Merge branch 'edge' into fix_text-area-style-issue

analyses-snapshot-testing/Makefile

@@ -3,12 +3,12 @@ CACHEBUST ?= $(shell date +%s)
 ANALYSIS_REF ?= edge
 PROTOCOL_NAMES ?= all
 OVERRIDE_PROTOCOL_NAMES ?= all
-OPENTRONS_VERSION ?= edge
+LOCAL_IMAGE_TAG ?= local
+ANALYZER_IMAGE_NAME ?= opentrons-analysis
 
-export OPENTRONS_VERSION # used for server
-export ANALYSIS_REF # used for analysis and snapshot test
-export PROTOCOL_NAMES # used for the snapshot test
-export OVERRIDE_PROTOCOL_NAMES # used for the snapshot test
+export ANALYSIS_REF # tag, branch or commit for the opentrons repository. Used as the image tag for the analyzer image
+export PROTOCOL_NAMES # tell the test which protocols to run
+export OVERRIDE_PROTOCOL_NAMES # tell the test which override protocols to run
 
 ifeq ($(CI), true)
 	PYTHON=python
@@ -93,23 +93,47 @@ build-base-image:
 
 .PHONY: build-opentrons-analysis
 build-opentrons-analysis:
-	@echo "Building docker image for $(ANALYSIS_REF)"
-	@echo "The image will be named opentrons-analysis:$(ANALYSIS_REF)"
-	@echo "If you want to build a different version, run 'make build-opentrons-analysis ANALYSIS_REF=<version>'"
-	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) --build-arg ANALYSIS_REF=$(ANALYSIS_REF) --build-arg CACHEBUST=$(CACHEBUST) -t opentrons-analysis:$(ANALYSIS_REF) -f citools/Dockerfile.analyze citools/.
+	@echo "Building docker image for opentrons repository reference$(ANALYSIS_REF)"
+	@echo "The image will be named $(ANALYZER_IMAGE_NAME):$(ANALYSIS_REF)"
+	@echo "If you want to build a different version, run 'make build-opentrons-analysis ANALYSIS_REF=<tag, branch, or commit>'"
+	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) --build-arg ANALYSIS_REF=$(ANALYSIS_REF) --build-arg CACHEBUST=$(CACHEBUST) -t $(ANALYZER_IMAGE_NAME):$(ANALYSIS_REF) -f citools/Dockerfile.analyze citools/.
 
-.PHONY: local-build
-local-build:
+.PHONY: build-local
+build-local:
 	@echo "Building docker image for your local opentrons code"
-	@echo "The image will be named opentrons-analysis:local"
-	@echo "For a fresh build, run 'make local-build NO_CACHE=1'"
-	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) $(BUILD_FLAGS) -t opentrons-analysis:local -f citools/Dockerfile.local .. || true
+	@echo "This image will be named $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG)"
+	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) -t $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG) -f citools/Dockerfile.local ..
 	@echo "Build complete"
 
+.PHONY: snapshot-test-local
+snapshot-test-local: ANALYSIS_REF=$(LOCAL_IMAGE_TAG)
+snapshot-test-local: build-base-image build-local
+	@echo "This target is overriding the ANALYSIS_REF to the LOCAL_IMAGE_TAG: $(LOCAL_IMAGE_TAG)"
+	@echo "ANALYSIS_REF is $(ANALYSIS_REF). The the test maps this env variable to the image tag."
+	@echo "The image the test will use is $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG)"
+	@echo "PROTOCOL_NAMES is $(PROTOCOL_NAMES)"
+	@echo "OVERRIDE_PROTOCOL_NAMES is $(OVERRIDE_PROTOCOL_NAMES)"
+	$(PYTHON) -m pipenv run pytest -k analyses_snapshot_test -vv
+
+.PHONY: snapshot-test-update-local
+snapshot-test-update-local: ANALYSIS_REF=$(LOCAL_IMAGE_TAG)
+snapshot-test-update-local: build-base-image build-local
+	@echo "This target is overriding the ANALYSIS_REF to the LOCAL_IMAGE_TAG: $(LOCAL_IMAGE_TAG)"
+	@echo "ANALYSIS_REF is $(ANALYSIS_REF). The the test maps this env variable to the image tag."
+	@echo "The image the test will use is $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG)"
+	@echo "PROTOCOL_NAMES is $(PROTOCOL_NAMES)"
+	@echo "OVERRIDE_PROTOCOL_NAMES is $(OVERRIDE_PROTOCOL_NAMES)"
+	$(PYTHON) -m pipenv run pytest -k analyses_snapshot_test --snapshot-update
+
 .PHONY: generate-protocols
 generate-protocols:
 	$(PYTHON) -m pipenv run python -m automation.data.protocol_registry
 
+# Tools for running the robot server in a container
+
+OPENTRONS_VERSION ?= edge
+export OPENTRONS_VERSION # used for the robot server image as the tag, branch or commit for the opentrons repository
+
 .PHONY: build-rs
 build-rs:
 	@echo "Building docker image for opentrons-robot-server:$(OPENTRONS_VERSION)"

analyses-snapshot-testing/README.md

@@ -4,7 +4,7 @@
 
 1. Follow the instructions in [DEV_SETUP.md](../DEV_SETUP.md)
 1. `cd analyses-snapshot-testing`
-1. use pyenv to install python 3.12 and set it as the local python version for this directory
+1. use pyenv to install python 3.13 and set it as the local python version for this directory
 1. `make setup`
 1. Have docker installed and ready
 
@@ -72,10 +72,17 @@ cd analyses-snapshot-testing \
 
 > This copies in your local code to the container and runs the analyses battery against it.
 
-1. `make build-base-image`
-1. `make build-local`
-1. `make local-snapshot-test`
+`cd PYENV_ROOT && git pull` - make sure pyenv is up to date so you may install python 3.13.0
+`pyenv install 3.13.0` - install python 3.13.0
+`cd <OPENTRONS_REPO_ROOT>/analyses-snapshot-testing` - navigate to the analyses-snapshot-testing directory
+`pyenv local 3.13.0` - set the local python version to 3.13.0
+`make setup` - install the requirements
+`make snapshot-test-local` - this target builds the base image, builds the local code into the base image, then runs the analyses battery against the image you just created
 
 You have the option to specify one or many protocols to run the analyses on. This is also described above [Running the tests against specific protocols](#running-the-tests-against-specific-protocols)
 
-- `make local-snapshot-test PROTOCOL_NAMES=Flex_S_v2_19_Illumina_DNA_PCR_Free OVERRIDE_PROTOCOL_NAMES=none`
+- `make snapshot-test-local PROTOCOL_NAMES=Flex_S_v2_19_Illumina_DNA_PCR_Free OVERRIDE_PROTOCOL_NAMES=none`
+
+### Updating the snapshots locally
+
+- `make snapshot-test-update-local` - this target builds the base image, builds the local code into the base image, then runs the analyses battery against the image you just created, updating the snapshots by passing the `--update-snapshots` flag to the test

api/docs/v2/versioning.rst

@@ -134,6 +134,10 @@ This table lists the correspondence between Protocol API versions and robot soft
 Changes in API Versions
 =======================
 
+Version 2.21
+------------
+- :ref:`Liquid presence detection <lpd>` now only checks on the first aspiration of the :py:meth:`.mix` cycle. 
+
 Version 2.20
 ------------
 

api/src/opentrons/hardware_control/backends/ot3controller.py

@@ -1008,6 +1008,7 @@ def _lookup_serial_key(pipette_name: FirmwarePipetteName) -> str:
         lookup_name = {
             FirmwarePipetteName.p1000_single: "P1KS",
             FirmwarePipetteName.p1000_multi: "P1KM",
+            FirmwarePipetteName.p1000_multi_em: "P1KP",
             FirmwarePipetteName.p50_single: "P50S",
             FirmwarePipetteName.p50_multi: "P50M",
             FirmwarePipetteName.p1000_96: "P1KH",

api/src/opentrons/hardware_control/dev_types.py

@@ -100,6 +100,8 @@ class PipetteDict(InstrumentDict):
     pipette_bounding_box_offsets: PipetteBoundingBoxOffsetDefinition
     current_nozzle_map: NozzleMap
     lld_settings: Optional[Dict[str, Dict[str, float]]]
+    plunger_positions: Dict[str, float]
+    shaft_ul_per_mm: float
 
 
 class PipetteStateDict(TypedDict):

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

@@ -28,7 +28,7 @@
     CommandPreconditionViolated,
 )
 from opentrons_shared_data.pipette.ul_per_mm import (
-    piecewise_volume_conversion,
+    calculate_ul_per_mm,
     PIPETTING_FUNCTION_FALLBACK_VERSION,
     PIPETTING_FUNCTION_LATEST_VERSION,
 )
@@ -584,21 +584,9 @@ def get_nominal_tip_overlap_dictionary_by_configuration(
     # want this to unbounded.
     @functools.lru_cache(maxsize=100)
     def ul_per_mm(self, ul: float, action: UlPerMmAction) -> float:
-        if action == "aspirate":
-            fallback = self._active_tip_settings.aspirate.default[
-                PIPETTING_FUNCTION_FALLBACK_VERSION
-            ]
-            sequence = self._active_tip_settings.aspirate.default.get(
-                self._pipetting_function_version, fallback
-            )
-        else:
-            fallback = self._active_tip_settings.dispense.default[
-                PIPETTING_FUNCTION_FALLBACK_VERSION
-            ]
-            sequence = self._active_tip_settings.dispense.default.get(
-                self._pipetting_function_version, fallback
-            )
-        return piecewise_volume_conversion(ul, sequence)
+        return calculate_ul_per_mm(
+            ul, action, self._active_tip_settings, self._pipetting_function_version
+        )
 
     def __str__(self) -> str:
         return "{} current volume {}ul critical point: {} at {}".format(

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

@@ -260,6 +260,13 @@ def get_attached_instrument(self, mount: MountType) -> PipetteDict:
                 "pipette_bounding_box_offsets"
             ] = instr.config.pipette_bounding_box_offsets
             result["lld_settings"] = instr.config.lld_settings
+            result["plunger_positions"] = {
+                "top": instr.plunger_positions.top,
+                "bottom": instr.plunger_positions.bottom,
+                "blow_out": instr.plunger_positions.blow_out,
+                "drop_tip": instr.plunger_positions.drop_tip,
+            }
+            result["shaft_ul_per_mm"] = instr.config.shaft_ul_per_mm
         return cast(PipetteDict, result)
 
     @property

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

@@ -27,7 +27,7 @@
     InvalidInstrumentData,
 )
 from opentrons_shared_data.pipette.ul_per_mm import (
-    piecewise_volume_conversion,
+    calculate_ul_per_mm,
     PIPETTING_FUNCTION_FALLBACK_VERSION,
     PIPETTING_FUNCTION_LATEST_VERSION,
 )
@@ -529,23 +529,13 @@ def tip_presence_responses(self) -> int:
     # want this to unbounded.
     @functools.lru_cache(maxsize=100)
     def ul_per_mm(self, ul: float, action: UlPerMmAction) -> float:
-        if action == "aspirate":
-            fallback = self._active_tip_settings.aspirate.default[
-                PIPETTING_FUNCTION_FALLBACK_VERSION
-            ]
-            sequence = self._active_tip_settings.aspirate.default.get(
-                self._pipetting_function_version, fallback
-            )
-        elif action == "blowout":
-            return self._config.shaft_ul_per_mm
-        else:
-            fallback = self._active_tip_settings.dispense.default[
-                PIPETTING_FUNCTION_FALLBACK_VERSION
-            ]
-            sequence = self._active_tip_settings.dispense.default.get(
-                self._pipetting_function_version, fallback
-            )
-        return piecewise_volume_conversion(ul, sequence)
+        return calculate_ul_per_mm(
+            ul,
+            action,
+            self._active_tip_settings,
+            self._pipetting_function_version,
+            self._config.shaft_ul_per_mm,
+        )
 
     def __str__(self) -> str:
         return "{} current volume {}ul critical point: {} at {}".format(
@@ -585,6 +575,7 @@ def as_dict(self) -> "Pipette.DictType":
                 "versioned_tip_overlap": self.tip_overlap,
                 "back_compat_names": self._config.pipette_backcompat_names,
                 "supported_tips": self.liquid_class.supported_tips,
+                "shaft_ul_per_mm": self._config.shaft_ul_per_mm,
             }
         )
         return self._config_as_dict

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

@@ -282,6 +282,13 @@ def get_attached_instrument(self, mount: OT3Mount) -> PipetteDict:
                 "pipette_bounding_box_offsets"
             ] = instr.config.pipette_bounding_box_offsets
             result["lld_settings"] = instr.config.lld_settings
+            result["plunger_positions"] = {
+                "top": instr.plunger_positions.top,
+                "bottom": instr.plunger_positions.bottom,
+                "blow_out": instr.plunger_positions.blow_out,
+                "drop_tip": instr.plunger_positions.drop_tip,
+            }
+            result["shaft_ul_per_mm"] = instr.config.shaft_ul_per_mm
         return cast(PipetteDict, result)
 
     @property

api/src/opentrons/hardware_control/ot3api.py

@@ -776,7 +776,7 @@ async def _update_position_estimation(
         """
         Function to update motor estimation for a set of axes
         """
-
+        await self._backend.update_motor_status()
         if axes:
             checked_axes = [ax for ax in axes if ax in Axis]
         else:

api/src/opentrons/protocol_api/__init__.py

@@ -30,7 +30,16 @@
 )
 from .disposal_locations import TrashBin, WasteChute
 from ._liquid import Liquid, LiquidClass
-from ._types import OFF_DECK
+from ._types import (
+    OFF_DECK,
+    PLUNGER_BLOWOUT,
+    PLUNGER_TOP,
+    PLUNGER_BOTTOM,
+    PLUNGER_DROPTIP,
+    ASPIRATE_ACTION,
+    DISPENSE_ACTION,
+    BLOWOUT_ACTION,
+)
 from ._nozzle_layout import (
     COLUMN,
     PARTIAL_COLUMN,
@@ -69,12 +78,22 @@
     "Liquid",
     "LiquidClass",
     "Parameters",
+    # Partial Tip types
     "COLUMN",
     "PARTIAL_COLUMN",
     "SINGLE",
     "ROW",
     "ALL",
+    # Deck location types
     "OFF_DECK",
+    # Pipette plunger types
+    "PLUNGER_BLOWOUT",
+    "PLUNGER_TOP",
+    "PLUNGER_BOTTOM",
+    "PLUNGER_DROPTIP",
+    "ASPIRATE_ACTION",
+    "DISPENSE_ACTION",
+    "BLOWOUT_ACTION",
     "RuntimeParameterRequiredError",
     "CSVParameter",
     # For internal Opentrons use only:

api/src/opentrons/protocol_api/_types.py

@@ -17,3 +17,27 @@ class OffDeckType(enum.Enum):
 
 See :ref:`off-deck-location` for details on using ``OFF_DECK`` with :py:obj:`ProtocolContext.move_labware()`.
 """
+
+
+class PlungerPositionTypes(enum.Enum):
+    PLUNGER_TOP = "top"
+    PLUNGER_BOTTOM = "bottom"
+    PLUNGER_BLOWOUT = "blow_out"
+    PLUNGER_DROPTIP = "drop_tip"
+
+
+PLUNGER_TOP: Final = PlungerPositionTypes.PLUNGER_TOP
+PLUNGER_BOTTOM: Final = PlungerPositionTypes.PLUNGER_BOTTOM
+PLUNGER_BLOWOUT: Final = PlungerPositionTypes.PLUNGER_BLOWOUT
+PLUNGER_DROPTIP: Final = PlungerPositionTypes.PLUNGER_DROPTIP
+
+
+class PipetteActionTypes(enum.Enum):
+    ASPIRATE_ACTION = "aspirate"
+    DISPENSE_ACTION = "dispense"
+    BLOWOUT_ACTION = "blowout"
+
+
+ASPIRATE_ACTION: Final = PipetteActionTypes.ASPIRATE_ACTION
+DISPENSE_ACTION: Final = PipetteActionTypes.DISPENSE_ACTION
+BLOWOUT_ACTION: Final = PipetteActionTypes.BLOWOUT_ACTION

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

@@ -1,13 +1,16 @@
-from typing import Optional, Dict
+from typing import Optional, Dict, Union
 from opentrons.hardware_control import SyncHardwareAPI
 
 from opentrons.types import Mount, MountType, Point, AxisType, AxisMapType
+from opentrons_shared_data.pipette import types as pip_types
+from opentrons.protocol_api._types import PipetteActionTypes, PlungerPositionTypes
 from opentrons.protocol_engine import commands as cmd
 from opentrons.protocol_engine.clients import SyncClient as EngineClient
 from opentrons.protocol_engine.types import DeckPoint, MotorAxis
 
 from opentrons.protocol_api.core.robot import AbstractRobot
 
+
 _AXIS_TYPE_TO_MOTOR_AXIS = {
     AxisType.X: MotorAxis.X,
     AxisType.Y: MotorAxis.Y,
@@ -39,12 +42,57 @@ def __init__(
     def _convert_to_engine_mount(self, axis_map: AxisMapType) -> Dict[MotorAxis, float]:
         return {_AXIS_TYPE_TO_MOTOR_AXIS[ax]: dist for ax, dist in axis_map.items()}
 
-    def get_pipette_type_from_engine(self, mount: Mount) -> Optional[str]:
+    def get_pipette_type_from_engine(
+        self, mount: Union[Mount, str]
+    ) -> Optional[pip_types.PipetteNameType]:
         """Get the pipette attached to the given mount."""
-        engine_mount = MountType[mount.name]
+        if isinstance(mount, Mount):
+            engine_mount = MountType[mount.name]
+        else:
+            if mount.lower() == "right":
+                engine_mount = MountType.RIGHT
+            else:
+                engine_mount = MountType.LEFT
         maybe_pipette = self._engine_client.state.pipettes.get_by_mount(engine_mount)
         return maybe_pipette.pipetteName if maybe_pipette else None
 
+    def get_plunger_position_from_name(
+        self, mount: Mount, position_name: PlungerPositionTypes
+    ) -> float:
+        engine_mount = MountType[mount.name]
+        maybe_pipette = self._engine_client.state.pipettes.get_by_mount(engine_mount)
+        if not maybe_pipette:
+            return 0.0
+        return self._engine_client.state.pipettes.lookup_plunger_position_name(
+            maybe_pipette.id, position_name.value
+        )
+
+    def get_plunger_position_from_volume(
+        self, mount: Mount, volume: float, action: PipetteActionTypes, robot_type: str
+    ) -> float:
+        engine_mount = MountType[mount.name]
+        maybe_pipette = self._engine_client.state.pipettes.get_by_mount(engine_mount)
+        if not maybe_pipette:
+            raise RuntimeError(
+                f"Cannot load plunger position as no pipette is attached to {mount}"
+            )
+        convert_volume = (
+            self._engine_client.state.pipettes.lookup_volume_to_mm_conversion(
+                maybe_pipette.id, volume, action.value
+            )
+        )
+        plunger_bottom = (
+            self._engine_client.state.pipettes.lookup_plunger_position_name(
+                maybe_pipette.id, "bottom"
+            )
+        )
+        mm = volume / convert_volume
+        if robot_type == "OT-2 Standard":
+            position = plunger_bottom + mm
+        else:
+            position = plunger_bottom - mm
+        return round(position, 6)
+
     def move_to(self, mount: Mount, destination: Point, speed: Optional[float]) -> None:
         engine_mount = MountType[mount.name]
         engine_destination = DeckPoint(