Merge branch 'edge' into E2E_Transfer_and_Command_update

abr-testing/Pipfile

@@ -20,6 +20,7 @@ pandas = "*"
 pandas-stubs = "*"
 paramiko = "*"
 prettier = "*"
+pydantic = "==2.9.0"
 
 [dev-packages]
 atomicwrites = "==1.4.1"

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

@@ -1397,7 +1397,11 @@ async def clean_up(self) -> None:
             return
 
         if hasattr(self, "_event_watcher"):
-            if loop.is_running() and self._event_watcher:
+            if (
+                loop.is_running()
+                and self._event_watcher
+                and not self._event_watcher.closed
+            ):
                 self._event_watcher.close()
 
         messenger = getattr(self, "_messenger", None)

api/src/opentrons/protocol_api/validation.py

@@ -14,13 +14,15 @@
 from math import isinf, isnan
 from typing_extensions import TypeGuard
 
-from opentrons_shared_data.labware.labware_definition import LabwareRole
+from opentrons_shared_data.labware.labware_definition import (
+    LabwareDefinition,
+    LabwareRole,
+)
 from opentrons_shared_data.pipette.types import PipetteNameType
 from opentrons_shared_data.robot.types import RobotType
 
 from opentrons.protocols.api_support.types import APIVersion, ThermocyclerStep
 from opentrons.protocols.api_support.util import APIVersionError
-from opentrons.protocols.models import LabwareDefinition
 from opentrons.protocols.advanced_control.transfers.common import TransferTipPolicyV2
 from opentrons.types import (
     Mount,

api/src/opentrons/protocol_engine/actions/actions.py

@@ -8,12 +8,12 @@
 from enum import Enum
 from typing import List, Optional, Union
 
-from opentrons.protocols.models import LabwareDefinition
+from opentrons_shared_data.errors import EnumeratedError
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
+
 from opentrons.hardware_control.types import DoorState
 from opentrons.hardware_control.modules import LiveData
 
-from opentrons_shared_data.errors import EnumeratedError
-
 from ..commands import (
     Command,
     CommandCreate,

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

@@ -2,10 +2,10 @@
 from dataclasses import dataclass
 from typing import Optional, overload, Union, List
 
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
 from opentrons_shared_data.pipette.types import PipetteNameType
 
 from opentrons.calibration_storage.helpers import uri_from_details
-from opentrons.protocols.models import LabwareDefinition
 from opentrons.types import MountType
 from opentrons.hardware_control import HardwareControlAPI
 from opentrons.hardware_control.modules import (

api/src/opentrons/protocol_engine/protocol_engine.py

@@ -2,20 +2,21 @@
 from contextlib import AsyncExitStack
 from logging import getLogger
 from typing import Dict, Optional, Union, AsyncGenerator, Callable
-from opentrons.protocol_engine.actions.actions import (
-    ResumeFromRecoveryAction,
-    SetErrorRecoveryPolicyAction,
-)
 
-from opentrons.protocols.models import LabwareDefinition
-from opentrons.hardware_control import HardwareControlAPI
-from opentrons.hardware_control.modules import AbstractModule as HardwareModuleAPI
-from opentrons.hardware_control.types import PauseType as HardwarePauseType
 from opentrons_shared_data.errors import (
     ErrorCodes,
     EnumeratedError,
 )
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
 
+from opentrons.hardware_control import HardwareControlAPI
+from opentrons.hardware_control.modules import AbstractModule as HardwareModuleAPI
+from opentrons.hardware_control.types import PauseType as HardwarePauseType
+
+from .actions.actions import (
+    ResumeFromRecoveryAction,
+    SetErrorRecoveryPolicyAction,
+)
 from .errors import ProtocolCommandFailedError, ErrorOccurrence, CommandNotAllowedError
 from .errors.exceptions import EStopActivatedError
 from .error_recovery_policy import ErrorRecoveryPolicy

api/src/opentrons/protocol_engine/resources/deck_data_provider.py

@@ -10,7 +10,7 @@
     DEFAULT_DECK_DEFINITION_VERSION,
 )
 from opentrons_shared_data.deck.types import DeckDefinitionV5
-from opentrons.protocols.models import LabwareDefinition
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
 from opentrons.types import DeckSlotName
 
 from ..types import (

api/src/opentrons/protocol_engine/resources/labware_data_provider.py

@@ -6,7 +6,8 @@
 import logging
 from anyio import to_thread
 
-from opentrons.protocols.models import LabwareDefinition
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
+
 from opentrons.protocols.labware import get_labware_definition
 
 # TODO (lc 09-26-2022) We should conditionally import ot2 or ot3 calibration

api/src/opentrons/protocol_engine/resources/labware_validation.py

@@ -1,7 +1,9 @@
 """Validation file for labware role and location checking functions."""
 
-from opentrons_shared_data.labware.labware_definition import LabwareRole
-from opentrons.protocols.models import LabwareDefinition
+from opentrons_shared_data.labware.labware_definition import (
+    LabwareDefinition,
+    LabwareRole,
+)
 
 
 def is_flex_trash(load_name: str) -> bool:

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

@@ -82,19 +82,12 @@ def _circular_frustum_polynomial_roots(
 
 
 def _volume_from_height_circular(
-    target_height: float,
-    total_frustum_height: float,
-    bottom_radius: float,
-    top_radius: float,
+    target_height: float, segment: ConicalFrustum
 ) -> float:
     """Find the volume given a height within a circular frustum."""
-    a, b, c = _circular_frustum_polynomial_roots(
-        bottom_radius=bottom_radius,
-        top_radius=top_radius,
-        total_frustum_height=total_frustum_height,
-    )
-    volume = a * (target_height**3) + b * (target_height**2) + c * target_height
-    return volume
+    heights = segment.height_to_volume_table.keys()
+    best_fit_height = min(heights, key=lambda x: abs(x - target_height))
+    return segment.height_to_volume_table[best_fit_height]
 
 
 def _volume_from_height_rectangular(
@@ -138,26 +131,12 @@ def _volume_from_height_squared_cone(
 
 
 def _height_from_volume_circular(
-    volume: float,
-    total_frustum_height: float,
-    bottom_radius: float,
-    top_radius: float,
+    target_volume: float, segment: ConicalFrustum
 ) -> float:
-    """Find the height given a volume within a circular frustum."""
-    a, b, c = _circular_frustum_polynomial_roots(
-        bottom_radius=bottom_radius,
-        top_radius=top_radius,
-        total_frustum_height=total_frustum_height,
-    )
-    d = volume * -1
-    x_intercept_roots = (a, b, c, d)
-
-    height_from_volume_roots = roots(x_intercept_roots)
-    height = _reject_unacceptable_heights(
-        potential_heights=list(height_from_volume_roots),
-        max_height=total_frustum_height,
-    )
-    return height
+    """Find the height given a volume within a squared cone segment."""
+    volumes = segment.volume_to_height_table.keys()
+    best_fit_volume = min(volumes, key=lambda x: abs(x - target_volume))
+    return segment.volume_to_height_table[best_fit_volume]
 
 
 def _height_from_volume_rectangular(
@@ -243,9 +222,7 @@ def _get_segment_capacity(segment: WellSegment) -> float:
             return (
                 _volume_from_height_circular(
                     target_height=section_height,
-                    total_frustum_height=section_height,
-                    bottom_radius=(segment.bottomDiameter / 2),
-                    top_radius=(segment.topDiameter / 2),
+                    segment=segment,
                 )
                 * segment.count
             )
@@ -293,12 +270,7 @@ def height_at_volume_within_section(
                 radius_of_curvature=section.radiusOfCurvature,
             )
         case ConicalFrustum():
-            return _height_from_volume_circular(
-                volume=target_volume_relative,
-                top_radius=(section.bottomDiameter / 2),
-                bottom_radius=(section.topDiameter / 2),
-                total_frustum_height=section_height,
-            )
+            return _height_from_volume_circular(target_volume_relative, section)
         case CuboidalFrustum():
             return _height_from_volume_rectangular(
                 volume=target_volume_relative,
@@ -334,10 +306,7 @@ def volume_at_height_within_section(
         case ConicalFrustum():
             return (
                 _volume_from_height_circular(
-                    target_height=target_height_relative,
-                    total_frustum_height=section_height,
-                    bottom_radius=(section.bottomDiameter / 2),
-                    top_radius=(section.topDiameter / 2),
+                    target_height=target_height_relative, segment=section
                 )
                 * section.count
             )
@@ -427,7 +396,7 @@ def _find_height_in_partial_frustum(
         if (
             bottom_section_volume
             < target_volume
-            < (bottom_section_volume + section_volume)
+            <= (bottom_section_volume + section_volume)
         ):
             relative_target_volume = target_volume - bottom_section_volume
             section_height = section.topHeight - section.bottomHeight

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

@@ -11,10 +11,10 @@
 
 from opentrons_shared_data.errors.exceptions import InvalidStoredData
 from opentrons_shared_data.labware.constants import WELL_NAME_PATTERN
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
 from opentrons_shared_data.deck.types import CutoutFixture
 from opentrons_shared_data.pipette import PIPETTE_X_SPAN
 from opentrons_shared_data.pipette.types import ChannelCount
-from opentrons.protocols.models import LabwareDefinition
 
 from .. import errors
 from ..errors import (

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

@@ -20,14 +20,15 @@
 from opentrons_shared_data.deck.types import DeckDefinitionV5
 from opentrons_shared_data.gripper.constants import LABWARE_GRIP_FORCE
 from opentrons_shared_data.labware.labware_definition import (
-    LabwareRole,
     InnerWellGeometry,
+    LabwareDefinition,
+    LabwareRole,
+    WellDefinition,
 )
 from opentrons_shared_data.pipette.types import LabwareUri
 
 from opentrons.types import DeckSlotName, StagingSlotName, MountType
 from opentrons.protocols.api_support.constants import OPENTRONS_NAMESPACE
-from opentrons.protocols.models import LabwareDefinition, WellDefinition
 from opentrons.calibration_storage.helpers import uri_from_details
 
 from .. import errors
@@ -524,7 +525,6 @@ def get_well_definition(
         will be used.
         """
         definition = self.get_definition(labware_id)
-
         if well_name is None:
             well_name = definition.ordering[0][0]
 

api/src/opentrons/protocol_reader/extract_labware_definitions.py

@@ -6,7 +6,7 @@
 
 import anyio
 
-from opentrons.protocols.models import LabwareDefinition
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
 
 from .protocol_source import ProtocolFileRole, ProtocolSource, ProtocolType
 

api/src/opentrons/protocol_reader/file_format_validator.py

@@ -14,7 +14,7 @@
 )
 from opentrons_shared_data.errors.exceptions import PythonException
 
-from opentrons.protocols.models import JsonProtocol as JsonProtocolUpToV5
+from opentrons.protocols.models.json_protocol import Model as JsonProtocolUpToV5
 
 from .file_identifier import (
     IdentifiedFile,

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

@@ -1,21 +0,0 @@
-# Convenience re-exports of models that are especially common or important.
-# More detailed sub-models are always available through the underlying
-# submodules.
-#
-# If re-exporting something, its name should still make sense when it's separated
-# from the name of its parent submodule. e.g. re-exporting models.json_protocol.Labware
-# as models.Labware could be confusing.
-
-# TODO(mc, 2022-03-11): remove this re-export when it won't break pickling
-# https://opentrons.atlassian.net/browse/RSS-94
-from opentrons_shared_data.labware.labware_definition import (
-    LabwareDefinition,
-    WellDefinition,
-)
-from .json_protocol import Model as JsonProtocol
-
-__all__ = [
-    "LabwareDefinition",
-    "WellDefinition",
-    "JsonProtocol",
-]

api/tests/opentrons/hardware_control/backends/test_ot3_controller.py

@@ -145,7 +145,18 @@ def mock_messenger(can_message_notifier: MockCanMessageNotifier) -> mock.AsyncMo
 
 @pytest.fixture
 def mock_can_driver(mock_messenger: mock.AsyncMock) -> AbstractCanDriver:
-    return mock.AsyncMock(spec=AbstractCanDriver)
+    driver = mock.AsyncMock(spec=AbstractCanDriver)
+
+    # ignoring this type error because this is a very weird function that will in fact
+    # do nothing, but has to have the yield in there for the compiler to make it a
+    # generator function
+    async def _fake_message_retrieve(d):  # type: ignore[no-untyped-def]
+        while True:
+            await asyncio.sleep(1)
+        yield
+
+    driver.__aiter__ = _fake_message_retrieve
+    return driver
 
 
 @pytest.fixture
@@ -160,15 +171,19 @@ def mock_eeprom_driver() -> EEPROMDriver:
 
 
 @pytest.fixture
-def controller(
+async def controller(
     mock_config: OT3Config,
     mock_can_driver: AbstractCanDriver,
     mock_eeprom_driver: EEPROMDriver,
-) -> OT3Controller:
-    with (mock.patch("opentrons.hardware_control.backends.ot3controller.OT3GPIO")):
-        return OT3Controller(
+) -> AsyncIterator[OT3Controller]:
+    with mock.patch("opentrons.hardware_control.backends.ot3controller.OT3GPIO"):
+        controller = OT3Controller(
             mock_config, mock_can_driver, eeprom_driver=mock_eeprom_driver
         )
+        try:
+            yield controller
+        finally:
+            await controller.clean_up()
 
 
 @pytest.fixture

api/tests/opentrons/protocol_api/test_validation.py

@@ -9,6 +9,7 @@
 
 from opentrons.protocols.advanced_control.transfers.common import TransferTipPolicyV2
 from opentrons_shared_data.labware.labware_definition import (
+    LabwareDefinition,
     LabwareRole,
     Parameters as LabwareDefinitionParameters,
 )
@@ -33,7 +34,6 @@
     HeaterShakerModuleModel,
     ThermocyclerStep,
 )
-from opentrons.protocols.models import LabwareDefinition
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocols.api_support.util import APIVersionError
 from opentrons.protocol_api import (

api/tests/opentrons/protocol_engine/commands/test_load_labware.py

@@ -6,8 +6,9 @@
 import pytest
 from decoy import Decoy
 
+from opentrons_shared_data.labware.labware_definition import LabwareDefinition
+
 from opentrons.types import DeckSlotName
-from opentrons.protocols.models import LabwareDefinition
 
 from opentrons.protocol_engine.errors import (
     LabwareIsNotAllowedInLocationError,

api/tests/opentrons/protocol_engine/commands/test_move_labware.py

@@ -7,7 +7,11 @@
 import pytest
 from decoy import Decoy, matchers
 
-from opentrons_shared_data.labware.labware_definition import Parameters, Dimensions
+from opentrons_shared_data.labware.labware_definition import (
+    LabwareDefinition,
+    Parameters,
+    Dimensions,
+)
 from opentrons_shared_data.errors.exceptions import (
     EnumeratedError,
     FailedGripperPickupError,
@@ -18,7 +22,6 @@
 
 from opentrons.protocol_engine.state import update_types
 from opentrons.types import DeckSlotName, Point
-from opentrons.protocols.models import LabwareDefinition
 from opentrons.protocol_engine import errors, Config
 from opentrons.protocol_engine.resources import labware_validation
 from opentrons.protocol_engine.resources.model_utils import ModelUtils