opentrons 8.1.0__py2.py3-none-any.whl → 8.2.0__py2.py3-none-any.whl

opentrons/hardware_control/modules/tempdeck.py

@@ -2,9 +2,12 @@ from __future__ import annotations
 
 import asyncio
 import logging
-from typing import Mapping, Optional
+from typing import Dict, Optional
 
-from opentrons.hardware_control.modules.types import TemperatureStatus
+from opentrons.hardware_control.modules.types import (
+    ModuleDisconnectedCallback,
+    TemperatureStatus,
+)
 from opentrons.hardware_control.poller import Reader, Poller
 from typing_extensions import Final
 from opentrons.drivers.types import Temperature
@@ -15,7 +18,7 @@ from opentrons.drivers.temp_deck import (
 )
 from opentrons.drivers.rpi_drivers.types import USBPort
 from opentrons.hardware_control.execution_manager import ExecutionManager
-from opentrons.hardware_control.modules import update, mod_abc, types
+from opentrons.hardware_control.modules import update, mod_abc, types, errors
 
 log = logging.getLogger(__name__)
 
@@ -26,7 +29,7 @@ SIM_TEMP_POLL_INTERVAL_SECS = TEMP_POLL_INTERVAL_SECS / 20.0
 class TempDeck(mod_abc.AbstractModule):
     """Hardware control interface for an attached Temperature Module."""
 
-    MODULE_TYPE = types.ModuleType.TEMPERATURE
+    MODULE_TYPE = types.ModuleType["TEMPERATURE"]
     FIRST_GEN2_REVISION = 20
 
     @classmethod
@@ -40,6 +43,7 @@ class TempDeck(mod_abc.AbstractModule):
         simulating: bool = False,
         sim_model: Optional[str] = None,
         sim_serial_number: Optional[str] = None,
+        disconnected_callback: ModuleDisconnectedCallback = None,
     ) -> "TempDeck":
         """
         Build a TempDeck
@@ -52,6 +56,7 @@ class TempDeck(mod_abc.AbstractModule):
             poll_interval_seconds: Poll interval override.
             simulating: whether to build a simulating driver
             sim_model: The model name used by simulator
+            disconnected_callback: Callback to inform the module controller that the device was disconnected
 
         Returns:
             Tempdeck instance
@@ -77,6 +82,7 @@ class TempDeck(mod_abc.AbstractModule):
             poller=poller,
             device_info=await driver.get_device_info(),
             hw_control_loop=hw_control_loop,
+            disconnected_callback=disconnected_callback,
         )
 
         try:
@@ -94,8 +100,9 @@ class TempDeck(mod_abc.AbstractModule):
         driver: AbstractTempDeckDriver,
         reader: TempDeckReader,
         poller: Poller,
-        device_info: Mapping[str, str],
+        device_info: Dict[str, str],
         hw_control_loop: asyncio.AbstractEventLoop,
+        disconnected_callback: ModuleDisconnectedCallback = None,
     ) -> None:
         """Constructor"""
         super().__init__(
@@ -103,6 +110,7 @@ class TempDeck(mod_abc.AbstractModule):
             usb_port=usb_port,
             hw_control_loop=hw_control_loop,
             execution_manager=execution_manager,
+            disconnected_callback=disconnected_callback,
         )
         self._device_info = device_info
         self._driver = driver
@@ -182,7 +190,7 @@ class TempDeck(mod_abc.AbstractModule):
         await self._reader.read()
 
     @property
-    def device_info(self) -> Mapping[str, str]:
+    def device_info(self) -> Dict[str, str]:
         return self._device_info
 
     @property
@@ -211,7 +219,7 @@ class TempDeck(mod_abc.AbstractModule):
     async def prep_for_update(self) -> str:
         model = self._device_info and self._device_info.get("model")
         if model in ("temp_deck_v1", "temp_deck_v1.1", "temp_deck_v2"):
-            raise types.UpdateError(
+            raise errors.UpdateError(
                 "This Temperature Module can't be updated."
                 "Please contact Opentrons Support."
             )

opentrons/hardware_control/modules/thermocycler.py

@@ -2,12 +2,15 @@ from __future__ import annotations
 
 import asyncio
 import logging
-from typing import Callable, Optional, List, Dict, Mapping
+from typing import Callable, Optional, List, Dict, Mapping, Union, cast
 from opentrons.drivers.rpi_drivers.types import USBPort
 from opentrons.drivers.types import ThermocyclerLidStatus, Temperature, PlateTemperature
 from opentrons.hardware_control.modules.lid_temp_status import LidTemperatureStatus
 from opentrons.hardware_control.modules.plate_temp_status import PlateTemperatureStatus
-from opentrons.hardware_control.modules.types import TemperatureStatus
+from opentrons.hardware_control.modules.types import (
+    ModuleDisconnectedCallback,
+    TemperatureStatus,
+)
 from opentrons.hardware_control.poller import Reader, Poller
 
 from ..execution_manager import ExecutionManager
@@ -64,6 +67,7 @@ class Thermocycler(mod_abc.AbstractModule):
         simulating: bool = False,
         sim_model: Optional[str] = None,
         sim_serial_number: Optional[str] = None,
+        disconnected_callback: ModuleDisconnectedCallback = None,
     ) -> "Thermocycler":
         """
         Build and connect to a Thermocycler
@@ -77,6 +81,7 @@ class Thermocycler(mod_abc.AbstractModule):
             simulating: whether to build a simulating driver
             loop: Loop
             sim_model: The model name used by simulator
+            disconnected_callback: Callback to inform the module controller that the device was disconnected
 
         Returns:
             Thermocycler instance.
@@ -102,6 +107,7 @@ class Thermocycler(mod_abc.AbstractModule):
             device_info=await driver.get_device_info(),
             hw_control_loop=hw_control_loop,
             execution_manager=execution_manager,
+            disconnected_callback=disconnected_callback,
         )
 
         try:
@@ -121,6 +127,7 @@ class Thermocycler(mod_abc.AbstractModule):
         poller: Poller,
         device_info: Dict[str, str],
         hw_control_loop: asyncio.AbstractEventLoop,
+        disconnected_callback: ModuleDisconnectedCallback = None,
     ) -> None:
         """
         Constructor
@@ -134,6 +141,7 @@ class Thermocycler(mod_abc.AbstractModule):
             poller: A poll controller for reads.
             device_info: The thermocycler device info.
             hw_control_loop: The event loop running in the hardware control thread.
+            disconnected_callback: Callback to inform the module controller that the device was disconnected
         """
         self._driver = driver
         super().__init__(
@@ -141,6 +149,7 @@ class Thermocycler(mod_abc.AbstractModule):
             usb_port=usb_port,
             hw_control_loop=hw_control_loop,
             execution_manager=execution_manager,
+            disconnected_callback=disconnected_callback,
         )
         self._device_info = device_info
         self._reader = reader
@@ -354,6 +363,39 @@ class Thermocycler(mod_abc.AbstractModule):
         self.make_cancellable(task)
         await task
 
+    async def execute_profile(
+        self,
+        profile: List[Union[types.ThermocyclerCycle, types.ThermocyclerStep]],
+        volume: Optional[float] = None,
+    ) -> None:
+        """Begin a set temperature profile, with both repeating and non-repeating steps.
+
+        Args:
+            profile: The temperature profile to follow.
+            volume: Optional volume
+
+        Returns: None
+        """
+        await self.wait_for_is_running()
+        self._total_cycle_count = 0
+        self._total_step_count = 0
+        self._current_cycle_index = 0
+        self._current_step_index = 0
+        for step_or_cycle in profile:
+            if "steps" in step_or_cycle:
+                # basically https://github.com/python/mypy/issues/14766
+                this_cycle = cast(types.ThermocyclerCycle, step_or_cycle)
+                self._total_cycle_count += this_cycle["repetitions"]
+                self._total_step_count += (
+                    len(this_cycle["steps"]) * this_cycle["repetitions"]
+                )
+            else:
+                self._total_step_count += 1
+                self._total_cycle_count += 1
+        task = self._loop.create_task(self._execute_profile(profile, volume))
+        self.make_cancellable(task)
+        await task
+
     async def set_lid_temperature(self, temperature: float) -> None:
         """Set the lid temperature in degrees Celsius"""
         await self.wait_for_is_running()
@@ -565,7 +607,7 @@ class Thermocycler(mod_abc.AbstractModule):
         self,
         steps: List[types.ThermocyclerStep],
         repetitions: int,
-        volume: Optional[float] = None,
+        volume: Optional[float],
     ) -> None:
         """
         Execute cycles.
@@ -583,6 +625,30 @@ class Thermocycler(mod_abc.AbstractModule):
                 self._current_step_index = step_idx + 1  # science starts at 1
                 await self._execute_cycle_step(step, volume)
 
+    async def _execute_profile(
+        self,
+        profile: List[Union[types.ThermocyclerCycle, types.ThermocyclerStep]],
+        volume: Optional[float],
+    ) -> None:
+        """
+        Execute profiles.
+
+        Profiles command a thermocycler pattern that can contain multiple cycles and out-of-cycle steps.
+        """
+        self._current_cycle_index = 0
+        self._current_step_index = 0
+        for step_or_cycle in profile:
+            self._current_cycle_index += 1
+            if "repetitions" in step_or_cycle:
+                # basically https://github.com/python/mypy/issues/14766
+                this_cycle = cast(types.ThermocyclerCycle, step_or_cycle)
+                for rep in range(this_cycle["repetitions"]):
+                    for step in this_cycle["steps"]:
+                        self._current_step_index += 1
+                        await self._execute_cycle_step(step, volume)
+            else:
+                await self._execute_cycle_step(step_or_cycle, volume)
+
     # TODO(mc, 2022-10-13): why does this exist?
     # Do the driver and poller really need to be disconnected?
     # Could we accomplish the same thing by latching the error state

opentrons/hardware_control/modules/types.py

@@ -3,6 +3,7 @@ from enum import Enum
 from dataclasses import dataclass
 from typing import (
     Dict,
+    List,
     NamedTuple,
     Callable,
     Any,
@@ -38,12 +39,20 @@ class ThermocyclerStep(ThermocyclerStepBase, total=False):
     hold_time_minutes: float
 
 
+class ThermocyclerCycle(TypedDict):
+    steps: List[ThermocyclerStep]
+    repetitions: int
+
+
 UploadFunction = Callable[[str, str, Dict[str, Any]], Awaitable[Tuple[bool, str]]]
 
 
+ModuleDisconnectedCallback = Optional[Callable[[str, str | None], None]]
+
+
 class LiveData(TypedDict):
     status: str
-    data: Dict[str, Union[float, str, bool, None]]
+    data: Dict[str, Union[float, str, bool, List[int], None]]
 
 
 class ModuleType(str, Enum):
@@ -135,6 +144,7 @@ def module_model_from_string(model_string: str) -> ModuleModel:
 class ModuleAtPort:
     port: str
     name: str
+    serial: Optional[str] = None
     usb_port: USBPort = USBPort(name="", port_number=0)
 
 
@@ -159,10 +169,6 @@ class BundledFirmware(NamedTuple):
         return f"<BundledFirmware {self.version}, path={self.path}>"
 
 
-class UpdateError(RuntimeError):
-    pass
-
-
 class ModuleInfo(NamedTuple):
     model: str  # A module model such as "magneticModuleV2"
     fw_version: str  # The version of the firmware

opentrons/hardware_control/modules/update.py

@@ -4,7 +4,8 @@ import os
 from pathlib import Path
 from glob import glob
 from typing import Any, AsyncGenerator, Dict, Tuple, Union
-from .types import UpdateError
+
+from .errors import UpdateError
 from .mod_abc import AbstractModule
 from opentrons.hardware_control.threaded_async_lock import ThreadedAsyncLock
 from contextlib import asynccontextmanager
@@ -33,6 +34,7 @@ async def update_firmware(
         kwargs: Dict[str, Any] = {
             "stdout": asyncio.subprocess.PIPE,
             "stderr": asyncio.subprocess.PIPE,
+            "module": module,
         }
         successful, res = await module.bootloader()(
             flash_port_or_dfu_serial, str(firmware_file), kwargs
@@ -139,7 +141,8 @@ async def upload_via_avrdude(
         "-b{}".format(BAUDRATE),
         "-D",
         "-Uflash:w:{}:i".format(firmware_file_path),
-        **kwargs,
+        stdout=kwargs["stdout"],
+        stderr=kwargs["stderr"],
     )
     await proc.wait()
 
@@ -191,8 +194,9 @@ async def upload_via_bossa(
         "--offset=0x2000",
         f"{firmware_file_path}",
     ]
-
-    proc = await asyncio.create_subprocess_exec(*bossa_args, **kwargs)
+    proc = await asyncio.create_subprocess_exec(
+        *bossa_args, stdout=kwargs["stdout"], stderr=kwargs["stderr"]
+    )
     stdout, stderr = await proc.communicate()
     res = stdout.decode()
     if "Verify successful" in res:
@@ -231,7 +235,9 @@ async def upload_via_dfu(
         f"-D{firmware_file_path}",
         "-R",
     ]
-    proc = await asyncio.create_subprocess_exec(*dfu_args, **kwargs)
+    proc = await asyncio.create_subprocess_exec(
+        *dfu_args, stdout=kwargs["stdout"], stderr=kwargs["stderr"]
+    )
     stdout, stderr = await proc.communicate()
     res = stdout.decode()
 

opentrons/hardware_control/modules/utils.py

@@ -6,7 +6,7 @@ from opentrons.drivers.rpi_drivers.types import USBPort
 
 from ..execution_manager import ExecutionManager
 
-from .types import ModuleType, SpeedStatus
+from .types import ModuleDisconnectedCallback, ModuleType, SpeedStatus
 from .mod_abc import AbstractModule
 from .tempdeck import TempDeck
 from .magdeck import MagDeck
@@ -46,6 +46,7 @@ async def build(
     execution_manager: ExecutionManager,
     sim_model: Optional[str] = None,
     sim_serial_number: Optional[str] = None,
+    disconnected_callback: ModuleDisconnectedCallback = None,
 ) -> AbstractModule:
     return await _MODULE_CLS_BY_TYPE[type].build(
         port=port,
@@ -55,6 +56,7 @@ async def build(
         execution_manager=execution_manager,
         sim_model=sim_model,
         sim_serial_number=sim_serial_number,
+        disconnected_callback=disconnected_callback,
     )
 
 

opentrons/hardware_control/ot3_calibration.py

@@ -819,13 +819,13 @@ async def find_pipette_offset(
     try:
         if reset_instrument_offset:
             await hcapi.reset_instrument_offset(mount)
-        await hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
+        hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
         offset = await _calibrate_mount(
             hcapi, mount, slot, method, raise_verify_error, probe=probe
         )
         return offset
     finally:
-        await hcapi.remove_tip(mount)
+        hcapi.remove_tip(mount)
 
 
 async def calibrate_pipette(
@@ -877,7 +877,7 @@ async def calibrate_module(
         if mount == OT3Mount.GRIPPER:
             hcapi.add_gripper_probe(GripperProbe.FRONT)
         else:
-            await hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
+            hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
 
         LOG.info(
             f"Starting module calibration for {module_id} at {nominal_position} using {mount}"
@@ -903,7 +903,7 @@ async def calibrate_module(
             hcapi.remove_gripper_probe()
             await hcapi.ungrip()
         else:
-            await hcapi.remove_tip(mount)
+            hcapi.remove_tip(mount)
 
 
 async def calibrate_belts(
@@ -927,7 +927,7 @@ async def calibrate_belts(
         raise RuntimeError("Must use pipette mount, not gripper")
     try:
         hcapi.reset_deck_calibration()
-        await hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
+        hcapi.add_tip(mount, hcapi.config.calibration.probe_length)
         belt_attitude, alignment_details = await _determine_transform_matrix(
             hcapi, mount
         )
@@ -935,7 +935,7 @@ async def calibrate_belts(
         return belt_attitude, alignment_details
     finally:
         hcapi.load_deck_calibration()
-        await hcapi.remove_tip(mount)
+        hcapi.remove_tip(mount)
 
 
 def apply_machine_transform(