Merge branch 'edge' into fix_inherit_enumerated_errors

.gitignore

@@ -137,6 +137,7 @@ update-server/LICENSE
 shared-data/python/LICENSE
 shared-data/LICENSE
 robot-server/LICENSE
+performance-metrics/LICENSE
 
 # typescript incremental files
 *.tsbuildinfo

api-client/src/runs/types.ts

@@ -21,6 +21,8 @@ export const RUN_STATUS_FINISHING = 'finishing' as const
 export const RUN_STATUS_SUCCEEDED = 'succeeded' as const
 export const RUN_STATUS_BLOCKED_BY_OPEN_DOOR = 'blocked-by-open-door' as const
 export const RUN_STATUS_AWAITING_RECOVERY = 'awaiting-recovery' as const
+export const RUN_STATUS_AWAITING_RECOVERY_BLOCKED_BY_OPEN_DOOR = 'awaiting-recovery-blocked-by-open-door' as const
+export const RUN_STATUS_AWAITING_RECOVERY_PAUSED = 'awaiting-recovery-paused' as const
 
 export type RunStatus =
   | typeof RUN_STATUS_IDLE
@@ -33,6 +35,8 @@ export type RunStatus =
   | typeof RUN_STATUS_SUCCEEDED
   | typeof RUN_STATUS_BLOCKED_BY_OPEN_DOOR
   | typeof RUN_STATUS_AWAITING_RECOVERY
+  | typeof RUN_STATUS_AWAITING_RECOVERY_BLOCKED_BY_OPEN_DOOR
+  | typeof RUN_STATUS_AWAITING_RECOVERY_PAUSED
 
 export interface LegacyGoodRunData {
   id: string

api/Pipfile

@@ -11,6 +11,7 @@ opentrons-shared-data = { editable = true, path = "../shared-data/python" }
 opentrons = { editable = true, path = "." }
 opentrons-hardware = { editable = true, path = "./../hardware", extras=["FLEX"] }
 numpy = "==1.22.3"
+packaging = "==21.3"
 pyusb = "==1.2.1"
 
 [dev-packages]

api/release-notes.md

@@ -6,6 +6,16 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
+## Opentrons Robot Software Changes in 7.3.1
+
+Welcome to the v7.3.1 release of the Opentrons robot software!
+
+### Improved Features
+
+- Updated values for how much a tip overlaps with the pipette nozzle when the pipette picks up tips, in order to make protocols more reliable. These new values only apply to JSON protocols and Python protocols specifying API version 2.19.
+
+---
+
 ## Opentrons Robot Software Changes in 7.3.0
 
 Welcome to the v7.3.0 release of the Opentrons robot software!

api/setup.py

@@ -66,6 +66,7 @@ def get_version():
     "typing-extensions>=4.0.0,<5",
     "click>=8.0.0,<9",
     'importlib-metadata >= 1.0 ; python_version < "3.8"',
+    "packaging>=21.0",
 ]
 
 EXTRAS = {

api/src/opentrons/hardware_control/api.py

@@ -65,7 +65,7 @@
     RobotCalibration,
 )
 from .protocols import HardwareControlInterface
-from .instruments.ot2.pipette_handler import PipetteHandlerProvider, PickUpTipSpec
+from .instruments.ot2.pipette_handler import PipetteHandlerProvider
 from .instruments.ot2.instrument_calibration import load_pipette_offset
 from .motion_utilities import (
     target_position_from_absolute,
@@ -1155,8 +1155,21 @@ async def update_nozzle_configuration_for_mount(
     async def tip_pickup_moves(
         self,
         mount: top_types.Mount,
-        spec: PickUpTipSpec,
+        presses: Optional[int] = None,
+        increment: Optional[float] = None,
     ) -> None:
+        spec, _ = self.plan_check_pick_up_tip(
+            mount=mount, presses=presses, increment=increment
+        )
+        self._backend.set_active_current(spec.plunger_currents)
+        target_absolute = target_position_from_plunger(
+            mount, spec.plunger_prep_pos, self._current_position
+        )
+        await self._move(
+            target_absolute,
+            home_flagged_axes=False,
+        )
+
         for press in spec.presses:
             with self._backend.save_current():
                 self._backend.set_active_current(press.current)
@@ -1176,6 +1189,11 @@ 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,
@@ -1189,7 +1207,7 @@ async def pick_up_tip(
         """
 
         spec, _add_tip_to_instrs = self.plan_check_pick_up_tip(
-            mount, tip_length, presses, increment
+            mount=mount, presses=presses, increment=increment, tip_length=tip_length
         )
         self._backend.set_active_current(spec.plunger_currents)
         target_absolute = target_position_from_plunger(
@@ -1200,7 +1218,24 @@ async def pick_up_tip(
             home_flagged_axes=False,
         )
 
-        await self.tip_pickup_moves(mount, spec)
+        for press in spec.presses:
+            with self._backend.save_current():
+                self._backend.set_active_current(press.current)
+                target_down = target_position_from_relative(
+                    mount, press.relative_down, self._current_position
+                )
+                await self._move(target_down, speed=press.speed)
+            target_up = target_position_from_relative(
+                mount, press.relative_up, self._current_position
+            )
+            await self._move(target_up)
+        # neighboring tips tend to get stuck in the space between
+        # the volume chamber and the drop-tip sleeve on p1000.
+        # This extra shake ensures those tips are removed
+        for rel_point, speed in spec.shake_off_list:
+            await self.move_rel(mount, rel_point, speed=speed)
+
+        await self.retract(mount, spec.retract_target)
         _add_tip_to_instrs()
 
         if prep_after:

api/src/opentrons/hardware_control/dev_types.py

@@ -84,6 +84,7 @@ class PipetteDict(InstrumentDict):
     tip_length: float
     working_volume: float
     tip_overlap: Dict[str, float]
+    versioned_tip_overlap: Dict[str, Dict[str, float]]
     available_volume: float
     return_tip_height: float
     default_aspirate_flow_rates: Dict[str, float]

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

@@ -631,9 +631,8 @@ def as_dict(self) -> "Pipette.DictType":
                 "default_dispense_flow_rates": self.dispense_flow_rates_lookup,
                 "tip_length": self.current_tip_length,
                 "return_tip_height": self.active_tip_settings.default_return_tip_height,
-                "tip_overlap": self.tip_overlap[
-                    "v0"
-                ],  # TODO(cb, 2024-06-11): hard coded to "v0" - when versioned tip overlaps are fully integrated this must change
+                "tip_overlap": self.tip_overlap["v0"],
+                "versioned_tip_overlap": self.tip_overlap,
                 "back_compat_names": self._config.pipette_backcompat_names,
                 "supported_tips": self.liquid_class.supported_tips,
             }

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

@@ -212,6 +212,7 @@ def get_attached_instrument(self, mount: MountType) -> PipetteDict:
                 "blow_out_flow_rate",
                 "working_volume",
                 "tip_overlap",
+                "versioned_tip_overlap",
                 "available_volume",
                 "return_tip_height",
                 "default_aspirate_flow_rates",
@@ -744,28 +745,28 @@ def build_one_shake() -> List[Tuple[top_types.Point, Optional[float]]]:
     def plan_check_pick_up_tip(
         self,
         mount: top_types.Mount,
-        tip_length: float,
         presses: Optional[int],
         increment: Optional[float],
+        tip_length: float = 0,
     ) -> Tuple[PickUpTipSpec, Callable[[], None]]:
         ...
 
     @overload
     def plan_check_pick_up_tip(
         self,
         mount: OT3Mount,
-        tip_length: float,
         presses: Optional[int],
         increment: Optional[float],
+        tip_length: float = 0,
     ) -> Tuple[PickUpTipSpec, Callable[[], None]]:
         ...
 
     def plan_check_pick_up_tip(  # type: ignore[no-untyped-def]
         self,
         mount,
-        tip_length,
         presses,
         increment,
+        tip_length=0,
     ):
         # Prechecks: ready for pickup tip and press/increment are valid
         instrument = self.get_pipette(mount)

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

@@ -581,6 +581,7 @@ def as_dict(self) -> "Pipette.DictType":
                 "tip_length": self.current_tip_length,
                 "return_tip_height": self.active_tip_settings.default_return_tip_height,
                 "tip_overlap": self.tip_overlap["v0"],
+                "versioned_tip_overlap": self.tip_overlap,
                 "back_compat_names": self._config.pipette_backcompat_names,
                 "supported_tips": self.liquid_class.supported_tips,
             }

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

@@ -228,6 +228,7 @@ def get_attached_instrument(self, mount: OT3Mount) -> PipetteDict:
                 "blow_out_flow_rate",
                 "working_volume",
                 "tip_overlap",
+                "versioned_tip_overlap",
                 "available_volume",
                 "return_tip_height",
                 "default_aspirate_flow_rates",

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

@@ -2,7 +2,7 @@
 import asyncio
 import logging
 import re
-from typing import ClassVar, Mapping, Optional, TypeVar
+from typing import ClassVar, Mapping, Optional, TypeVar, cast
 from packaging.version import InvalidVersion, parse, Version
 from opentrons.config import IS_ROBOT, ROBOT_FIRMWARE_DIR
 from opentrons.drivers.rpi_drivers.types import USBPort
@@ -18,9 +18,14 @@
 def parse_fw_version(version: str) -> Version:
     try:
         device_version = parse(version)
+        # This is a patch for older versions of packaging - they would try and parse old
+        # kidns of versions and return a LegacyVersion object. We can't check for that
+        # explicitly because they removed it in modern versions of packaging.
+        if not isinstance(device_version, Version):
+            raise InvalidVersion()
     except InvalidVersion:
         device_version = parse("v0.0.0")
-    return device_version
+    return cast(Version, device_version)
 
 
 class AbstractModule(abc.ABC):

api/src/opentrons/hardware_control/ot3api.py

@@ -1799,7 +1799,7 @@ async def hold_jaw_width(self, jaw_width_mm: int) -> None:
 
     async def tip_pickup_moves(
         self,
-        mount: OT3Mount,
+        mount: Union[top_types.Mount, OT3Mount],
         presses: Optional[int] = None,
         increment: Optional[float] = None,
     ) -> None:
@@ -2191,6 +2191,15 @@ 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],
@@ -2209,7 +2218,7 @@ def add_tip_to_instr() -> None:
 
         await self._move_to_plunger_bottom(realmount, rate=1.0)
 
-        await self.tip_pickup_moves(realmount, presses, increment)
+        await self.tip_pickup_moves(mount, presses, increment)
 
         add_tip_to_instr()
 

api/src/opentrons/hardware_control/protocols/__init__.py

@@ -59,6 +59,9 @@ class HardwareControlInterface(
     def get_robot_type(self) -> Type[OT2RobotType]:
         return OT2RobotType
 
+    def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
+        ...
+
 
 class FlexHardwareControlInterface(
     ModuleProvider,
@@ -90,6 +93,9 @@ def motor_status_ok(self, axis: Axis) -> bool:
     def encoder_status_ok(self, axis: Axis) -> bool:
         ...
 
+    def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
+        ...
+
 
 __all__ = [
     "HardwareControlAPI",

api/src/opentrons/hardware_control/protocols/liquid_handler.py

@@ -130,6 +130,14 @@ async def blow_out(
         """
         ...
 
+    async def tip_pickup_moves(
+        self,
+        mount: MountArgType,
+        presses: Optional[int] = None,
+        increment: Optional[float] = None,
+    ) -> None:
+        ...
+
     async def pick_up_tip(
         self,
         mount: MountArgType,

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

@@ -35,7 +35,7 @@
 from opentrons.protocol_api._nozzle_layout import NozzleLayout
 from opentrons.hardware_control.nozzle_manager import NozzleConfigurationType
 from opentrons.hardware_control.nozzle_manager import NozzleMap
-from . import deck_conflict
+from . import deck_conflict, overlap_versions
 
 from ..instrument import AbstractInstrument
 from .well import WellCore
@@ -782,7 +782,13 @@ def set_flow_rate(
 
     def configure_for_volume(self, volume: float) -> None:
         self._engine_client.execute_command(
-            cmd.ConfigureForVolumeParams(pipetteId=self._pipette_id, volume=volume)
+            cmd.ConfigureForVolumeParams(
+                pipetteId=self._pipette_id,
+                volume=volume,
+                tipOverlapNotAfterVersion=overlap_versions.overlap_for_api_version(
+                    self._protocol_core.api_version
+                ),
+            )
         )
 
     def prepare_to_aspirate(self) -> None:

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

@@ -0,0 +1,16 @@
+"""Mappings between API versions and overlap versions."""
+from functools import lru_cache
+from typing_extensions import Final
+from opentrons.protocols.api_support.types import APIVersion
+
+_OVERLAP_VERSION_MAP: Final = {APIVersion(2, 0): "v0", APIVersion(2, 19): "v1"}
+
+
+@lru_cache(1)
+def overlap_for_api_version(api_version: APIVersion) -> str:
+    """Get the overlap version for a specific API version."""
+    defined = list(reversed(sorted(_OVERLAP_VERSION_MAP.keys())))
+    for version in defined:
+        if version <= api_version:
+            return _OVERLAP_VERSION_MAP[version]
+    return _OVERLAP_VERSION_MAP[APIVersion(2, 0)]

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

@@ -68,8 +68,7 @@
     AbsorbanceReaderCore,
 )
 from .exceptions import InvalidModuleLocationError
-from . import load_labware_params
-from . import deck_conflict
+from . import load_labware_params, deck_conflict, overlap_versions
 
 if TYPE_CHECKING:
     from ...labware import Labware
@@ -497,7 +496,10 @@ def _get_module_core(
             )
 
     def load_instrument(
-        self, instrument_name: PipetteNameType, mount: Mount
+        self,
+        instrument_name: PipetteNameType,
+        mount: Mount,
+        liquid_presence_detection: bool = False,
     ) -> InstrumentCore:
         """Load an instrument into the protocol.
 
@@ -510,7 +512,14 @@ def load_instrument(
         """
         engine_mount = MountType[mount.name]
         load_result = self._engine_client.execute_command_without_recovery(
-            cmd.LoadPipetteParams(pipetteName=instrument_name, mount=engine_mount)
+            cmd.LoadPipetteParams(
+                pipetteName=instrument_name,
+                mount=engine_mount,
+                tipOverlapNotAfterVersion=overlap_versions.overlap_for_api_version(
+                    self._api_version
+                ),
+                liquidPresenceDetection=liquid_presence_detection,
+            )
         )
 
         return InstrumentCore(

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

@@ -346,7 +346,10 @@ def load_module(
         return module_core
 
     def load_instrument(
-        self, instrument_name: PipetteNameType, mount: Mount
+        self,
+        instrument_name: PipetteNameType,
+        mount: Mount,
+        liquid_presence_detection: bool = False,
     ) -> LegacyInstrumentCore:
         """Load an instrument."""
         attached = {