Merge branch 'edge' into fix_RQA-3434

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

@@ -79,49 +79,49 @@ jobs:
           files: ./coverage/lcov.info
           flags: protocol-designer
 
-  e2e-test:
-    name: 'pd e2e tests'
-    needs: ['js-unit-test']
-    timeout-minutes: 30
-    strategy:
-      matrix:
-        os: ['ubuntu-22.04']
-    runs-on: '${{ matrix.os }}'
-    steps:
-      - uses: 'actions/checkout@v3'
-        with:
-          fetch-depth: 0
-      # https://github.com/actions/checkout/issues/290
-      - name: 'Fix actions/checkout odd handling of tags'
-        if: startsWith(github.ref, 'refs/tags')
-        run: |
-          git fetch -f origin ${{ github.ref }}:${{ github.ref }}
-          git checkout ${{ github.ref }}
-      - uses: 'actions/setup-node@v3'
-        with:
-          node-version: '18.19.0'
-      - name: 'install udev for usb-detection'
-        if: startsWith(matrix.os, 'ubuntu')
-        run: |
-          # WORKAROUND: Remove microsoft debian repo due to https://github.com/microsoft/linux-package-repositories/issues/130. Remove line below after it is resolved
-          sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
-          sudo apt-get update && sudo apt-get install libudev-dev
-      - name: 'cache yarn cache'
-        uses: actions/cache@v3
-        with:
-          path: |
-            ${{ github.workspace }}/.yarn-cache
-            ${{ github.workspace }}/.npm-cache
-          key: js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-${{ hashFiles('yarn.lock') }}
-          restore-keys: |
-            js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-
-      - name: 'setup-js'
-        run: |
-          npm config set cache ./.npm-cache
-          yarn config set cache-folder ./.yarn-cache
-          make setup-js
-      - name: 'test-e2e'
-        run: make -C protocol-designer test-e2e
+  # e2e-test:
+  #   name: 'pd e2e tests'
+  #   needs: ['js-unit-test']
+  #   timeout-minutes: 30
+  #   strategy:
+  #     matrix:
+  #       os: ['ubuntu-22.04']
+  #   runs-on: '${{ matrix.os }}'
+  #   steps:
+  #     - uses: 'actions/checkout@v3'
+  #       with:
+  #         fetch-depth: 0
+  #     # https://github.com/actions/checkout/issues/290
+  #     - name: 'Fix actions/checkout odd handling of tags'
+  #       if: startsWith(github.ref, 'refs/tags')
+  #       run: |
+  #         git fetch -f origin ${{ github.ref }}:${{ github.ref }}
+  #         git checkout ${{ github.ref }}
+  #     - uses: 'actions/setup-node@v3'
+  #       with:
+  #         node-version: '18.19.0'
+  #     - name: 'install udev for usb-detection'
+  #       if: startsWith(matrix.os, 'ubuntu')
+  #       run: |
+  #         # WORKAROUND: Remove microsoft debian repo due to https://github.com/microsoft/linux-package-repositories/issues/130. Remove line below after it is resolved
+  #         sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
+  #         sudo apt-get update && sudo apt-get install libudev-dev
+  #     - name: 'cache yarn cache'
+  #       uses: actions/cache@v3
+  #       with:
+  #         path: |
+  #           ${{ github.workspace }}/.yarn-cache
+  #           ${{ github.workspace }}/.npm-cache
+  #         key: js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-${{ hashFiles('yarn.lock') }}
+  #         restore-keys: |
+  #           js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-
+  #     - name: 'setup-js'
+  #       run: |
+  #         npm config set cache ./.npm-cache
+  #         yarn config set cache-folder ./.yarn-cache
+  #         make setup-js
+  #     - name: 'test-e2e'
+  #       run: make -C protocol-designer test-e2e
   build-pd:
     name: 'build protocol designer artifact'
     needs: ['js-unit-test']

abr-testing/abr_testing/data_collection/abr_calibration_logs.py

@@ -82,7 +82,7 @@ def module_helper(
                 y = one_module["moduleOffset"]["offset"].get("y", "")
                 z = one_module["moduleOffset"]["offset"].get("z", "")
             except KeyError:
-                pass
+                continue
             if mod_serial in module_sheet_serials and modified in module_modify_dates:
                 continue
             module_row = (

api-client/src/runs/types.ts

@@ -8,6 +8,7 @@ import type {
   RunTimeCommand,
   RunTimeParameter,
   NozzleLayoutConfig,
+  OnDeckLabwareLocation,
 } from '@opentrons/shared-data'
 import type { ResourceLink, ErrorDetails } from '../types'
 export * from './commands/types'
@@ -117,7 +118,9 @@ export interface Runs {
 }
 
 export interface RunCurrentStateData {
+  estopEngaged: boolean
   activeNozzleLayouts: Record<string, NozzleLayoutValues> // keyed by pipetteId
+  placeLabwareState?: PlaceLabwareState
 }
 
 export const RUN_ACTION_TYPE_PLAY: 'play' = 'play'
@@ -209,3 +212,9 @@ export interface NozzleLayoutValues {
   activeNozzles: string[]
   config: NozzleLayoutConfig
 }
+
+export interface PlaceLabwareState {
+  labwareId: string
+  location: OnDeckLabwareLocation
+  shouldPlaceDown: boolean
+}

api/release-notes.md

@@ -8,6 +8,24 @@ By installing and using Opentrons software, you agree to the Opentrons End-User
 
 ---
 
+## Opentrons Robot Software Changes in 8.2.0
+
+Welcome to the v8.2.0 release of the Opentrons robot software! This release adds support for the Opentrons Absorbance Plate Reader Module.
+
+### New Features
+
+- Create and run Python protocols that use the Opentrons Absorbance Plate Reader.
+
+### Improved Features
+
+- Liquid presence detection no longer checks for liquid before every aspiration in a `mix()` command.
+
+### Bug Fixes
+
+- Error recovery no longer causes an `AssertionError` when a Python protocol changes the pipette speed.
+
+---
+
 ## Opentrons Robot Software Changes in 8.1.0
 
 Welcome to the v8.1.0 release of the Opentrons robot software!

api/src/opentrons/hardware_control/modules/absorbance_reader.py

@@ -272,12 +272,8 @@ def usb_port(self) -> USBPort:
         return self._usb_port
 
     async def deactivate(self, must_be_running: bool = True) -> None:
-        """Deactivate the module.
-
-        Contains an override to the `wait_for_is_running` step in cases where the
-        module must be deactivated regardless of context."""
-        await self._poller.stop()
-        await self._driver.disconnect()
+        """Deactivate the module."""
+        pass
 
     async def wait_for_is_running(self) -> None:
         if not self.is_simulated:
@@ -336,7 +332,8 @@ async def cleanup(self) -> None:
         Clean up, i.e. stop pollers, disconnect serial, etc in preparation for
         object destruction.
         """
-        await self.deactivate()
+        await self._poller.stop()
+        await self._driver.disconnect()
 
     async def set_sample_wavelength(
         self,

api/src/opentrons/motion_planning/__init__.py

@@ -6,6 +6,7 @@
     MINIMUM_Z_MARGIN,
     get_waypoints,
     get_gripper_labware_movement_waypoints,
+    get_gripper_labware_placement_waypoints,
 )
 
 from .types import Waypoint, MoveType
@@ -27,4 +28,5 @@
     "ArcOutOfBoundsError",
     "get_waypoints",
     "get_gripper_labware_movement_waypoints",
+    "get_gripper_labware_placement_waypoints",
 ]

api/src/opentrons/motion_planning/waypoints.py

@@ -181,3 +181,35 @@ def get_gripper_labware_movement_waypoints(
             )
         )
     return waypoints_with_jaw_status
+
+
+def get_gripper_labware_placement_waypoints(
+    to_labware_center: Point,
+    gripper_home_z: float,
+    drop_offset: Optional[Point],
+) -> List[GripperMovementWaypointsWithJawStatus]:
+    """Get waypoints for placing labware using a gripper."""
+    drop_offset = drop_offset or Point()
+
+    drop_location = to_labware_center + Point(
+        drop_offset.x, drop_offset.y, drop_offset.z
+    )
+
+    post_drop_home_pos = Point(drop_location.x, drop_location.y, gripper_home_z)
+
+    return [
+        GripperMovementWaypointsWithJawStatus(
+            position=Point(drop_location.x, drop_location.y, gripper_home_z),
+            jaw_open=False,
+            dropping=False,
+        ),
+        GripperMovementWaypointsWithJawStatus(
+            position=drop_location, jaw_open=False, dropping=False
+        ),
+        # Gripper ungrips here
+        GripperMovementWaypointsWithJawStatus(
+            position=post_drop_home_pos,
+            jaw_open=True,
+            dropping=True,
+        ),
+    ]

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

@@ -567,6 +567,7 @@ class AbsorbanceReaderCore(ModuleCore, AbstractAbsorbanceReaderCore):
 
     _sync_module_hardware: SynchronousAdapter[hw_modules.AbsorbanceReader]
     _initialized_value: Optional[List[int]] = None
+    _ready_to_initialize: bool = False
 
     def initialize(
         self,
@@ -575,6 +576,11 @@ def initialize(
         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."
+            )
+
         # TODO: check that the wavelengths are within the supported wavelengths
         self._engine_client.execute_command(
             cmd.absorbance_reader.InitializeParams(
@@ -586,7 +592,7 @@ def initialize(
         )
         self._initialized_value = wavelengths
 
-    def read(self, filename: Optional[str]) -> Dict[int, Dict[str, float]]:
+    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
@@ -633,6 +639,7 @@ def close_lid(
                 moduleId=self.module_id,
             )
         )
+        self._ready_to_initialize = True
 
     def open_lid(self) -> None:
         """Close the Absorbance Reader's lid."""

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

@@ -449,9 +449,10 @@ def load_module(
 
         # When the protocol engine is created, we add Module Lids as part of the deck fixed labware
         # If a valid module exists in the deck config. For analysis, we add the labware here since
-        # deck fixed labware is not created under the same conditions.
-        if self._engine_client.state.config.use_virtual_modules:
-            self._load_virtual_module_lid(module_core)
+        # deck fixed labware is not created under the same conditions. We also need to inject the Module
+        # lids when the module isnt already on the deck config, like when adding a new
+        # module during a protocol setup.
+        self._load_virtual_module_lid(module_core)
 
         self._module_cores_by_id[module_core.module_id] = module_core
 
@@ -461,20 +462,24 @@ def _load_virtual_module_lid(
         self, module_core: Union[ModuleCore, NonConnectedModuleCore]
     ) -> None:
         if isinstance(module_core, AbsorbanceReaderCore):
-            lid = self._engine_client.execute_command_without_recovery(
-                cmd.LoadLabwareParams(
-                    loadName="opentrons_flex_lid_absorbance_plate_reader_module",
-                    location=ModuleLocation(moduleId=module_core.module_id),
-                    namespace="opentrons",
-                    version=1,
-                    displayName="Absorbance Reader Lid",
-                )
+            substate = self._engine_client.state.modules.get_absorbance_reader_substate(
+                module_core.module_id
             )
+            if substate.lid_id is None:
+                lid = self._engine_client.execute_command_without_recovery(
+                    cmd.LoadLabwareParams(
+                        loadName="opentrons_flex_lid_absorbance_plate_reader_module",
+                        location=ModuleLocation(moduleId=module_core.module_id),
+                        namespace="opentrons",
+                        version=1,
+                        displayName="Absorbance Reader Lid",
+                    )
+                )
 
-            self._engine_client.add_absorbance_reader_lid(
-                module_id=module_core.module_id,
-                lid_id=lid.labwareId,
-            )
+                self._engine_client.add_absorbance_reader_lid(
+                    module_id=module_core.module_id,
+                    lid_id=lid.labwareId,
+                )
 
     def _create_non_connected_module_core(
         self, load_module_result: LoadModuleResult

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, filename: Optional[str]) -> Dict[int, Dict[str, float]]:
+    def read(self, filename: Optional[str] = None) -> Dict[int, Dict[str, float]]:
         """Get an absorbance reading from the Absorbance Reader."""
 
     @abstractmethod

api/src/opentrons/protocol_api/module_contexts.py

@@ -1035,7 +1035,9 @@ def initialize(
         )
 
     @requires_version(2, 21)
-    def read(self, export_filename: Optional[str]) -> Dict[int, Dict[str, float]]:
+    def read(
+        self, export_filename: Optional[str] = None
+    ) -> Dict[int, Dict[str, float]]:
         """Initiate read on the Absorbance Reader.
 
         Returns a dictionary of wavelengths to dictionary of values ordered by well name.

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

@@ -392,6 +392,7 @@
         unsafe.UpdatePositionEstimators,
         unsafe.UnsafeEngageAxes,
         unsafe.UnsafeUngripLabware,
+        unsafe.UnsafePlaceLabware,
     ],
     Field(discriminator="commandType"),
 ]
@@ -469,6 +470,7 @@
     unsafe.UpdatePositionEstimatorsParams,
     unsafe.UnsafeEngageAxesParams,
     unsafe.UnsafeUngripLabwareParams,
+    unsafe.UnsafePlaceLabwareParams,
 ]
 
 CommandType = Union[
@@ -544,6 +546,7 @@
     unsafe.UpdatePositionEstimatorsCommandType,
     unsafe.UnsafeEngageAxesCommandType,
     unsafe.UnsafeUngripLabwareCommandType,
+    unsafe.UnsafePlaceLabwareCommandType,
 ]
 
 CommandCreate = Annotated[
@@ -620,6 +623,7 @@
         unsafe.UpdatePositionEstimatorsCreate,
         unsafe.UnsafeEngageAxesCreate,
         unsafe.UnsafeUngripLabwareCreate,
+        unsafe.UnsafePlaceLabwareCreate,
     ],
     Field(discriminator="commandType"),
 ]
@@ -697,6 +701,7 @@
     unsafe.UpdatePositionEstimatorsResult,
     unsafe.UnsafeEngageAxesResult,
     unsafe.UnsafeUngripLabwareResult,
+    unsafe.UnsafePlaceLabwareResult,
 ]