Merge branch 'release-at-v7.2.1-into-edge' into edge

api/release-notes.md

@@ -6,6 +6,19 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
+## Opentrons Robot Software Changes in 7.2.1
+
+Welcome to the v7.2.1 release of the Opentrons robot software!
+
+### Bug Fixes
+
+- Fixed an issue where OT-2 tip length calibrations created before v4.1.0 would cause a "missing calibration data" error that you could only resolve by resetting calibration.
+- Fixed collision prediction being too conservative in certain conditions on Flex, leading to errors even when collisions wouldn't take place.
+- Flex now properly homes after an instrument collision.
+- `opentrons_simulate` now outputs entries for commands that drop tips in the default trash container in protocols that specify Python API version 2.16 or newer.
+
+---
+
 ## Opentrons Robot Software Changes in 7.2.0
 
 Welcome to the v7.2.0 release of the Opentrons robot software!

api/src/opentrons/calibration_storage/ot2/deck_attitude.py

@@ -79,7 +79,7 @@ def get_robot_deck_attitude() -> Optional[v1.DeckCalibrationModel]:
         pass
     except (json.JSONDecodeError, ValidationError):
         log.warning(
-            "Deck calibration is malformed. Please factory reset your calibrations."
+            "Deck calibration is malformed. Please factory reset your calibrations.",
+            exc_info=True,
         )
-        pass
     return None

api/src/opentrons/calibration_storage/ot2/pipette_offset.py

@@ -92,7 +92,8 @@ def get_pipette_offset(
         return None
     except (json.JSONDecodeError, ValidationError):
         log.warning(
-            f"Malformed calibrations for {pipette_id} on {mount}. Please factory reset your calibrations."
+            f"Malformed calibrations for {pipette_id} on {mount}. Please factory reset your calibrations.",
+            exc_info=True,
         )
         # TODO: Delete the bad calibration here maybe?
         return None

api/src/opentrons/calibration_storage/ot2/tip_length.py

@@ -37,28 +37,43 @@ def _convert_tip_length_model_to_dict(
 def tip_lengths_for_pipette(
     pipette_id: str,
 ) -> typing.Dict[LabwareUri, v1.TipLengthModel]:
-    tip_lengths = {}
     try:
         tip_length_filepath = config.get_tip_length_cal_path() / f"{pipette_id}.json"
         all_tip_lengths_for_pipette = io.read_cal_file(tip_length_filepath)
-        for tiprack_identifier, data in all_tip_lengths_for_pipette.items():
-            # We normally key these calibrations by their tip rack URI,
-            # but older software had them keyed by their tip rack hash.
-            # Migrate from the old format, if necessary.
-            if "/" not in tiprack_identifier:
-                data["definitionHash"] = tiprack_identifier
-                tiprack_identifier = data.pop("uri")
-            try:
-                tip_lengths[LabwareUri(tiprack_identifier)] = v1.TipLengthModel(**data)
-            except (json.JSONDecodeError, ValidationError):
-                log.warning(
-                    f"Tip length calibration is malformed for {tiprack_identifier} on {pipette_id}"
-                )
-                pass
-        return tip_lengths
     except FileNotFoundError:
         log.debug(f"Tip length calibrations not found for {pipette_id}")
-        return tip_lengths
+        return {}
+    except json.JSONDecodeError:
+        log.warning(
+            f"Tip length calibration is malformed for {pipette_id}", exc_info=True
+        )
+        return {}
+
+    tip_lengths: typing.Dict[LabwareUri, v1.TipLengthModel] = {}
+
+    for tiprack_identifier, data in all_tip_lengths_for_pipette.items():
+        # We normally key these calibrations by their tip rack URI,
+        # but older software had them keyed by their tip rack hash.
+        # Migrate from the old format, if necessary.
+        tiprack_identifier_is_uri = "/" in tiprack_identifier
+        if not tiprack_identifier_is_uri:
+            data["definitionHash"] = tiprack_identifier
+            uri = data.pop("uri", None)
+            if uri is None:
+                # We don't have a way to migrate old records without a URI,
+                # so skip over them.
+                continue
+            else:
+                tiprack_identifier = uri
+
+        try:
+            tip_lengths[LabwareUri(tiprack_identifier)] = v1.TipLengthModel(**data)
+        except ValidationError:
+            log.warning(
+                f"Tip length calibration is malformed for {tiprack_identifier} on {pipette_id}",
+                exc_info=True,
+            )
+    return tip_lengths
 
 
 def load_tip_length_calibration(

api/src/opentrons/calibration_storage/ot3/deck_attitude.py

@@ -77,7 +77,7 @@ def get_robot_belt_attitude() -> Optional[v1.BeltCalibrationModel]:
         pass
     except (json.JSONDecodeError, ValidationError):
         log.warning(
-            "Belt calibration is malformed. Please factory reset your calibrations."
+            "Belt calibration is malformed. Please factory reset your calibrations.",
+            exc_info=True,
         )
-        pass
     return None

api/src/opentrons/calibration_storage/ot3/module_offset.py

@@ -108,7 +108,8 @@ def get_module_offset(
         return None
     except (json.JSONDecodeError, ValidationError):
         log.warning(
-            f"Malformed calibrations for {module_id} on slot {slot}. Please factory reset your calibrations."
+            f"Malformed calibrations for {module_id} on slot {slot}. Please factory reset your calibrations.",
+            exc_info=True,
         )
         return None
 
@@ -130,7 +131,8 @@ def load_all_module_offsets() -> List[v1.ModuleOffsetModel]:
             )
         except (json.JSONDecodeError, ValidationError):
             log.warning(
-                f"Malformed module calibrations for {file}. Please factory reset your calibrations."
+                f"Malformed module calibrations for {file}. Please factory reset your calibrations.",
+                exc_info=True,
             )
             continue
     return calibrations

api/src/opentrons/calibration_storage/ot3/pipette_offset.py

@@ -89,6 +89,7 @@ def get_pipette_offset(
         return None
     except (json.JSONDecodeError, ValidationError):
         log.warning(
-            f"Malformed calibrations for {pipette_id} on {mount}. Please factory reset your calibrations."
+            f"Malformed calibrations for {pipette_id} on {mount}. Please factory reset your calibrations.",
+            exc_info=True,
         )
         return None

api/src/opentrons/config/robot_configs.py

@@ -148,7 +148,7 @@ def _load_json(filename: Union[str, Path]) -> Dict[str, Any]:
         log.warning("{0} not found. Loading defaults".format(filename))
         res = {}
     except json.decoder.JSONDecodeError:
-        log.warning("{0} is corrupt. Loading defaults".format(filename))
+        log.warning("{0} is corrupt. Loading defaults".format(filename), exc_info=True)
         res = {}
     return cast(Dict[str, Any], res)
 

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

@@ -78,9 +78,6 @@ def __init__(self, message: str) -> None:
     x=A12_column_back_right_bound.x - _NOZZLE_PITCH * 11, y=506.2
 )
 
-# Arbitrary safety margin in z-direction
-Z_SAFETY_MARGIN = 10
-
 _FLEX_TC_LID_BACK_LEFT_PT = Point(
     x=FLEX_TC_LID_COLLISION_ZONE["back_left"]["x"],
     y=FLEX_TC_LID_COLLISION_ZONE["back_left"]["y"],
@@ -332,7 +329,7 @@ def _slot_has_potential_colliding_object(
             slot_highest_z = engine_state.geometry.get_highest_z_in_slot(
                 StagingSlotLocation(slotName=surrounding_slot)
             )
-        return slot_highest_z + Z_SAFETY_MARGIN > pipette_bounds[0].z
+        return slot_highest_z >= pipette_bounds[0].z
     return False
 
 

api/src/opentrons/protocol_api/instrument_context.py

@@ -1149,6 +1149,7 @@ def home_plunger(self) -> InstrumentContext:
         self._core.home_plunger()
         return self
 
+    # TODO (spp, 2024-03-08): verify if ok to & change source & dest types to AdvancedLiquidHandling
     @publisher.publish(command=cmds.distribute)
     @requires_version(2, 0)
     def distribute(
@@ -1188,6 +1189,7 @@ def distribute(
 
         return self.transfer(volume, source, dest, **kwargs)
 
+    # TODO (spp, 2024-03-08): verify if ok to & change source & dest types to AdvancedLiquidHandling
     @publisher.publish(command=cmds.consolidate)
     @requires_version(2, 0)
     def consolidate(

api/tests/opentrons/calibration_storage/test_tip_length_ot2.py

@@ -113,3 +113,31 @@ def test_delete_all_tip_calibration(starting_calibration_data: Any) -> None:
     clear_tip_length_calibration()
     assert tip_lengths_for_pipette("pip1") == {}
     assert tip_lengths_for_pipette("pip2") == {}
+
+
+def test_uriless_calibrations_are_dropped(ot_config_tempdir: object) -> None:
+    """Legacy records without a `uri` field should be silently ignored."""
+
+    data = {
+        "ed323db6ca1ddf197aeb20667c1a7a91c89cfb2f931f45079d483928da056812": {
+            "tipLength": 123,
+            "lastModified": "2021-01-11T00:34:29.291073+00:00",
+            "source": "user",
+            "status": {"markedBad": False},
+        },
+        "130e17bb7b2f0c0472dcc01c1ff6f600ca1a6f9f86a90982df56c4bf43776824": {
+            "tipLength": 456,
+            "lastModified": "2021-05-12T22:16:14.249567+00:00",
+            "source": "user",
+            "status": {"markedBad": False},
+            "uri": "opentrons/opentrons_96_filtertiprack_200ul/1",
+        },
+    }
+
+    io.save_to_file(config.get_tip_length_cal_path(), "pipette1234", data)
+    result = tip_lengths_for_pipette("pipette1234")
+    assert len(result) == 1
+    assert (
+        result[LabwareUri("opentrons/opentrons_96_filtertiprack_200ul/1")].tipLength
+        == 456
+    )

api/tests/opentrons/protocol_api_integration/test_pipette_movement_deck_conflicts.py

@@ -99,6 +99,36 @@ def test_deck_conflicts_for_96_ch_a12_column_configuration() -> None:
     instrument.dispense(50, accessible_plate.wells_by_name()["A1"])
 
 
+@pytest.mark.ot3_only
+def test_close_shave_deck_conflicts_for_96_ch_a12_column_configuration() -> None:
+    """Shouldn't raise errors for "almost collision"s."""
+    protocol_context = simulate.get_protocol_api(version="2.16", robot_type="Flex")
+    res12 = protocol_context.load_labware("nest_12_reservoir_15ml", "C3")
+
+    # Mag block and tiprack adapter are very close to the destination reservoir labware
+    protocol_context.load_module("magneticBlockV1", "D2")
+    protocol_context.load_labware(
+        "opentrons_flex_96_tiprack_200ul",
+        "B3",
+        adapter="opentrons_flex_96_tiprack_adapter",
+    )
+    tiprack_8 = protocol_context.load_labware("opentrons_flex_96_tiprack_200ul", "B2")
+    hs = protocol_context.load_module("heaterShakerModuleV1", "D1")
+    hs_adapter = hs.load_adapter("opentrons_96_deep_well_adapter")
+    deepwell = hs_adapter.load_labware("nest_96_wellplate_2ml_deep")
+    protocol_context.load_trash_bin("A3")
+    p1000_96 = protocol_context.load_instrument("flex_96channel_1000")
+    p1000_96.configure_nozzle_layout(style=COLUMN, start="A12", tip_racks=[tiprack_8])
+
+    hs.close_labware_latch()  # type: ignore[union-attr]
+    p1000_96.distribute(
+        15,
+        res12.wells()[0],
+        deepwell.rows()[0],
+        disposal_vol=0,
+    )
+
+
 @pytest.mark.ot3_only
 def test_deck_conflicts_for_96_ch_a1_column_configuration() -> None:
     """It should raise errors for expected deck conflicts."""

app-shell/build/release-notes.md

@@ -6,6 +6,16 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
+## Opentrons App Changes in 7.2.1
+
+Welcome to the v7.2.1 release of the Opentrons App!
+
+### Bug Fixes
+
+- Fixed a memory leak that could cause the app to crash.
+
+---
+
 ## Opentrons App Changes in 7.2.0
 
 Welcome to the v7.2.0 release of the Opentrons App!

app/src/organisms/Devices/ProtocolRun/SetupGripperCalibrationItem.tsx

@@ -26,7 +26,7 @@ export function SetupGripperCalibrationItem({
   gripperData,
   runId,
 }: SetupGripperCalibrationItemProps): JSX.Element | null {
-  const { t } = useTranslation('protocol_setup')
+  const { t, i18n } = useTranslation('protocol_setup')
   const [
     openWizardFlowType,
     setOpenWizardFlowType,
@@ -47,7 +47,7 @@ export function SetupGripperCalibrationItem({
             setOpenWizardFlowType(GRIPPER_FLOW_TYPES.ATTACH)
           }}
         >
-          {t('attach_gripper')}
+          {i18n.format(t('attach_gripper'), 'capitalize')}
         </TertiaryButton>
       </Flex>
     )

app/src/redux/shell/remote.ts

@@ -34,20 +34,50 @@ export function appShellRequestor<Data>(
   return remote.ipcRenderer.invoke('usb:request', configProxy)
 }
 
-export function appShellListener(
-  hostname: string | null,
-  topic: NotifyTopic,
+interface CallbackStore {
+  [hostname: string]: {
+    [topic in NotifyTopic]: Array<(data: NotifyResponseData) => void>
+  }
+}
+const callbackStore: CallbackStore = {}
+
+interface AppShellListener {
+  hostname: string
+  topic: NotifyTopic
   callback: (data: NotifyResponseData) => void
-): void {
-  remote.ipcRenderer.on(
-    'notify',
-    (_, shellHostname, shellTopic, shellMessage) => {
-      if (
-        hostname === shellHostname &&
-        (topic === shellTopic || shellTopic === 'ALL_TOPICS')
-      ) {
-        callback(shellMessage)
+  isDismounting?: boolean
+}
+export function appShellListener({
+  hostname,
+  topic,
+  callback,
+  isDismounting = false,
+}: AppShellListener): CallbackStore {
+  if (isDismounting) {
+    const callbacks = callbackStore[hostname]?.[topic]
+    if (callbacks != null) {
+      callbackStore[hostname][topic] = callbacks.filter(cb => cb !== callback)
+      if (!callbackStore[hostname][topic].length) {
+        // eslint-disable-next-line @typescript-eslint/no-dynamic-delete
+        delete callbackStore[hostname][topic]
+        if (!Object.keys(callbackStore[hostname]).length) {
+          // eslint-disable-next-line @typescript-eslint/no-dynamic-delete
+          delete callbackStore[hostname]
+        }
       }
     }
-  )
+  } else {
+    callbackStore[hostname] = callbackStore[hostname] ?? {}
+    callbackStore[hostname][topic] ??= []
+    callbackStore[hostname][topic].push(callback)
+  }
+  return callbackStore
 }
+
+// Instantiate the notify listener at runtime.
+remote.ipcRenderer.on(
+  'notify',
+  (_, shellHostname, shellTopic, shellMessage) => {
+    callbackStore[shellHostname]?.[shellTopic]?.forEach(cb => cb(shellMessage))
+  }
+)

app/src/redux/shell/types.ts

@@ -6,19 +6,19 @@ export interface Remote {
   ipcRenderer: {
     invoke: (channel: string, ...args: unknown[]) => Promise<any>
     send: (channel: string, ...args: unknown[]) => void
-    on: (
-      channel: string,
-      listener: (
-        event: IpcMainEvent,
-        hostname: string,
-        topic: NotifyTopic,
-        message: NotifyResponseData | NotifyNetworkError,
-        ...args: unknown[]
-      ) => void
-    ) => void
+    on: (channel: string, listener: IpcListener) => void
+    off: (channel: string, listener: IpcListener) => void
   }
 }
 
+export type IpcListener = (
+  event: IpcMainEvent,
+  hostname: string,
+  topic: NotifyTopic,
+  message: NotifyResponseData | NotifyNetworkError,
+  ...args: unknown[]
+) => void
+
 export interface NotifyRefetchData {
   refetchUsingHTTP: boolean
 }