Merge branch 'edge' into second_probe_command

Resolve conflicts in:
* api/src/opentrons/protocol_engine/commands/liquid_probe.py
* api/tests/opentrons/protocol_engine/commands/test_liquid_probe.py

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

@@ -207,6 +207,7 @@ jobs:
     needs: [determine-build-type]
     if: needs.determine-build-type.outputs.variants != '[]'
     strategy:
+      fail-fast: false
       matrix:
         os: ['windows-2022', 'ubuntu-22.04', 'macos-latest']
         variant: ${{fromJSON(needs.determine-build-type.outputs.variants)}}

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -464,6 +464,7 @@ def get_run_error_info_from_robot(
     email = args.email[0]
     board_id = args.board_id[0]
     reporter_id = args.reporter_id[0]
+    file_paths = read_robot_logs.get_logs(storage_directory, ip)
     ticket = jira_tool.JiraTicket(url, api_token, email)
     ticket.issues_on_board(board_id)
     users_file_path = ticket.get_jira_users(storage_directory)
@@ -496,7 +497,6 @@ def get_run_error_info_from_robot(
     saved_file_path_calibration, calibration = read_robot_logs.get_calibration_offsets(
         ip, storage_directory
     )
-    file_paths = read_robot_logs.get_logs(storage_directory, ip)
 
     print(f"Making ticket for {summary}.")
     # TODO: make argument or see if I can get rid of with using board_id.

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -569,23 +569,32 @@ def get_calibration_offsets(
 
 def get_logs(storage_directory: str, ip: str) -> List[str]:
     """Get Robot logs."""
-    log_types = ["api.log", "server.log", "serial.log", "touchscreen.log"]
+    log_types: List[Dict[str, Any]] = [
+        {"log type": "api.log", "records": 1000},
+        {"log type": "server.log", "records": 10000},
+        {"log type": "serial.log", "records": 10000},
+        {"log type": "touchscreen.log", "records": 1000},
+    ]
     all_paths = []
     for log_type in log_types:
         try:
+            log_type_name = log_type["log type"]
+            print(log_type_name)
+            log_records = int(log_type["records"])
+            print(log_records)
             response = requests.get(
-                f"http://{ip}:31950/logs/{log_type}",
-                headers={"log_identifier": log_type},
-                params={"records": 5000},
+                f"http://{ip}:31950/logs/{log_type_name}",
+                headers={"log_identifier": log_type_name},
+                params={"records": log_records},
             )
             response.raise_for_status()
             log_data = response.text
-            log_name = ip + "_" + log_type.split(".")[0] + ".log"
+            log_name = ip + "_" + log_type_name.split(".")[0] + ".log"
             file_path = os.path.join(storage_directory, log_name)
             with open(file_path, mode="w", encoding="utf-8") as file:
                 file.write(log_data)
         except RuntimeError:
-            print(f"Request exception. Did not save {log_type}")
+            print(f"Request exception. Did not save {log_type_name}")
             continue
         all_paths.append(file_path)
     # Get weston.log using scp

api/src/opentrons/config/defaults_ot3.py

@@ -23,8 +23,8 @@
 DEFAULT_MODULE_OFFSET = [0.0, 0.0, 0.0]
 
 DEFAULT_LIQUID_PROBE_SETTINGS: Final[LiquidProbeSettings] = LiquidProbeSettings(
-    mount_speed=10,
-    plunger_speed=5,
+    mount_speed=5,
+    plunger_speed=20,
     plunger_impulse_time=0.2,
     sensor_threshold_pascals=15,
     output_option=OutputOptions.sync_buffer_to_csv,
@@ -328,7 +328,7 @@ def _build_default_liquid_probe(
         or output_option is OutputOptions.stream_to_csv
     ):
         data_files = _build_log_files_with_default(
-            from_conf.get("data_files", {}), default.data_files
+            from_conf.get("data_files", None), default.data_files
         )
     return LiquidProbeSettings(
         mount_speed=from_conf.get("mount_speed", default.mount_speed),

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

@@ -194,7 +194,6 @@
     PipetteLiquidNotFoundError,
     CommunicationError,
     PythonException,
-    UnsupportedHardwareCommand,
 )
 
 from .subsystem_manager import SubsystemManager
@@ -1363,17 +1362,6 @@ async def liquid_probe(
         probe: InstrumentProbeType = InstrumentProbeType.PRIMARY,
         force_both_sensors: bool = False,
     ) -> float:
-        if output_option == OutputOptions.sync_buffer_to_csv:
-            if (
-                self._subsystem_manager.device_info[
-                    SubSystem.of_mount(mount)
-                ].revision.tertiary
-                != "1"
-            ):
-                raise UnsupportedHardwareCommand(
-                    "Liquid Probe not supported on this pipette firmware"
-                )
-
         head_node = axis_to_node(Axis.by_mount(mount))
         tool = sensor_node_for_pipette(OT3Mount(mount.value))
         csv_output = bool(output_option.value & OutputOptions.stream_to_csv.value)

api/src/opentrons/hardware_control/ot3api.py

@@ -2636,10 +2636,13 @@ async def liquid_probe(
         pos = await self.gantry_position(checked_mount, refresh=True)
         while (probe_start_pos.z - pos.z) < max_z_dist:
             # safe distance so we don't accidentally aspirate liquid if we're already close to liquid
-            safe_plunger_pos = pos._replace(z=(pos.z + 2))
+            safe_plunger_pos = top_types.Point(pos.x, pos.y, pos.z + 2)
             # overlap amount we want to use between passes
-            pass_start_pos = pos._replace(z=(pos.z + 0.5))
-
+            pass_start_pos = top_types.Point(pos.x, pos.y, pos.z + 0.5)
+            max_z_time = (
+                max_z_dist - (probe_start_pos.z - safe_plunger_pos.z)
+            ) / probe_settings.mount_speed
+            pass_travel = min(max_z_time * probe_settings.plunger_speed, p_travel)
             # Prep the plunger
             await self.move_to(checked_mount, safe_plunger_pos)
             if probe_settings.aspirate_while_sensing:
@@ -2655,7 +2658,7 @@ async def liquid_probe(
                     checked_mount,
                     probe_settings,
                     probe if probe else InstrumentProbeType.PRIMARY,
-                    p_travel,
+                    pass_travel,
                 )
                 # if we made it here without an error we found the liquid
                 error = None

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

@@ -838,13 +838,12 @@ def retract(self) -> None:
         z_axis = self._engine_client.state.pipettes.get_z_axis(self._pipette_id)
         self._engine_client.execute_command(cmd.HomeParams(axes=[z_axis]))
 
-    def liquid_probe_with_recovery(self, well_core: WellCore) -> None:
+    def liquid_probe_with_recovery(self, well_core: WellCore, loc: Location) -> None:
         labware_id = well_core.labware_id
         well_name = well_core.get_name()
         well_location = WellLocation(
             origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=0)
         )
-
         self._engine_client.execute_command(
             cmd.LiquidProbeParams(
                 labwareId=labware_id,
@@ -854,13 +853,16 @@ def liquid_probe_with_recovery(self, well_core: WellCore) -> None:
             )
         )
 
-    def liquid_probe_without_recovery(self, well_core: WellCore) -> float:
+        self._protocol_core.set_last_location(location=loc, mount=self.get_mount())
+
+    def liquid_probe_without_recovery(
+        self, well_core: WellCore, loc: Location
+    ) -> float:
         labware_id = well_core.labware_id
         well_name = well_core.get_name()
         well_location = WellLocation(
             origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=0)
         )
-
         result = self._engine_client.execute_command_without_recovery(
             cmd.LiquidProbeParams(
                 labwareId=labware_id,
@@ -870,5 +872,7 @@ def liquid_probe_without_recovery(self, well_core: WellCore) -> float:
             )
         )
 
+        self._protocol_core.set_last_location(location=loc, mount=self.get_mount())
+
         if result is not None and isinstance(result, LiquidProbeResult):
             return result.z_position

api/src/opentrons/protocol_api/core/instrument.py

@@ -306,12 +306,16 @@ def retract(self) -> None:
         ...
 
     @abstractmethod
-    def liquid_probe_with_recovery(self, well_core: WellCoreType) -> None:
+    def liquid_probe_with_recovery(
+        self, well_core: WellCoreType, loc: types.Location
+    ) -> None:
         """Do a liquid probe to detect the presence of liquid in the well."""
         ...
 
     @abstractmethod
-    def liquid_probe_without_recovery(self, well_core: WellCoreType) -> float:
+    def liquid_probe_without_recovery(
+        self, well_core: WellCoreType, loc: types.Location
+    ) -> float:
         """Do a liquid probe to find the level of the liquid in the well."""
         ...
 

api/src/opentrons/protocol_api/core/legacy/legacy_instrument_core.py

@@ -566,10 +566,14 @@ def retract(self) -> None:
         """Retract this instrument to the top of the gantry."""
         self._protocol_interface.get_hardware.retract(self._mount)  # type: ignore [attr-defined]
 
-    def liquid_probe_with_recovery(self, well_core: WellCore) -> None:
+    def liquid_probe_with_recovery(
+        self, well_core: WellCore, loc: types.Location
+    ) -> None:
         """This will never be called because it was added in API 2.20."""
         assert False, "liquid_probe_with_recovery only supported in API 2.20 & later"
 
-    def liquid_probe_without_recovery(self, well_core: WellCore) -> float:
+    def liquid_probe_without_recovery(
+        self, well_core: WellCore, loc: types.Location
+    ) -> float:
         """This will never be called because it was added in API 2.20."""
         assert False, "liquid_probe_without_recovery only supported in API 2.20 & later"

api/src/opentrons/protocol_api/core/legacy_simulator/legacy_instrument_core.py

@@ -484,10 +484,14 @@ def retract(self) -> None:
         """Retract this instrument to the top of the gantry."""
         self._protocol_interface.get_hardware.retract(self._mount)  # type: ignore [attr-defined]
 
-    def liquid_probe_with_recovery(self, well_core: WellCore) -> None:
+    def liquid_probe_with_recovery(
+        self, well_core: WellCore, loc: types.Location
+    ) -> None:
         """This will never be called because it was added in API 2.20."""
         assert False, "liquid_probe_with_recovery only supported in API 2.20 & later"
 
-    def liquid_probe_without_recovery(self, well_core: WellCore) -> float:
+    def liquid_probe_without_recovery(
+        self, well_core: WellCore, loc: types.Location
+    ) -> float:
         """This will never be called because it was added in API 2.20."""
         assert False, "liquid_probe_without_recovery only supported in API 2.20 & later"

api/src/opentrons/protocol_api/instrument_context.py

@@ -9,7 +9,6 @@
     CommandParameterLimitViolated,
     UnexpectedTipRemovalError,
 )
-from opentrons.protocol_engine.errors.exceptions import WellDoesNotExistError
 from opentrons.legacy_broker import LegacyBroker
 from opentrons.hardware_control.dev_types import PipetteDict
 from opentrons import types
@@ -226,7 +225,6 @@ def aspirate(
 
         well: Optional[labware.Well] = None
         move_to_location: types.Location
-
         last_location = self._get_last_location_by_api_version()
         try:
             target = validation.validate_location(
@@ -264,6 +262,14 @@ def aspirate(
             c_vol = self._core.get_available_volume() if not volume else volume
         flow_rate = self._core.get_aspirate_flow_rate(rate)
 
+        if (
+            self.api_version >= APIVersion(2, 20)
+            and well is not None
+            and self.liquid_presence_detection
+        ):
+            self.require_liquid_presence(well=well)
+            self.prepare_to_aspirate()
+
         with publisher.publish_context(
             broker=self.broker,
             command=cmds.aspirate(
@@ -2105,11 +2111,11 @@ def detect_liquid_presence(self, well: labware.Well) -> bool:
 
         :returns: A boolean.
         """
-        if not isinstance(well, labware.Well):
-            raise WellDoesNotExistError("You must provide a valid well to check.")
+        loc = well.top()
         try:
-            self._core.liquid_probe_without_recovery(well._core)
+            self._core.liquid_probe_without_recovery(well._core, loc)
         except ProtocolCommandFailedError as e:
+            # if we handle the error, we change the protocl state from error to valid
             if isinstance(e.original_error, LiquidNotFoundError):
                 return False
             raise e
@@ -2122,10 +2128,8 @@ def require_liquid_presence(self, well: labware.Well) -> None:
 
         :returns: None.
         """
-        if not isinstance(well, labware.Well):
-            raise WellDoesNotExistError("You must provide a valid well to check.")
-
-        self._core.liquid_probe_with_recovery(well._core)
+        loc = well.top()
+        self._core.liquid_probe_with_recovery(well._core, loc)
 
     @requires_version(2, 20)
     def measure_liquid_height(self, well: labware.Well) -> float:
@@ -2137,8 +2141,6 @@ def measure_liquid_height(self, well: labware.Well) -> float:
 
         This is intended for Opentrons internal use only and is not a guaranteed API.
         """
-        if not isinstance(well, labware.Well):
-            raise WellDoesNotExistError("You must provide a valid well to check.")
-
-        height = self._core.liquid_probe_without_recovery(well._core)
+        loc = well.top()
+        height = self._core.liquid_probe_without_recovery(well._core, loc)
         return height

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

@@ -11,7 +11,7 @@
 
 from pydantic import Field
 
-from ..types import CurrentWell, DeckPoint
+from ..types import DeckPoint
 from .pipetting_common import (
     LiquidNotFoundError,
     LiquidNotFoundErrorInternalData,
@@ -97,6 +97,8 @@ async def execute(self, params: LiquidProbeParams) -> _LiquidProbeExecuteReturn:
         Raises:
             TipNotAttachedError: as an undefined error, if there is not tip attached to
                 the pipette.
+            TipNotEmptyError: as an undefined error, if the tip starts with liquid
+                in it.
             MustHomeError: as an undefined error, if the plunger is not in a valid
                 position.
         """
@@ -118,19 +120,12 @@ async def execute(self, params: LiquidProbeParams) -> _LiquidProbeExecuteReturn:
                 message="Current position of pipette is invalid. Please home."
             )
 
-        current_well = CurrentWell(
-            pipette_id=pipette_id,
-            labware_id=labware_id,
-            well_name=well_name,
-        )
-
         # liquid_probe process start position
         position = await self._movement.move_to_well(
             pipette_id=pipette_id,
             labware_id=labware_id,
             well_name=well_name,
             well_location=params.wellLocation,
-            current_well=current_well,
         )
 
         try:

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

@@ -30,7 +30,7 @@ class PipettingHandler(TypingProtocol):
     """Liquid handling commands."""
 
     def get_is_empty(self, pipette_id: str) -> bool:
-        """Get whether a pipette has a working volume equal to 0."""
+        """Get whether a pipette has an aspirated volume equal to 0."""
 
     def get_is_ready_to_aspirate(self, pipette_id: str) -> bool:
         """Get whether a pipette is ready to aspirate."""
@@ -81,8 +81,8 @@ def __init__(self, state_view: StateView, hardware_api: HardwareControlAPI) -> N
         self._hardware_api = hardware_api
 
     def get_is_empty(self, pipette_id: str) -> bool:
-        """Get whether a pipette has a working volume equal to 0."""
-        return self._state_view.pipettes.get_working_volume(pipette_id) == 0
+        """Get whether a pipette has an aspirated volume equal to 0."""
+        return self._state_view.pipettes.get_aspirated_volume(pipette_id) == 0
 
     def get_is_ready_to_aspirate(self, pipette_id: str) -> bool:
         """Get whether a pipette is ready to aspirate."""
@@ -234,8 +234,8 @@ def __init__(
         self._state_view = state_view
 
     def get_is_empty(self, pipette_id: str) -> bool:
-        """Get whether a pipette has a working volume equal to 0."""
-        return self._state_view.pipettes.get_working_volume(pipette_id) == 0
+        """Get whether a pipette has an aspirated volume equal to 0."""
+        return self._state_view.pipettes.get_aspirated_volume(pipette_id) == 0
 
     def get_is_ready_to_aspirate(self, pipette_id: str) -> bool:
         """Get whether a pipette is ready to aspirate."""

api/src/opentrons/protocol_engine/state/pipettes.py

@@ -637,7 +637,7 @@ def get_current_tip_lld_settings(self, pipette_id: str) -> float:
         if attached_tip is None or attached_tip.volume is None:
             return 0
         lld_settings = self.get_pipette_lld_settings(pipette_id)
-        tipVolume = str(attached_tip.volume)
+        tipVolume = "t" + str(int(attached_tip.volume))
         if (
             lld_settings is None
             or lld_settings[tipVolume] is None

api/tests/opentrons/hardware_control/test_ot3_api.py

@@ -806,9 +806,6 @@ async def test_liquid_probe(
     )
     await ot3_hardware.cache_pipette(mount, instr_data, None)
     pipette = ot3_hardware.hardware_pipettes[mount.to_mount()]
-    plunger_positions = ot3_hardware._pipette_handler.get_pipette(
-        mount
-    ).plunger_positions
 
     assert pipette
     await ot3_hardware.add_tip(mount, 100)
@@ -841,7 +838,7 @@ async def test_liquid_probe(
         mock_move_to_plunger_bottom.assert_called_once()
         mock_liquid_probe.assert_called_once_with(
             mount,
-            plunger_positions.bottom - plunger_positions.top,
+            3.0,
             fake_settings_aspirate.mount_speed,
             (fake_settings_aspirate.plunger_speed * -1),
             fake_settings_aspirate.sensor_threshold_pascals,