opentrons 8.2.0a2__tar.gz → 8.2.0a3__tar.gz

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.2.0a2
+Version: 8.2.0a3
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Author: Opentrons
 Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 License-File: ../LICENSE
-Requires-Dist: opentrons-shared-data==8.2.0a2
+Requires-Dist: opentrons-shared-data==8.2.0a3
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -34,9 +34,9 @@ Requires-Dist: pyusb==1.2.1
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.2.0a2; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.2.0a3; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.2.0a2; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.2.0a3; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/drivers/absorbance_reader/async_byonoy.py

@@ -23,7 +23,8 @@ from opentrons.hardware_control.modules.errors import AbsorbanceReaderDisconnect
 
 
 SN_PARSER = re.compile(r'ATTRS{serial}=="(?P<serial>.+?)"')
-VERSION_PARSER = re.compile(r"Absorbance (?P<version>V\d+\.\d+\.\d+)")
+# match semver V0.0.0 (old format) or one integer (latest format)
+VERSION_PARSER = re.compile(r"(?P<version>(V\d+\.\d+\.\d+|^\d+$))")
 SERIAL_PARSER = re.compile(r"(?P<serial>(OPT|BYO)[A-Z]{3}[0-9]+)")
 
 
@@ -156,10 +157,10 @@ class AsyncByonoy:
             func=partial(self._interface.get_device_information, handle),
         )
         self._raise_if_error(err.name, f"Error getting device information: {err}")
-        serial_match = SERIAL_PARSER.fullmatch(device_info.sn)
-        version_match = VERSION_PARSER.match(device_info.version)
+        serial_match = SERIAL_PARSER.match(device_info.sn)
+        version_match = VERSION_PARSER.search(device_info.version)
         serial = serial_match["serial"].strip() if serial_match else "OPTMAA00000"
-        version = version_match["version"].lower() if version_match else "v0.0.0"
+        version = version_match["version"].lower() if version_match else "v0"
         info = {
             "serial": serial,
             "version": version,

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/hardware_control/backends/ot3utils.py

@@ -652,6 +652,7 @@ _gripper_jaw_state_lookup: Dict[FirmwareGripperjawState, GripperJawState] = {
     FirmwareGripperjawState.force_controlling_home: GripperJawState.HOMED_READY,
     FirmwareGripperjawState.force_controlling: GripperJawState.GRIPPING,
     FirmwareGripperjawState.position_controlling: GripperJawState.HOLDING,
+    FirmwareGripperjawState.stopped: GripperJawState.STOPPED,
 }
 
 

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/hardware_control/modules/absorbance_reader.py

@@ -312,6 +312,8 @@ class AbsorbanceReader(mod_abc.AbstractModule):
         log.debug(f"Updating {self.name}: {self.port} with {firmware_file_path}")
         self._updating = True
         success, res = await self._driver.update_firmware(firmware_file_path)
+        # it takes time for the plate reader to re-init after an update.
+        await asyncio.sleep(10)
         self._device_info = await self._driver.get_device_info()
         await self._poller.start()
         self._updating = False

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/hardware_control/types.py

@@ -625,6 +625,8 @@ class GripperJawState(enum.Enum):
     #: the gripper is actively force-control gripping something
     HOLDING = enum.auto()
     #: the gripper is in position-control mode
+    STOPPED = enum.auto()
+    #: the gripper has been homed before but is stopped now
 
 
 class InstrumentProbeType(enum.Enum):

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_api/module_contexts.py

@@ -581,7 +581,7 @@ class ThermocyclerContext(ModuleContext):
                                  individual well of the loaded labware, in µL.
                                  If not specified, the default is 25 µL.
 
-        .. note:
+        .. note::
 
             If ``hold_time_minutes`` and ``hold_time_seconds`` are not
             specified, the Thermocycler will proceed to the next command
@@ -605,7 +605,7 @@ class ThermocyclerContext(ModuleContext):
         :param temperature: A value between 37 and 110, representing the target
                             temperature in °C.
 
-        .. note:
+        .. note::
 
             The Thermocycler will proceed to the next command immediately after
             ``temperature`` has been reached.
@@ -635,13 +635,13 @@ class ThermocyclerContext(ModuleContext):
                                  individual well of the loaded labware, in µL.
                                  If not specified, the default is 25 µL.
 
-        .. note:
+        .. note::
 
             Unlike with :py:meth:`set_block_temperature`, either or both of
             ``hold_time_minutes`` and ``hold_time_seconds`` must be defined
             and for each step.
 
-        .. note:
+        .. note::
 
             Before API Version 2.21, Thermocycler profiles run with this command
             would be listed in the app as having a number of repetitions equal to
@@ -991,7 +991,7 @@ class MagneticBlockContext(ModuleContext):
 
 
 class AbsorbanceReaderContext(ModuleContext):
-    """An object representing a connected Absorbance Reader Module.
+    """An object representing a connected Absorbance Plate Reader Module.
 
     It should not be instantiated directly; instead, it should be
     created through :py:meth:`.ProtocolContext.load_module`.
@@ -1009,17 +1009,21 @@ class AbsorbanceReaderContext(ModuleContext):
 
     @requires_version(2, 21)
     def close_lid(self) -> None:
-        """Close the lid of the Absorbance Reader."""
+        """Use the Flex Gripper to close the lid of the Absorbance Plate Reader.
+
+        You must call this method before initializing the reader, even if the reader was
+        in the closed position at the start of the protocol.
+        """
         self._core.close_lid()
 
     @requires_version(2, 21)
     def open_lid(self) -> None:
-        """Open the lid of the Absorbance Reader."""
+        """Use the Flex Gripper to open the lid of the Absorbance Plate Reader."""
         self._core.open_lid()
 
     @requires_version(2, 21)
     def is_lid_on(self) -> bool:
-        """Return ``True`` if the Absorbance Reader's lid is currently closed."""
+        """Return ``True`` if the Absorbance Plate Reader's lid is currently closed."""
         return self._core.is_lid_on()
 
     @requires_version(2, 21)
@@ -1029,19 +1033,28 @@ class AbsorbanceReaderContext(ModuleContext):
         wavelengths: List[int],
         reference_wavelength: Optional[int] = None,
     ) -> None:
-        """Take a zero reading on the Absorbance Plate Reader Module.
+        """Prepare the Absorbance Plate Reader to read a plate.
+
+        See :ref:`absorbance-initialization` for examples.
 
         :param mode: Either ``"single"`` or ``"multi"``.
 
-             - In single measurement mode, :py:meth:`.AbsorbanceReaderContext.read` uses
-               one sample wavelength and an optional reference wavelength.
-             - In multiple measurement mode, :py:meth:`.AbsorbanceReaderContext.read` uses
-               a list of up to six sample wavelengths.
-        :param wavelengths: A list of wavelengths, in mm, to measure.
-             - Must contain only one item when initializing a single measurement.
-             - Must contain one to six items when initializing a multiple measurement.
-        :param reference_wavelength: An optional reference wavelength, in mm. Cannot be
-             used with multiple measurements.
+            - In single measurement mode, :py:meth:`.AbsorbanceReaderContext.read` uses
+              one sample wavelength and an optional reference wavelength.
+            - In multiple measurement mode, :py:meth:`.AbsorbanceReaderContext.read` uses
+              a list of up to six sample wavelengths.
+        :param wavelengths: A list of wavelengths, in nm, to measure.
+
+            - In the default hardware configuration, each wavelength must be one of
+              ``450`` (blue), ``562`` (green), ``600`` (orange), or ``650`` (red). In
+              custom hardware configurations, the module may accept other integers
+              between 350 and 1000.
+            - The list must contain only one item when initializing a single measurement.
+            - The list can contain one to six items when initializing a multiple measurement.
+        :param reference_wavelength: An optional reference wavelength, in nm. If provided,
+            :py:meth:`.AbsorbanceReaderContext.read` will read at the reference
+            wavelength and then subtract the reference wavelength values from the
+            measurement wavelength values. Can only be used with single measurements.
         """
         self._core.initialize(
             mode, wavelengths, reference_wavelength=reference_wavelength
@@ -1051,16 +1064,33 @@ class AbsorbanceReaderContext(ModuleContext):
     def read(
         self, export_filename: Optional[str] = None
     ) -> Dict[int, Dict[str, float]]:
-        """Initiate read on the Absorbance Reader.
+        """Read a plate on the Absorbance Plate Reader.
+
+        This method always returns a dictionary of measurement data. It optionally will
+        save a CSV file of the results to the Flex filesystem, which you can access from
+        the Recent Protocol Runs screen in the Opentrons App. These files are `only` saved
+        if you specify ``export_filename``.
+
+        In simulation, the values for each well key in the dictionary are set to zero, and
+        no files are written.
+
+        .. note::
+
+            Avoid divide-by-zero errors when simulating and using the results of this
+            method later in the protocol. If you divide by any of the measurement
+            values, use :py:meth:`.ProtocolContext.is_simulating` to use alternate dummy
+            data or skip the division step.
 
-        Returns a dictionary of wavelengths to dictionary of values ordered by well name.
+        :param export_filename: An optional file basename. If provided, this method
+            will write a CSV file for each measurement in the read operation. File
+            names will use the value of this parameter, the measurement wavelength
+            supplied in :py:meth:`~.AbsorbanceReaderContext.initialize`, and a
+            ``.csv`` extension. For example, when reading at wavelengths 450 and 562
+            with ``export_filename="my_data"``, there will be two output files:
+            ``my_data_450.csv`` and ``my_data_562.csv``.
 
-        :param export_filename: Optional, if a filename is provided a CSV file will be saved
-             as a result of the read action containing measurement data. The filename will
-             be modified to include the wavelength used during measurement. If multiple
-             measurements are taken, then a file will be generated for each wavelength provided.
+            See :ref:`absorbance-csv` for information on working with these CSV files.
 
-        Example: If `export_filename="my_data"` and wavelengths 450 and 531 are used during
-        measurement, the output files will be "my_data_450.csv" and "my_data_531.csv".
+        :returns: A dictionary of wavelengths to dictionary of values ordered by well name.
         """
         return self._core.read(filename=export_filename)

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/commands/aspirate_in_place.py

@@ -83,10 +83,11 @@ class AspirateInPlaceImplementation(
             TipNotAttachedError: if no tip is attached to the pipette.
             PipetteNotReadyToAspirateError: pipette plunger is not ready.
         """
+        state_update = StateUpdate()
+
         ready_to_aspirate = self._pipetting.get_is_ready_to_aspirate(
             pipette_id=params.pipetteId,
         )
-
         if not ready_to_aspirate:
             raise PipetteNotReadyToAspirateError(
                 "Pipette cannot aspirate in place because of a previous blow out."
@@ -94,11 +95,10 @@ class AspirateInPlaceImplementation(
                 " so the plunger can be reset in a known safe position."
             )
 
-        state_update = StateUpdate()
         current_location = self._state_view.pipettes.get_current_location()
+        current_position = await self._gantry_mover.get_position(params.pipetteId)
 
         try:
-            current_position = await self._gantry_mover.get_position(params.pipetteId)
             volume = await self._pipetting.aspirate_in_place(
                 pipette_id=params.pipetteId,
                 volume=params.volume,

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/commands/command.py

@@ -185,7 +185,9 @@ class BaseCommand(
     )
     error: Union[
         _ErrorT,
-        # ErrorOccurrence here is for undefined errors not captured by _ErrorT.
+        # ErrorOccurrence here is a catch-all for undefined errors not captured by
+        # _ErrorT, or defined errors that don't parse into _ErrorT because, for example,
+        # they are from an older software version that was missing some fields.
         ErrorOccurrence,
         None,
     ] = Field(

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/commands/dispense_in_place.py

@@ -76,8 +76,8 @@ class DispenseInPlaceImplementation(
         """Dispense without moving the pipette."""
         state_update = StateUpdate()
         current_location = self._state_view.pipettes.get_current_location()
+        current_position = await self._gantry_mover.get_position(params.pipetteId)
         try:
-            current_position = await self._gantry_mover.get_position(params.pipetteId)
             volume = await self._pipetting.dispense_in_place(
                 pipette_id=params.pipetteId,
                 volume=params.volume,

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/commands/drop_tip.py

@@ -145,6 +145,7 @@ class DropTipImplementation(AbstractCommandImpl[DropTipParams, _ExecuteReturn]):
                         error=exception,
                     )
                 ],
+                errorInfo={"retryLocation": position},
             )
             state_update_if_false_positive = update_types.StateUpdate()
             state_update_if_false_positive.update_pipette_tip_state(
@@ -165,7 +166,7 @@ class DropTipImplementation(AbstractCommandImpl[DropTipParams, _ExecuteReturn]):
             )
 
 
-class DropTip(BaseCommand[DropTipParams, DropTipResult, ErrorOccurrence]):
+class DropTip(BaseCommand[DropTipParams, DropTipResult, TipPhysicallyAttachedError]):
     """Drop tip command model."""
 
     commandType: DropTipCommandType = "dropTip"

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/commands/drop_tip_in_place.py

@@ -18,7 +18,7 @@ from ..resources.model_utils import ModelUtils
 from ..state import update_types
 
 if TYPE_CHECKING:
-    from ..execution import TipHandler
+    from ..execution import TipHandler, GantryMover
 
 
 DropTipInPlaceCommandType = Literal["dropTipInPlace"]
@@ -57,15 +57,19 @@ class DropTipInPlaceImplementation(
         self,
         tip_handler: TipHandler,
         model_utils: ModelUtils,
+        gantry_mover: GantryMover,
         **kwargs: object,
     ) -> None:
         self._tip_handler = tip_handler
         self._model_utils = model_utils
+        self._gantry_mover = gantry_mover
 
     async def execute(self, params: DropTipInPlaceParams) -> _ExecuteReturn:
         """Drop a tip using the requested pipette."""
         state_update = update_types.StateUpdate()
 
+        retry_location = await self._gantry_mover.get_position(params.pipetteId)
+
         try:
             await self._tip_handler.drop_tip(
                 pipette_id=params.pipetteId, home_after=params.homeAfter
@@ -85,6 +89,7 @@ class DropTipInPlaceImplementation(
                         error=exception,
                     )
                 ],
+                errorInfo={"retryLocation": retry_location},
             )
             return DefinedErrorData(
                 public=error,
@@ -99,7 +104,7 @@ class DropTipInPlaceImplementation(
 
 
 class DropTipInPlace(
-    BaseCommand[DropTipInPlaceParams, DropTipInPlaceResult, ErrorOccurrence]
+    BaseCommand[DropTipInPlaceParams, DropTipInPlaceResult, TipPhysicallyAttachedError]
 ):
     """Drop tip in place command model."""
 

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/commands/pick_up_tip.py

@@ -82,7 +82,7 @@ class TipPhysicallyMissingError(ErrorOccurrence):
     isDefined: bool = True
     errorType: Literal["tipPhysicallyMissing"] = "tipPhysicallyMissing"
     errorCode: str = ErrorCodes.TIP_PICKUP_FAILED.value.code
-    detail: str = "No tip detected."
+    detail: str = "No Tip Detected"
 
 
 _ExecuteReturn = Union[

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/commands/pipetting_common.py

@@ -148,7 +148,12 @@ class DestinationPositionResult(BaseModel):
 
 
 class ErrorLocationInfo(TypedDict):
-    """Holds a retry location for in-place error recovery."""
+    """Holds a retry location for in-place error recovery.
+
+    This is appropriate to pass to a `moveToCoordinates` command,
+    assuming the pipette has not been configured with a different nozzle layout
+    in the meantime.
+    """
 
     retryLocation: Tuple[float, float, float]
 
@@ -201,3 +206,5 @@ class TipPhysicallyAttachedError(ErrorOccurrence):
 
     errorCode: str = ErrorCodes.TIP_DROP_FAILED.value.code
     detail: str = ErrorCodes.TIP_DROP_FAILED.value.detail
+
+    errorInfo: ErrorLocationInfo

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_engine/errors/error_occurrence.py

@@ -12,8 +12,6 @@ from opentrons_shared_data.errors.exceptions import EnumeratedError
 log = getLogger(__name__)
 
 
-# TODO(mc, 2021-11-12): flesh this model out with structured error data
-# for each error type so client may produce better error messages
 class ErrorOccurrence(BaseModel):
     """An occurrence of a specific error during protocol execution."""
 
@@ -44,8 +42,15 @@ class ErrorOccurrence(BaseModel):
     id: str = Field(..., description="Unique identifier of this error occurrence.")
     createdAt: datetime = Field(..., description="When the error occurred.")
 
+    # Our Python should probably always set this to False--if we want it to be True,
+    # we should probably be using a more specific subclass of ErrorOccurrence anyway.
+    # However, we can't make this Literal[False], because we want this class to be able
+    # to act as a catch-all for parsing defined errors that might be missing some
+    # `errorInfo` fields because they were serialized by older software.
     isDefined: bool = Field(
-        default=False,  # default=False for database backwards compatibility.
+        # default=False for database backwards compatibility, so we can parse objects
+        # serialized before isDefined existed.
+        default=False,
         description=dedent(
             """\
             Whether this error is *defined.*

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocol_runner/run_orchestrator.py

@@ -418,6 +418,21 @@ class RunOrchestrator:
         """Get current nozzle maps keyed by pipette id."""
         return self._protocol_engine.state_view.tips.get_pipette_nozzle_maps()
 
+    def get_tip_attached(self) -> Dict[str, bool]:
+        """Get current tip state keyed by pipette id."""
+
+        def has_tip_attached(pipette_id: str) -> bool:
+            return (
+                self._protocol_engine.state_view.pipettes.get_attached_tip(pipette_id)
+                is not None
+            )
+
+        pipette_ids = (
+            pipette.id
+            for pipette in self._protocol_engine.state_view.pipettes.get_all()
+        )
+        return {pipette_id: has_tip_attached(pipette_id) for pipette_id in pipette_ids}
+
     def set_error_recovery_policy(self, policy: ErrorRecoveryPolicy) -> None:
         """Create error recovery policy for the run."""
         self._protocol_engine.set_error_recovery_policy(policy)

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons/protocols/parameters/csv_parameter_interface.py

@@ -60,7 +60,9 @@ class CSVParameter:
         as appropriate.
 
         :param detect_dialect: If ``True``, examine the file and try to assign it a
-            :py:class:`csv.Dialect` to improve parsing behavior.
+            :py:class:`csv.Dialect` to improve parsing behavior. Set this to ``False``
+            when using the file output of :py:meth:`.AbsorbanceReaderContext.read` as
+            a runtime parameter.
         :param kwargs: For advanced CSV handling, you can pass any of the
             `formatting parameters <https://docs.python.org/3/library/csv.html#csv-fmt-params>`_
             accepted by :py:func:`csv.reader` from the Python standard library.

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.2.0a2
+Version: 8.2.0a3
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Author: Opentrons
 Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 License-File: ../LICENSE
-Requires-Dist: opentrons-shared-data==8.2.0a2
+Requires-Dist: opentrons-shared-data==8.2.0a3
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -34,9 +34,9 @@ Requires-Dist: pyusb==1.2.1
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.2.0a2; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.2.0a3; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.2.0a2; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.2.0a3; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.2.0a2 → opentrons-8.2.0a3}/src/opentrons.egg-info/requires.txt

@@ -1,4 +1,4 @@
-opentrons-shared-data==8.2.0a2
+opentrons-shared-data==8.2.0a3
 aionotify==0.3.1
 anyio<4.0.0,>=3.6.1
 jsonschema<4.18.0,>=3.0.1
@@ -14,7 +14,7 @@ packaging>=21.0
 importlib-metadata>=1.0
 
 [flex-hardware]
-opentrons-hardware[FLEX]==8.2.0a2
+opentrons-hardware[FLEX]==8.2.0a3
 
 [ot2-hardware]
-opentrons-hardware==8.2.0a2
+opentrons-hardware==8.2.0a3