opentrons 8.6.0a11__py3-none-any.whl → 8.7.0__py3-none-any.whl

opentrons/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '8.6.0a11'
-__version_tuple__ = version_tuple = (8, 6, 0, 'a11')
+__version__ = version = '8.7.0'
+__version_tuple__ = version_tuple = (8, 7, 0)
 
 __commit_id__ = commit_id = None

opentrons/cli/analyze.py

@@ -1,4 +1,5 @@
 """Opentrons analyze CLI."""
+
 import click
 
 from anyio import run
@@ -24,7 +25,9 @@ from typing import (
 import logging
 import sys
 import json
+import gc
 
+from opentrons.protocol_engine import ProtocolEngine
 from opentrons.protocol_engine.types import (
     RunTimeParameter,
     CSVRuntimeParamPaths,
@@ -94,6 +97,18 @@ class _Output:
     help="Return analysis results as JSON, formatted for human eyes. Specify --human-json-output=- to use stdout, but be aware that Python protocols may contain print() which will make the output JSON invalid.",
     type=click.File(mode="wb"),
 )
+@click.option(
+    "--leaks",
+    help="Fail (via exit code) if the analysis engine has not been garbage collected after analysis is complete.",
+    is_flag=True,
+    default=False,
+)
+@click.option(
+    "--leaks-debug",
+    help="Drop into a PDB shell if a leak is detected",
+    is_flag=True,
+    default=False,
+)
 @click.option(
     "--check",
     help="Fail (via exit code) if the protocol had an error. If not specified, always succeed.",
@@ -133,6 +148,8 @@ def analyze(
     log_output: str,
     log_level: str,
     check: bool,
+    leaks: bool,
+    leaks_debug: bool,
 ) -> int:
     """Analyze a protocol.
 
@@ -147,7 +164,18 @@ def analyze(
 
     try:
         with _capture_logs(log_output, log_level):
-            sys.exit(run(_analyze, files, rtp_values, rtp_files, outputs, check))
+            sys.exit(
+                run(
+                    _analyze,
+                    files,
+                    rtp_values,
+                    rtp_files,
+                    outputs,
+                    check,
+                    leaks or leaks_debug,
+                    leaks_debug,
+                )
+            )
     except click.ClickException:
         raise
     except Exception as e:
@@ -344,12 +372,14 @@ async def _do_analyze(
     return await orchestrator.run(deck_configuration=[])
 
 
-async def _analyze(
+async def _analyze(  # noqa: C901
     files_and_dirs: Sequence[Path],
     rtp_values: str,
     rtp_files: str,
     outputs: Sequence[_Output],
     check: bool,
+    fail_on_leak: bool,
+    debug_on_leak: bool,
 ) -> int:
     input_files = _get_input_files(files_and_dirs)
     parsed_rtp_values = _get_runtime_parameter_values(rtp_values)
@@ -366,6 +396,32 @@ async def _analyze(
     analysis = await _do_analyze(protocol_source, parsed_rtp_values, rtp_paths)
     return_code = _get_return_code(analysis)
 
+    # This ugly code checks to see if an engine remains past garbage collection
+    # after analysis is complete.
+    # It should be here and open coded to make it a little easier to present
+    # the debug option.
+    if fail_on_leak or debug_on_leak:
+        gc.collect()
+        leaked_engine = next(
+            (obj for obj in gc.get_objects() if isinstance(obj, ProtocolEngine)), None
+        )
+        if leaked_engine:
+            if fail_on_leak:
+                print(
+                    "A ProtocolEngine instance exists even after garbage collection; "
+                    "some thing (likely in the protocol) has caused it to be leaked, "
+                    "likely by reference to the engine or something that refers to the "
+                    "engine after the run function ends.",
+                    file=sys.stderr,
+                )
+                return_code = -2
+            if debug_on_leak:
+                print(
+                    "You are now in an interactive PDB (https://docs.python.org/3.10/library/pdb.html) "
+                    "session; the leaked engine is bound to the variable leaked_engine."
+                )
+                breakpoint()
+
     if not outputs:
         return return_code
 

opentrons/drivers/asyncio/communication/serial_connection.py

@@ -462,7 +462,10 @@ class AsyncResponseSerialConnection(SerialConnection):
         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 @@ class AsyncResponseSerialConnection(SerialConnection):
         """
         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 @@ class AsyncResponseSerialConnection(SerialConnection):
             "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 @@ class AsyncResponseSerialConnection(SerialConnection):
         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}")

opentrons/drivers/flex_stacker/driver.py

@@ -461,7 +461,12 @@ class FlexStackerDriver(AbstractFlexStackerDriver):
         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:

opentrons/hardware_control/backends/flex_protocol.py

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

opentrons/hardware_control/backends/ot3controller.py

@@ -686,9 +686,9 @@ class OT3Controller(FlexBackend):
         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 @@ class OT3Controller(FlexBackend):
         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 @@ class OT3Controller(FlexBackend):
 
         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 @@ class OT3Controller(FlexBackend):
         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 @@ class OT3Controller(FlexBackend):
         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 @@ class OT3Controller(FlexBackend):
             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 @@ class OT3Controller(FlexBackend):
         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 @@ class OT3Controller(FlexBackend):
         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",

opentrons/hardware_control/backends/ot3simulator.py

@@ -781,7 +781,7 @@ class OT3Simulator(FlexBackend):
                 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 @@ class OT3Simulator(FlexBackend):
         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.

opentrons/hardware_control/dev_types.py

@@ -14,8 +14,9 @@ from opentrons_shared_data.pipette.types import (
     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):

opentrons/hardware_control/instruments/ot2/pipette_handler.py

@@ -267,6 +267,7 @@ class PipetteHandlerProvider(Generic[MountType]):
                 "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

opentrons/hardware_control/instruments/ot3/pipette_handler.py

@@ -294,6 +294,7 @@ class OT3PipetteHandler:
             }
             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

opentrons/hardware_control/ot3api.py

@@ -1462,6 +1462,7 @@ class OT3API(
         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 @@ class OT3API(
             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:

opentrons/hardware_control/protocols/gripper_controller.py

@@ -41,6 +41,7 @@ class GripperController(Protocol):
         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."""
 

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