=3)
                 p300 = protocol.load_instrument(
                     instrument_name="p300_single", 
-                    mount="right",
+                    mount="left",
                     tip_racks=[tiprack_1])
 
                 p300.pick_up_tip()
@@ -442,13 +442,13 @@ This protocol dispenses diluent to all wells of a Corning 96-well plate. Next, i
                     source = reservoir.wells()[i]
                     row = plate.rows()[i]
 
-                # transfer 30 µL of source to first well in column
-                pipette.transfer(30, source, row[0], mix_after=(3, 25))
+                    # transfer 30 µL of source to first well in column
+                    pipette.transfer(30, source, row[0], mix_after=(3, 25))
 
-                # dilute the sample down the column
-                pipette.transfer(
-                    30, row[:11], row[1:],
-                    mix_after=(3, 25))
+                    # dilute the sample down the column
+                    pipette.transfer(
+                        30, row[:11], row[1:],
+                        mix_after=(3, 25))
     
     .. tab:: OT-2
 
@@ -474,7 +474,7 @@ This protocol dispenses diluent to all wells of a Corning 96-well plate. Next, i
                     location=4)
                 p300 = protocol.load_instrument(
                     instrument_name="p300_single",
-                    mount="right",
+                    mount="left",
                     tip_racks=[tiprack_1, tiprack_2])
                 # Dispense diluent
                 p300.distribute(50, reservoir["A12"], plate.wells())
@@ -483,16 +483,15 @@ This protocol dispenses diluent to all wells of a Corning 96-well plate. Next, i
                 for i in range(8):
                     # save the source well and destination column to variables
                     source = reservoir.wells()[i]
-                    source = reservoir.wells()[i]
                     row = plate.rows()[i]
 
-                # transfer 30 µL of source to first well in column
-                p300.transfer(30, source, row[0], mix_after=(3, 25))
+                    # transfer 30 µL of source to first well in column
+                    p300.transfer(30, source, row[0], mix_after=(3, 25))
 
-                # dilute the sample down the column
-                p300.transfer(
-                    30, row[:11], row[1:],
-                    mix_after=(3, 25))
+                    # dilute the sample down the column
+                    p300.transfer(
+                        30, row[:11], row[1:],
+                        mix_after=(3, 25))
 
 Notice here how the code sample loops through the rows and uses slicing to distribute the diluent. For information about these features, see the Loops and Air Gaps examples above. See also, the :ref:`tutorial-commands` section of the Tutorial.
 

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/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]:
@@ -125,7 +129,7 @@ def _buildroot_config(level_value: int) -> Dict[str, Any]:
             },
             "sensor": {
                 "class": "logging.handlers.RotatingFileHandler",
-                "formatter": "basic",
+                "formatter": "message_only",
                 "filename": sensor_log_filename,
                 "maxBytes": 1000000,
                 "level": logging.DEBUG,

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,

app/src/assets/localization/en/pipette_wizard_flows.json

@@ -49,7 +49,7 @@
   "install_probe": "Take the calibration probe from its storage location. Ensure its collar is unlocked. Push the pipette ejector up and press the probe firmly onto the <bold>{{location}}</bold> pipette nozzle. Twist the collar to lock the probe. Test that the probe is secure by gently pulling it back and forth.",
   "loose_detach": "Loosen screws and detach ",
   "move_gantry_to_front": "Move gantry to front",
-  "must_detach_mounting_plate": "You must detach the mounting plate and reattach the z-axis carraige before using other pipettes. We do not recommend exiting this process before completion.",
+  "must_detach_mounting_plate": "You must detach the mounting plate and reattach the z-axis carriage before using other pipettes. We do not recommend exiting this process before completion.",
   "name_and_volume_detected": "{{name}} Pipette Detected",
   "next": "next",
   "ninety_six_channel": "{{ninetySix}} pipette",