Chore release 8.7.0 into release

api/release-notes.md

@@ -8,15 +8,32 @@ By installing and using Opentrons software, you agree to the Opentrons End-User
 
 ---
 
+## Opentrons Robot Software Changes in 8.7.0
+
+Welcome to the v8.7.0 release of the Opentrons robot software! This release adds improvements and bug fixes.
+
+### New Features
+
+Use Opentrons Tough Universal Lids on compatible well plates and reservoirs.
+
+### Improvements
+
+Transfer aqueous, viscous, or volatile liquids with the Opentrons Flex 96-Channel Pipette (1–200 μL) to apply optimized, liquid class transfer behavior to volumes as low as 1 µL.
+
+### Bug Fixes
+
+- Default pipette flow rates are correctly applied in all liquid transfers. Use `configure_for_volume()` to clear customized pipette flow rates.
+- The API no longer raises an error when partial tip pickup occurs in a slot adjacent to a loaded Flex Stacker Module.
+
 ## Opentrons Robot Software Changes in 8.6.0
 
 Welcome to the v8.6.0 release of the Opentrons robot software! This release adds support for the Flex Stacker Module, along with other new features and improvements.
 
-### New Features 
+### New Features
 
-- Automate labware storage with the Flex Stacker Module. Use new commands like `retrieve()` and `store()` to move well plates, reservoirs, or Flex tip racks to and from the Stacker during a protocol. 
-- This release adds support for the Opentrons Flex 96-Channel Pipette (1–200 μL) to transfer as little as 1 µL in a protocol. 
-- Control individual robot motors, like the gantry, extension mount, or gripper, with new  commands.  
+- Automate labware storage with the Flex Stacker Module. Use new commands like `retrieve()` and `store()` to move well plates, reservoirs, or Flex tip racks to and from the Stacker during a protocol.
+- This release adds support for the Opentrons Flex 96-Channel Pipette (1–200 μL) to transfer as little as 1 µL in a protocol.
+- Control individual robot motors, like the gantry, extension mount, or gripper, with new commands.
 
 ### Known Limitations
 
@@ -69,10 +86,10 @@ Welcome to the v8.4.0 release of the Opentrons robot software! This release incl
 
 ### New Features
 
-- Use new ``transfer_liquid``, ``distribute_liquid``, and ``consolidate_liquid`` commands on Flex to optimize liquid handling based on Opentrons-verified liquid classes. 
-- Stack multiple Opentrons Tough Auto-Sealing Lids on the deck. 
-- Move Opentrons Tough Auto-Sealing Lids or remove tip rack lids with the Flex Gripper. 
-- Aspirate or dispense in a well based on the liquid meniscus. 
+- Use new `transfer_liquid`, `distribute_liquid`, and `consolidate_liquid` commands on Flex to optimize liquid handling based on Opentrons-verified liquid classes.
+- Stack multiple Opentrons Tough Auto-Sealing Lids on the deck.
+- Move Opentrons Tough Auto-Sealing Lids or remove tip rack lids with the Flex Gripper.
+- Aspirate or dispense in a well based on the liquid meniscus.
 
 ### Improvements
 

api/src/opentrons/drivers/asyncio/communication/serial_connection.py

@@ -462,7 +462,10 @@ def __init__(
         self._async_error_ack = async_error_ack.lower()
 
     async def send_command(
-        self, command: CommandBuilder, retries: int = 0, timeout: Optional[float] = None
+        self,
+        command: CommandBuilder,
+        retries: int | None = None,
+        timeout: float | None = None,
     ) -> str:
         """
         Send a command and return the response.
@@ -478,12 +481,12 @@ async def send_command(
         """
         return await self.send_data(
             data=command.build(),
-            retries=retries or self._number_of_retries,
+            retries=retries if retries is not None else self._number_of_retries,
             timeout=timeout,
         )
 
     async def send_data(
-        self, data: str, retries: int = 0, timeout: Optional[float] = None
+        self, data: str, retries: int | None = None, timeout: float | None = None
     ) -> str:
         """
         Send data and return the response.
@@ -501,7 +504,8 @@ async def send_data(
             "timeout", timeout
         ):
             return await self._send_data(
-                data=data, retries=retries or self._number_of_retries
+                data=data,
+                retries=retries if retries is not None else self._number_of_retries,
             )
 
     async def _send_data(self, data: str, retries: int = 0) -> str:
@@ -517,7 +521,6 @@ async def _send_data(self, data: str, retries: int = 0) -> str:
         Raises: SerialException
         """
         data_encode = data.encode()
-        retries = retries or self._number_of_retries
 
         for retry in range(retries + 1):
             log.debug(f"{self._name}: Write -> {data_encode!r}")

api/src/opentrons/drivers/flex_stacker/driver.py

@@ -461,7 +461,12 @@ async def _get_tof_histogram_frame(
         command = GCODE.GET_TOF_MEASUREMENT.build_command().add_element(sensor.name)
         if resend:
             command.add_element("R")
-        resp = await self._connection.send_command(command)
+
+        # Note: We DONT want to auto resend the request if it fails, because the
+        # firmware will send the next frame id instead of the current one missed.
+        # So lets set `retries=0` so we only send the frame once and we can
+        # use the retry mechanism of the `get_tof_histogram` method instead.
+        resp = await self._connection.send_command(command, retries=0)
         return self.parse_get_tof_measurement(resp)
 
     async def get_tof_histogram(self, sensor: TOFSensor) -> TOFMeasurementResult:

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

@@ -451,6 +451,7 @@ def check_gripper_position_within_bounds(
         max_allowed_grip_error: float,
         hard_limit_lower: float,
         hard_limit_upper: float,
+        disable_geometry_grip_check: bool = False,
     ) -> None:
         ...
 

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

@@ -686,9 +686,9 @@ def _build_move_node_axis_runner(
         return (
             MoveGroupRunner(
                 move_groups=[move_group],
-                ignore_stalls=True
-                if not self._feature_flags.stall_detection_enabled
-                else False,
+                ignore_stalls=(
+                    True if not self._feature_flags.stall_detection_enabled else False
+                ),
             ),
             False,
         )
@@ -712,9 +712,9 @@ def _build_move_gear_axis_runner(
         return (
             MoveGroupRunner(
                 move_groups=[tip_motor_move_group],
-                ignore_stalls=True
-                if not self._feature_flags.stall_detection_enabled
-                else False,
+                ignore_stalls=(
+                    True if not self._feature_flags.stall_detection_enabled else False
+                ),
             ),
             True,
         )
@@ -939,9 +939,9 @@ async def home_tip_motors(
 
         runner = MoveGroupRunner(
             move_groups=[move_group],
-            ignore_stalls=True
-            if not self._feature_flags.stall_detection_enabled
-            else False,
+            ignore_stalls=(
+                True if not self._feature_flags.stall_detection_enabled else False
+            ),
         )
         try:
             positions = await runner.run(can_messenger=self._messenger)
@@ -976,9 +976,9 @@ async def tip_action(
         move_group = self._build_tip_action_group(origin, targets)
         runner = MoveGroupRunner(
             move_groups=[move_group],
-            ignore_stalls=True
-            if not self._feature_flags.stall_detection_enabled
-            else False,
+            ignore_stalls=(
+                True if not self._feature_flags.stall_detection_enabled else False
+            ),
         )
         try:
             positions = await runner.run(can_messenger=self._messenger)
@@ -1763,6 +1763,7 @@ def check_gripper_position_within_bounds(
         max_allowed_grip_error: float,
         hard_limit_lower: float,
         hard_limit_upper: float,
+        disable_geometry_grip_check: bool = False,
     ) -> None:
         """
         Check if the gripper is at the expected location.
@@ -1777,7 +1778,16 @@ def check_gripper_position_within_bounds(
             expected_grip_width + grip_width_uncertainty_wider
         )
         current_gripper_position = jaw_width
-        if isclose(current_gripper_position, hard_limit_lower):
+        log.info(
+            f"Checking gripper position: current {jaw_width}; max error {max_allowed_grip_error}; hard limits {hard_limit_lower}, {hard_limit_upper}; expected {expected_gripper_position_min}, {expected_grip_width}, {expected_gripper_position_max}; uncertainty {grip_width_uncertainty_narrower}, {grip_width_uncertainty_wider}"
+        )
+        if (
+            isclose(current_gripper_position, hard_limit_lower)
+            # this odd check handles internal backlash that can lead the position to read as if
+            # the gripper has overshot its lower bound; this is physically impossible and an
+            # artifact of the gearing, so it always indicates a hard stop
+            or current_gripper_position < hard_limit_lower
+        ):
             raise FailedGripperPickupError(
                 message="Failed to grip: jaws all the way closed",
                 details={
@@ -1796,6 +1806,7 @@ def check_gripper_position_within_bounds(
         if (
             current_gripper_position - expected_gripper_position_min
             < -max_allowed_grip_error
+            and not disable_geometry_grip_check
         ):
             raise FailedGripperPickupError(
                 message="Failed to grip: jaws closed too far",
@@ -1809,6 +1820,7 @@ def check_gripper_position_within_bounds(
         if (
             current_gripper_position - expected_gripper_position_max
             > max_allowed_grip_error
+            and not disable_geometry_grip_check
         ):
             raise FailedGripperPickupError(
                 message="Failed to grip: jaws could not close far enough",

api/src/opentrons/hardware_control/backends/ot3simulator.py

@@ -781,7 +781,7 @@ def subsystems(self) -> Dict[SubSystem, SubSystemState]:
                 next_fw_version=1,
                 fw_update_needed=False,
                 current_fw_sha="simulated",
-                pcba_revision="A1",
+                pcba_revision="A1.0",
                 update_state=None,
             )
             for axis in self._present_axes
@@ -848,6 +848,7 @@ def check_gripper_position_within_bounds(
         max_allowed_grip_error: float,
         hard_limit_lower: float,
         hard_limit_upper: float,
+        disable_geometry_grip_check: bool = False,
     ) -> None:
         # This is a (pretty bad) simulation of the gripper actually gripping something,
         # but it should work.

api/src/opentrons/hardware_control/dev_types.py

@@ -14,8 +14,9 @@
     PipetteModel,
     PipetteName,
     ChannelCount,
+    PipetteTipType,
+    LiquidClasses,
 )
-from opentrons_shared_data.pipette.types import PipetteTipType
 from opentrons_shared_data.pipette.pipette_definition import (
     PipetteConfigurations,
     SupportedTipsDefinition,
@@ -104,6 +105,7 @@ class PipetteDict(InstrumentDict):
     plunger_positions: Dict[str, float]
     shaft_ul_per_mm: float
     available_sensors: AvailableSensorDefinition
+    volume_mode: LiquidClasses  # LiquidClasses refer to volume mode in this context
 
 
 class PipetteStateDict(TypedDict):

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

@@ -267,6 +267,7 @@ def get_attached_instrument(self, mount: MountType) -> PipetteDict:
                 "drop_tip": instr.plunger_positions.drop_tip,
             }
             result["shaft_ul_per_mm"] = instr.config.shaft_ul_per_mm
+            result["volume_mode"] = instr.liquid_class_name
         return cast(PipetteDict, result)
 
     @property

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

@@ -294,6 +294,7 @@ def get_attached_instrument(self, mount: OT3Mount) -> PipetteDict:
             }
             result["shaft_ul_per_mm"] = instr.config.shaft_ul_per_mm
             result["available_sensors"] = instr.config.available_sensors
+            result["volume_mode"] = instr.liquid_class_name
         return cast(PipetteDict, result)
 
     @property

api/src/opentrons/hardware_control/ot3api.py

@@ -1462,6 +1462,7 @@ def raise_error_if_gripper_pickup_failed(
         expected_grip_width: float,
         grip_width_uncertainty_wider: float,
         grip_width_uncertainty_narrower: float,
+        disable_geometry_grip_check: bool = False,
     ) -> None:
         """Ensure that a gripper pickup succeeded.
 
@@ -1480,8 +1481,9 @@ def raise_error_if_gripper_pickup_failed(
             grip_width_uncertainty_narrower,
             gripper.jaw_width,
             gripper.max_allowed_grip_error,
-            gripper.max_jaw_width,
             gripper.min_jaw_width,
+            gripper.max_jaw_width,
+            disable_geometry_grip_check,
         )
 
     def gripper_jaw_can_home(self) -> bool:

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

@@ -41,6 +41,7 @@ def raise_error_if_gripper_pickup_failed(
         expected_grip_width: float,
         grip_width_uncertainty_wider: float,
         grip_width_uncertainty_narrower: float,
+        disable_geometry_grip_check: bool = False,
     ) -> None:
         """Ensure that a gripper pickup succeeded."""
 

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

@@ -0,0 +1,56 @@
+"""The versions of standard liquid classes that the Protocol API should load by default."""
+
+from typing import TypeAlias
+from opentrons.protocols.api_support.types import APIVersion
+
+
+DefaultLiquidClassVersions: TypeAlias = dict[APIVersion, dict[str, int]]
+
+
+# This:
+#
+# {
+#     APIVersion(2, 100): {
+#         "foo_liquid": 3,
+#     },
+#     APIVersion(2, 105): {
+#         "foo_liquid": 7
+#     }
+# }
+#
+# Means this:
+#
+# apiLevels        name              Default liquid class version
+# ---------------------------------------------------------------
+# <2.100           foo_liquid        1
+# >=2.100,<2.105   foo_liquid        3
+# >=2.105          foo_liquid        7
+# [any]            [anything else]   1
+DEFAULT_LIQUID_CLASS_VERSIONS: DefaultLiquidClassVersions = {
+    APIVersion(2, 26): {
+        "ethanol_80": 2,
+        "glycerol_50": 2,
+        "water": 2,
+    },
+}
+
+
+def get_liquid_class_version(
+    api_version: APIVersion,
+    liquid_class_name: str,
+) -> int:
+    """Return what version of a liquid class the Protocol API should load by default."""
+    default_lc_versions_newest_to_oldest = sorted(
+        DEFAULT_LIQUID_CLASS_VERSIONS.items(), key=lambda kv: kv[0], reverse=True
+    )
+    for (
+        breakpoint_api_version,
+        breakpoint_liquid_class_versions,
+    ) in default_lc_versions_newest_to_oldest:
+        if (
+            api_version >= breakpoint_api_version
+            and liquid_class_name in breakpoint_liquid_class_versions
+        ):
+            return breakpoint_liquid_class_versions[liquid_class_name]
+
+    return 1