opentrons 8.2.0__py2.py3-none-any.whl → 8.2.0a0__py2.py3-none-any.whl

opentrons/protocol_engine/state/modules.py

@@ -26,15 +26,13 @@ from opentrons.motion_planning.adjacent_slots_getters import (
     get_west_slot,
     get_adjacent_staging_slot,
 )
-from opentrons.protocol_engine.actions.get_state_update import get_state_updates
 from opentrons.protocol_engine.commands.calibration.calibrate_module import (
     CalibrateModuleResult,
 )
-from opentrons.protocol_engine.state import update_types
 from opentrons.protocol_engine.state.module_substates.absorbance_reader_substate import (
     AbsorbanceReaderMeasureMode,
 )
-from opentrons.types import DeckSlotName, MountType, StagingSlotName
+from opentrons.types import DeckSlotName, MountType
 from ..errors import ModuleNotConnectedError
 
 from ..types import (
@@ -69,6 +67,7 @@ from ..actions import (
     Action,
     SucceedCommandAction,
     AddModuleAction,
+    AddAbsorbanceReaderLidAction,
 )
 from ._abstract_store import HasState, HandlesActions
 from .module_substates import (
@@ -235,14 +234,13 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
                 requested_model=None,
                 module_live_data=action.module_live_data,
             )
-
-        for state_update in get_state_updates(action):
-            self._handle_state_update(state_update)
+        elif isinstance(action, AddAbsorbanceReaderLidAction):
+            self._update_absorbance_reader_lid_id(
+                module_id=action.module_id,
+                lid_id=action.lid_id,
+            )
 
     def _handle_command(self, command: Command) -> None:
-        # todo(mm, 2024-11-04): Delete this function. Port these isinstance()
-        # checks to the update_types.StateUpdate mechanism.
-
         if isinstance(command.result, LoadModuleResult):
             slot_name = command.params.location.slotName
             self._add_module_substate(
@@ -299,40 +297,38 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
         if isinstance(
             command.result,
             (
+                absorbance_reader.CloseLidResult,
+                absorbance_reader.OpenLidResult,
                 absorbance_reader.InitializeResult,
                 absorbance_reader.ReadAbsorbanceResult,
             ),
         ):
             self._handle_absorbance_reader_commands(command)
 
-    def _handle_state_update(self, state_update: update_types.StateUpdate) -> None:
-        if state_update.absorbance_reader_lid != update_types.NO_CHANGE:
-            module_id = state_update.absorbance_reader_lid.module_id
-            is_lid_on = state_update.absorbance_reader_lid.is_lid_on
-
-            # Get current values:
-            absorbance_reader_substate = self._state.substate_by_module_id[module_id]
-            assert isinstance(
-                absorbance_reader_substate, AbsorbanceReaderSubState
-            ), f"{module_id} is not an absorbance plate reader."
-            configured = absorbance_reader_substate.configured
-            measure_mode = absorbance_reader_substate.measure_mode
-            configured_wavelengths = absorbance_reader_substate.configured_wavelengths
-            reference_wavelength = absorbance_reader_substate.reference_wavelength
-            data = absorbance_reader_substate.data
+    def _update_absorbance_reader_lid_id(
+        self,
+        module_id: str,
+        lid_id: str,
+    ) -> None:
+        abs_substate = self._state.substate_by_module_id.get(module_id)
+        assert isinstance(
+            abs_substate, AbsorbanceReaderSubState
+        ), f"{module_id} is not an absorbance plate reader."
 
-            self._state.substate_by_module_id[module_id] = AbsorbanceReaderSubState(
-                module_id=AbsorbanceReaderId(module_id),
-                configured=configured,
-                measured=True,
-                is_lid_on=is_lid_on,
-                measure_mode=measure_mode,
-                configured_wavelengths=configured_wavelengths,
-                reference_wavelength=reference_wavelength,
-                data=data,
-            )
+        prev_state: AbsorbanceReaderSubState = abs_substate
+        self._state.substate_by_module_id[module_id] = AbsorbanceReaderSubState(
+            module_id=AbsorbanceReaderId(module_id),
+            configured=prev_state.configured,
+            measured=prev_state.measured,
+            is_lid_on=prev_state.is_lid_on,
+            data=prev_state.data,
+            measure_mode=prev_state.measure_mode,
+            configured_wavelengths=prev_state.configured_wavelengths,
+            reference_wavelength=prev_state.reference_wavelength,
+            lid_id=lid_id,
+        )
 
-    def _add_module_substate(
+    def _add_module_substate(  # noqa: C901
         self,
         module_id: str,
         serial_number: Optional[str],
@@ -391,6 +387,16 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
                 module_id=MagneticBlockId(module_id)
             )
         elif ModuleModel.is_absorbance_reader(actual_model):
+            lid_labware_id = None
+            slot = self._state.slot_by_module_id[module_id]
+            if slot is not None:
+                reader_addressable_area = f"absorbanceReaderV1{slot.value}"
+                for labware in self._state.deck_fixed_labware:
+                    if labware.location == AddressableAreaLocation(
+                        addressableAreaName=reader_addressable_area
+                    ):
+                        lid_labware_id = labware.labware_id
+                        break
             self._state.substate_by_module_id[module_id] = AbsorbanceReaderSubState(
                 module_id=AbsorbanceReaderId(module_id),
                 configured=False,
@@ -400,6 +406,7 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
                 measure_mode=None,
                 configured_wavelengths=None,
                 reference_wavelength=None,
+                lid_id=lid_labware_id,
             )
 
     def _update_additional_slots_occupied_by_thermocycler(
@@ -593,6 +600,8 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
         command: Union[
             absorbance_reader.Initialize,
             absorbance_reader.ReadAbsorbance,
+            absorbance_reader.CloseLid,
+            absorbance_reader.OpenLid,
         ],
     ) -> None:
         module_id = command.params.moduleId
@@ -607,6 +616,8 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
         configured_wavelengths = absorbance_reader_substate.configured_wavelengths
         reference_wavelength = absorbance_reader_substate.reference_wavelength
         is_lid_on = absorbance_reader_substate.is_lid_on
+        lid_id = absorbance_reader_substate.lid_id
+        data = absorbance_reader_substate.data
 
         if isinstance(command.result, absorbance_reader.InitializeResult):
             self._state.substate_by_module_id[module_id] = AbsorbanceReaderSubState(
@@ -614,6 +625,7 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
                 configured=True,
                 measured=False,
                 is_lid_on=is_lid_on,
+                lid_id=lid_id,
                 measure_mode=AbsorbanceReaderMeasureMode(command.params.measureMode),
                 configured_wavelengths=command.params.sampleWavelengths,
                 reference_wavelength=command.params.referenceWavelength,
@@ -625,12 +637,39 @@ class ModuleStore(HasState[ModuleState], HandlesActions):
                 configured=configured,
                 measured=True,
                 is_lid_on=is_lid_on,
+                lid_id=lid_id,
                 measure_mode=measure_mode,
                 configured_wavelengths=configured_wavelengths,
                 reference_wavelength=reference_wavelength,
                 data=command.result.data,
             )
 
+        elif isinstance(command.result, absorbance_reader.OpenLidResult):
+            self._state.substate_by_module_id[module_id] = AbsorbanceReaderSubState(
+                module_id=AbsorbanceReaderId(module_id),
+                configured=configured,
+                measured=True,
+                is_lid_on=False,
+                lid_id=lid_id,
+                measure_mode=measure_mode,
+                configured_wavelengths=configured_wavelengths,
+                reference_wavelength=reference_wavelength,
+                data=data,
+            )
+
+        elif isinstance(command.result, absorbance_reader.CloseLidResult):
+            self._state.substate_by_module_id[module_id] = AbsorbanceReaderSubState(
+                module_id=AbsorbanceReaderId(module_id),
+                configured=configured,
+                measured=True,
+                is_lid_on=True,
+                lid_id=lid_id,
+                measure_mode=measure_mode,
+                configured_wavelengths=configured_wavelengths,
+                reference_wavelength=reference_wavelength,
+                data=data,
+            )
+
 
 class ModuleView(HasState[ModuleState]):
     """Read-only view of computed module state."""
@@ -844,21 +883,12 @@ class ModuleView(HasState[ModuleState]):
         """Get the specified module's dimensions."""
         return self.get_definition(module_id).dimensions
 
-    def get_nominal_offset_to_child(
+    def get_nominal_module_offset(
         self,
         module_id: str,
-        # todo(mm, 2024-11-07): A method of one view taking a sibling view as an argument
-        # is unusual, and may be bug-prone if the order in which the views are updated
-        # matters. If we need to compute something that depends on module info and
-        # addressable area info, can we do that computation in GeometryView instead of
-        # here?
         addressable_areas: AddressableAreaView,
     ) -> LabwareOffsetVector:
-        """Get the nominal offset from a module's location to its child labware's location.
-
-        Includes the slot-specific transform. Does not include the child's
-        Labware Position Check offset.
-        """
+        """Get the module's nominal offset vector computed with slot transform."""
         if (
             self.state.deck_type == DeckType.OT2_STANDARD
             or self.state.deck_type == DeckType.OT2_SHORT_TRASH
@@ -966,7 +996,7 @@ class ModuleView(HasState[ModuleState]):
         default_lw_offset_point = self.get_definition(module_id).labwareOffset.z
         z_difference = module_height - default_lw_offset_point
 
-        nominal_transformed_lw_offset_z = self.get_nominal_offset_to_child(
+        nominal_transformed_lw_offset_z = self.get_nominal_module_offset(
             module_id=module_id, addressable_areas=addressable_areas
         ).z
         calibration_offset = self.get_module_calibration_offset(module_id)
@@ -1094,8 +1124,8 @@ class ModuleView(HasState[ModuleState]):
 
     def should_dodge_thermocycler(
         self,
-        from_slot: Union[DeckSlotName, StagingSlotName],
-        to_slot: Union[DeckSlotName, StagingSlotName],
+        from_slot: DeckSlotName,
+        to_slot: DeckSlotName,
     ) -> bool:
         """Decide if the requested path would cross the thermocycler, if installed.
 
@@ -1268,10 +1298,7 @@ class ModuleView(HasState[ModuleState]):
                 row = chr(ord("A") + i // 12)  # Convert index to row (A-H)
                 col = (i % 12) + 1  # Convert index to column (1-12)
                 well_key = f"{row}{col}"
-                truncated_value = float(
-                    "{:.5}".format(str(value))
-                )  # Truncate the returned value to the third decimal place
-                well_map[well_key] = truncated_value
+                well_map[well_key] = value
             return well_map
         else:
             raise ValueError(

opentrons/protocol_engine/state/motion.py

@@ -2,7 +2,7 @@
 from dataclasses import dataclass
 from typing import List, Optional, Union
 
-from opentrons.types import MountType, Point, StagingSlotName
+from opentrons.types import MountType, Point
 from opentrons.hardware_control.types import CriticalPoint
 from opentrons.motion_planning.adjacent_slots_getters import (
     get_east_west_slots,
@@ -277,13 +277,9 @@ class MotionView:
         current_location = self._pipettes.get_current_location()
         if current_location is not None:
             if isinstance(current_location, CurrentWell):
-                ancestor = self._geometry.get_ancestor_slot_name(
+                pipette_deck_slot = self._geometry.get_ancestor_slot_name(
                     current_location.labware_id
-                )
-                if isinstance(ancestor, StagingSlotName):
-                    # Staging Area Slots cannot intersect with the h/s
-                    return False
-                pipette_deck_slot = ancestor.as_int()
+                ).as_int()
             else:
                 pipette_deck_slot = (
                     self._addressable_areas.get_addressable_area_base_slot(
@@ -303,13 +299,9 @@ class MotionView:
         current_location = self._pipettes.get_current_location()
         if current_location is not None:
             if isinstance(current_location, CurrentWell):
-                ancestor = self._geometry.get_ancestor_slot_name(
+                pipette_deck_slot = self._geometry.get_ancestor_slot_name(
                     current_location.labware_id
-                )
-                if isinstance(ancestor, StagingSlotName):
-                    # Staging Area Slots cannot intersect with the h/s
-                    return False
-                pipette_deck_slot = ancestor.as_int()
+                ).as_int()
             else:
                 pipette_deck_slot = (
                     self._addressable_areas.get_addressable_area_base_slot(
@@ -332,10 +324,6 @@ class MotionView:
         """Get a list of touch points for a touch tip operation."""
         mount = self._pipettes.get_mount(pipette_id)
         labware_slot = self._geometry.get_ancestor_slot_name(labware_id)
-        if isinstance(labware_slot, StagingSlotName):
-            raise errors.LocationIsStagingSlotError(
-                "Cannot perform Touch Tip on labware in Staging Area Slot."
-            )
         next_to_module = self._modules.is_edge_move_unsafe(mount, labware_slot)
         edge_path_type = self._labware.get_edge_path_type(
             labware_id, well_name, mount, labware_slot, next_to_module

opentrons/protocol_engine/state/update_types.py

@@ -205,14 +205,6 @@ class LiquidOperatedUpdate:
     volume_added: float | ClearType
 
 
-@dataclasses.dataclass
-class AbsorbanceReaderLidUpdate:
-    """An update to an absorbance reader's lid location."""
-
-    module_id: str
-    is_lid_on: bool
-
-
 @dataclasses.dataclass
 class StateUpdate:
     """Represents an update to perform on engine state."""
@@ -239,8 +231,6 @@ class StateUpdate:
 
     liquid_operated: LiquidOperatedUpdate | NoChangeType = NO_CHANGE
 
-    absorbance_reader_lid: AbsorbanceReaderLidUpdate | NoChangeType = NO_CHANGE
-
     # These convenience functions let the caller avoid the boilerplate of constructing a
     # complicated dataclass tree.
 
@@ -416,9 +406,3 @@ class StateUpdate:
             well_name=well_name,
             volume_added=volume_added,
         )
-
-    def set_absorbance_reader_lid(self, module_id: str, is_lid_on: bool) -> None:
-        """Update an absorbance reader's lid location. See `AbsorbanceReaderLidUpdate`."""
-        self.absorbance_reader_lid = AbsorbanceReaderLidUpdate(
-            module_id=module_id, is_lid_on=is_lid_on
-        )

opentrons/protocol_runner/run_orchestrator.py

@@ -418,21 +418,6 @@ 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/protocols/parameters/csv_parameter_interface.py

@@ -60,9 +60,7 @@ 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. Set this to ``False``
-            when using the file output of :py:meth:`.AbsorbanceReaderContext.read` as
-            a runtime parameter.
+            :py:class:`csv.Dialect` to improve parsing behavior.
         :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/util/logging_config.py

@@ -5,7 +5,7 @@ from typing import Any, Dict
 
 from opentrons.config import CONFIG, ARCHITECTURE, SystemArchitecture
 
-if ARCHITECTURE is SystemArchitecture.YOCTO:
+if ARCHITECTURE is SystemArchitecture.BUILDROOT:
     from opentrons_hardware.sensors import SENSOR_LOG_NAME
 else:
     # we don't use the sensor log on ot2 or host

{opentrons-8.2.0.dist-info → opentrons-8.2.0a0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.2.0
+Version: 8.2.0a0
 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 ==8.2.0
+Requires-Dist: opentrons-shared-data ==8.2.0a0
 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: packaging >=21.0
 Requires-Dist: importlib-metadata >=1.0 ; python_version < "3.8"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[flex] ==8.2.0 ; extra == 'flex-hardware'
+Requires-Dist: opentrons-hardware[flex] ==8.2.0a0 ; extra == 'flex-hardware'
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware ==8.2.0 ; extra == 'ot2-hardware'
+Requires-Dist: opentrons-hardware ==8.2.0a0 ; extra == 'ot2-hardware'
 
 .. _Full API Documentation: http://docs.opentrons.com