Merge branch 'edge' into pick_up_tip_testing

.github/actions/python/pypi-deploy/action.yaml

@@ -28,7 +28,7 @@ runs:
           fi
         fi
         status=0
-        QUIET=1 BUILD_NUMBER=${OT_BUILD} make -C ${{ inputs.project }} clean deploy twine_repository_url=${{ inputs.repository_url }} pypi_username=opentrons pypi_password=${{ inputs.password }} || status=$?
+        CI=1 QUIET=1 BUILD_NUMBER=${OT_BUILD} make -C ${{ inputs.project }} clean deploy twine_repository_url=${{ inputs.repository_url }} pypi_username=opentrons pypi_password=${{ inputs.password }} || status=$?
         if [[ ${status} != 0 ]] && [[ ${{ inputs.repository_url }} =~ "test.pypi.org" ]]; then
           echo "upload failures allowed to test pypi"
           exit 0

api/Makefile

@@ -199,8 +199,8 @@ emulator:
 	-$(python) -m opentrons.hardware_control.emulation.app
 
 .PHONY: deploy
-deploy: wheel
-	$(call python_upload_package,$(twine_auth_args),$(twine_repository_url),$(wheel_file))
+deploy: wheel sdist
+	$(call python_upload_package,$(twine_auth_args),$(twine_repository_url),$(wheel_file),$(sdist_file))
 
 # User must currently specify host, e.g.: `make term host=169.254.202.176`
 .PHONY: term

api/Pipfile

@@ -3,42 +3,48 @@ url = "https://pypi.python.org/simple"
 verify_ssl = true
 name = "pypi"
 
+[packages]
+jsonschema = "==4.17.3"
+pydantic = "==1.10.12"
+anyio = "==3.7.1"
+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"
+
 [dev-packages]
 # atomicwrites and colorama are pytest dependencies on windows,
 # spec'd here to force lockfile inclusion
 # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177
 atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" }
 colorama = { version = "==0.4.4", markers="sys_platform=='win32'" }
-coverage = "==5.1"
-mypy = "==0.981"
+coverage = "==7.4.1"
+mypy = "==1.8.0"
 numpydoc = "==0.9.1"
-pytest = "==7.0.1"
-pytest-asyncio = "~=0.16"
-pytest-cov = "==2.10.1"
+pytest = "==7.4.4"
+pytest-asyncio = "~=0.23.0"
+pytest-cov = "==4.1.0"
 pytest-lazy-fixture = "==0.6.3"
 pytest-xdist = "~=2.5.0"
 sphinx = "==5.0.1"
 twine = "==4.0.0"
 wheel = "==0.37.0"
-typeguard = "==2.13.1"
+typeguard = "==4.1.5"
 sphinx-substitution-extensions = "==2020.9.30.0"
 sphinxext-opengraph = "==0.8.1"
 sphinx-tabs = ">=3.4.1,<4"
-mock = "~=4.0.3"
-flake8 = "~=3.9.0"
-flake8-annotations = "~=2.6.2"
-flake8-docstrings = "~=1.6.0"
-flake8-noqa = "~=1.2.1"
-decoy = "~=1.11"
+mock = "==5.1.0"
+flake8 = "==7.0.0"
+flake8-annotations = "~=3.0.1"
+flake8-docstrings = "~=1.7.0"
+flake8-noqa = "~=1.4.0"
+decoy = "==2.1.1"
 black = "==22.3.0"
-types-mock = "==4.0.1"
+types-mock = "~=5.1.0"
 types-setuptools = "==57.0.2"
-opentrons-shared-data = { editable = true, path = "../shared-data/python" }
-opentrons = { editable = true, path = "." }
-opentrons-hardware = { editable = true, path = "./../hardware", extras=["FLEX"] }
 # specify typing-extensions explicitly to force lockfile inclusion on Python >= 3.8
 typing-extensions = ">=4.0.0,<5"
 pytest-profiling = "~=1.7.0"
 # TODO(mc, 2022-03-31): upgrade sphinx, remove this subdep pin
 jinja2 = ">=2.3,<3.1"
-hypothesis = ">=6.36,<7"
+hypothesis = "==6.96.1"

api/mypy.ini

@@ -4,7 +4,7 @@ show_error_codes = True
 warn_unused_configs = True
 strict = True
 # TODO(mc, 2021-09-12): work through and remove these exclusions
-exclude = tests/opentrons/(hardware_control/test_(?!ot3).*py|hardware_control/integration/|hardware_control/emulation/|hardware_control/modules/|protocols/advanced_control/|protocols/api_support/|protocols/duration/|protocols/execution/|protocols/fixtures/|protocols/geometry/)
+exclude = tests/opentrons/(hardware_control/test_(?!(ot3|module_control)).*py|hardware_control/integration/|hardware_control/emulation/|hardware_control/modules/|protocols/advanced_control/|protocols/api_support/|protocols/duration/|protocols/execution/|protocols/fixtures/|protocols/geometry/)
 
 [pydantic-mypy]
 init_forbid_extra = True

api/setup.py

@@ -60,11 +60,11 @@ def get_version():
 INSTALL_REQUIRES = [
     f"opentrons-shared-data=={VERSION}",
     "aionotify==0.2.0",
-    "anyio==3.6.1",
-    "jsonschema==3.0.2",
-    "numpy>=1.15.1,<2",
-    "pydantic==1.9.2",
-    "pyserial==3.5",
+    "anyio>=3.6.1,<4.0.0",
+    "jsonschema>=3.0.1,<4.18.0",
+    "numpy>=1.20.0,<2",
+    "pydantic>=1.10.9,<2.0.0",
+    "pyserial>=3.5",
     "typing-extensions>=4.0.0,<5",
     "click>=8.0.0,<9",
     'importlib-metadata >= 1.0 ; python_version < "3.8"',

api/src/opentrons/calibration_storage/helpers.py

@@ -5,7 +5,7 @@
 labware calibration to its designated file location.
 """
 import json
-from typing import Any, Union, List, Dict, TYPE_CHECKING, cast
+from typing import Any, Union, List, Dict, TYPE_CHECKING, cast, Tuple
 from dataclasses import is_dataclass, asdict
 
 
@@ -18,10 +18,7 @@
     from opentrons_shared_data.pipette.dev_types import LabwareUri
 
 
-DictionaryFactoryType = Union[List, Dict]
-
-
-def dict_filter_none(data: DictionaryFactoryType) -> Dict[str, Any]:
+def dict_filter_none(data: List[Tuple[str, Any]]) -> Dict[str, Any]:
     """
     Helper function to filter out None keys from a dataclass
     before saving to file.

api/src/opentrons/calibration_storage/ot2/models/v1.py

@@ -51,7 +51,7 @@ class DeckCalibrationModel(BaseModel):
     attitude: types.AttitudeMatrix = Field(
         ..., description="Attitude matrix for deck found from calibration."
     )
-    last_modified: datetime = Field(
+    last_modified: typing.Optional[datetime] = Field(
         default=None, description="The last time this deck was calibrated."
     )
     source: types.SourceType = Field(

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

@@ -7,7 +7,7 @@
 from typing import Optional, AsyncGenerator, Union
 from typing_extensions import Literal
 
-from serial import Serial, serial_for_url  # type: ignore[import]
+from serial import Serial, serial_for_url  # type: ignore[import-untyped]
 
 TimeoutProperties = Union[Literal["write_timeout"], Literal["timeout"]]
 

api/src/opentrons/drivers/rpi_drivers/gpio.py

@@ -7,7 +7,7 @@
 from . import RevisionPinsError
 from .types import gpio_group, PinDir, GPIOPin
 
-import gpiod  # type: ignore[import]
+import gpiod  # type: ignore[import-not-found]
 
 """
 Raspberry Pi GPIO control module

api/src/opentrons/drivers/serial_communication.py

@@ -1,12 +1,12 @@
 from typing import List, Optional, Iterator
 
-import serial  # type: ignore[import]
+import serial  # type: ignore[import-untyped]
 from serial import Serial
-from serial.tools import list_ports  # type: ignore[import]
+from serial.tools import list_ports  # type: ignore[import-untyped]
 import contextlib
 import logging
 
-from serial.tools.list_ports_common import ListPortInfo  # type: ignore[import]
+from serial.tools.list_ports_common import ListPortInfo  # type: ignore[import-untyped]
 
 log = logging.getLogger(__name__)
 

api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py

@@ -18,7 +18,7 @@
 from math import isclose
 
 from opentrons.drivers.serial_communication import get_ports_by_name
-from serial.serialutil import SerialException  # type: ignore[import]
+from serial.serialutil import SerialException  # type: ignore[import-untyped]
 
 from opentrons.drivers.smoothie_drivers.connection import SmoothieConnection
 from opentrons.drivers.smoothie_drivers.constants import (

api/src/opentrons/drivers/smoothie_drivers/simulator.py

@@ -57,11 +57,11 @@ async def update_pipette_config(
         - endstop debounce M365.2 (NOT for zprobe debounce)
         - retract from endstop distance M365.3
         """
-        pass
+        return {}
 
     @property
     def current(self) -> Dict[str, float]:
-        pass
+        return {}
 
     @property
     def speed(self) -> None:

api/src/opentrons/hardware_control/api.py

@@ -762,7 +762,7 @@ async def move_to(
             top_types.Point(0, 0, 0),
         )
 
-        await self._cache_and_maybe_retract_mount(mount)
+        await self.prepare_for_mount_movement(mount)
         await self._move(target_position, speed=speed, max_speeds=max_speeds)
 
     async def move_axes(
@@ -822,7 +822,7 @@ async def move_rel(
                 detail={"mount": str(mount), "unhomed_axes": str(unhomed)},
             )
 
-        await self._cache_and_maybe_retract_mount(mount)
+        await self.prepare_for_mount_movement(mount)
         await self._move(
             target_position,
             speed=speed,
@@ -842,6 +842,9 @@ async def _cache_and_maybe_retract_mount(self, mount: top_types.Mount) -> None:
             await self.retract(self._last_moved_mount, 10)
         self._last_moved_mount = mount
 
+    async def prepare_for_mount_movement(self, mount: top_types.Mount) -> None:
+        await self._cache_and_maybe_retract_mount(mount)
+
     @ExecutionManagerProvider.wait_for_running
     async def _move(
         self,

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

@@ -19,7 +19,7 @@
 from pathlib import Path
 
 try:
-    import aionotify  # type: ignore[import]
+    import aionotify  # type: ignore[import-untyped]
 except (OSError, ModuleNotFoundError):
     aionotify = None
 

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

@@ -54,7 +54,7 @@
 from .tip_presence_manager import TipPresenceManager
 
 try:
-    import aionotify  # type: ignore[import]
+    import aionotify  # type: ignore[import-untyped]
 except (OSError, ModuleNotFoundError):
     aionotify = None
 
@@ -653,6 +653,7 @@ async def move(
             if not self._feature_flags.stall_detection_enabled
             else False,
         )
+
         mounts_moving = [
             k
             for k in moving_axes_in_move_group(move_group)
@@ -1224,7 +1225,6 @@ async def probe(self, axis: Axis, distance: float) -> OT3AxisMap[float]:
 
     async def clean_up(self) -> None:
         """Clean up."""
-
         try:
             loop = asyncio.get_event_loop()
         except RuntimeError:
@@ -1233,6 +1233,15 @@ async def clean_up(self) -> None:
         if hasattr(self, "_event_watcher"):
             if loop.is_running() and self._event_watcher:
                 self._event_watcher.close()
+
+        messenger = getattr(self, "_messenger", None)
+        if messenger:
+            await messenger.stop()
+
+        usb_messenger = getattr(self, "_usb_messenger", None)
+        if usb_messenger:
+            await usb_messenger.stop()
+
         return None
 
     @staticmethod

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

@@ -446,7 +446,7 @@ async def home_tip_motors(
     def _attached_to_mount(
         self, mount: OT3Mount, expected_instr: Optional[PipetteName]
     ) -> OT3AttachedInstruments:
-        init_instr = self._attached_instruments.get(mount, {"model": None, "id": None})  # type: ignore
+        init_instr = self._attached_instruments.get(mount, {"model": None, "id": None})
         if mount is OT3Mount.GRIPPER:
             return self._attached_gripper_to_mount(cast(GripperSpec, init_instr))
         return self._attached_pipette_to_mount(

api/src/opentrons/hardware_control/dev_types.py

@@ -95,7 +95,7 @@ class PipetteDict(InstrumentDict):
     has_tip: bool
     default_push_out_volume: Optional[float]
     supported_tips: Dict[PipetteTipType, SupportedTipsDefinition]
-    current_nozzle_map: Optional[NozzleMap]
+    current_nozzle_map: NozzleMap  # spp: why was this Optional?
 
 
 class PipetteStateDict(TypedDict):

api/src/opentrons/hardware_control/execution_manager.py

@@ -74,7 +74,9 @@ async def wait_for_is_running(self) -> None:
         async with self._condition:
             if self._state == ExecutionState.PAUSED:
                 await self._condition.wait()
-                if self._state == ExecutionState.CANCELLED:
+                # type-ignore needed because this is a reentrant function and narrowing cannot
+                # apply
+                if self._state == ExecutionState.CANCELLED:  # type: ignore[comparison-overlap]
                     raise ExecutionCancelledError
             elif self._state == ExecutionState.CANCELLED:
                 raise ExecutionCancelledError

api/src/opentrons/hardware_control/instruments/instrument_abc.py

@@ -12,11 +12,13 @@ class AbstractInstrument(ABC, Generic[InstrumentConfig]):
     """Defines the common methods of an instrument."""
 
     @property
+    @abstractmethod
     def model(self) -> str:
         """Return model of the instrument."""
         ...
 
     @property
+    @abstractmethod
     def config(self) -> InstrumentConfig:
         """Instrument config in dataclass format."""
         ...

api/src/opentrons/hardware_control/nozzle_manager.py

@@ -192,6 +192,20 @@ def front_nozzle_offset(self) -> Point:
         front_left = next(iter(self.columns.values()))[-1]
         return self.map_store[front_left]
 
+    @property
+    def front_right_nozzle_offset(self) -> Point:
+        """The offset for the front_right nozzle."""
+        # Front-right-most nozzle of the 96 channel in a given configuration
+        # and Front-most nozzle of the 8-channel
+        return self.map_store[self.front_right]
+
+    @property
+    def back_left_nozzle_offset(self) -> Point:
+        """The offset for the back_left nozzle."""
+        # Back-left-most nozzle of the 96-channel in a given configuration
+        # and back-most nozzle of the 8-channel
+        return self.map_store[self.back_left]
+
     @property
     def tip_count(self) -> int:
         """The total number of active nozzles in the configuration, and thus the number of tips that will be picked up."""

api/src/opentrons/hardware_control/ot3_calibration.py

@@ -9,7 +9,7 @@
 from enum import Enum
 from math import floor, copysign
 from logging import getLogger
-from opentrons.util.linal import solve_attitude, SolvePoints
+from opentrons.util.linal import solve_attitude, SolvePoints, DoubleMatrix
 
 from .types import OT3Mount, Axis, GripperProbe
 from opentrons.types import Point
@@ -952,8 +952,10 @@ def apply_machine_transform(
     -------
     Attitude matrix with regards to machine coordinate system.
     """
-    belt_attitude_arr = np.array(belt_attitude)
-    machine_transform_arr = np.array(defaults_ot3.DEFAULT_MACHINE_TRANSFORM)
+    belt_attitude_arr: DoubleMatrix = np.array(belt_attitude)
+    machine_transform_arr: DoubleMatrix = np.array(
+        defaults_ot3.DEFAULT_MACHINE_TRANSFORM
+    )
     deck_attitude_arr = np.dot(belt_attitude_arr, machine_transform_arr)
     deck_attitude = deck_attitude_arr.round(4).tolist()
     return deck_attitude  # type: ignore[no-any-return]
@@ -991,7 +993,7 @@ def validate_attitude_deck_calibration(
     TODO(pm, 5/9/2023): As with the OT2, expand on this method,
     or create another method to diagnose bad instrument offset data
     """
-    curr_cal = np.array(deck_cal.attitude)
+    curr_cal: DoubleMatrix = np.array(deck_cal.attitude)
     row, _ = curr_cal.shape
     rank: int = np.linalg.matrix_rank(curr_cal)
     if row != rank: