opentrons 8.3.0a1__py2.py3-none-any.whl → 8.3.0a4__py2.py3-none-any.whl

opentrons/protocol_engine/execution/hardware_stopper.py

@@ -65,7 +65,7 @@ class HardwareStopper:
             axes=[MotorAxis.X, MotorAxis.Y, MotorAxis.LEFT_Z, MotorAxis.RIGHT_Z]
         )
 
-    async def _drop_tip(self) -> None:
+    async def _try_to_drop_tips(self) -> None:
         """Drop currently attached tip, if any, into trash after a run cancel."""
         attached_tips = self._state_store.pipettes.get_all_attached_tips()
 
@@ -134,9 +134,9 @@ class HardwareStopper:
             PostRunHardwareState.HOME_THEN_DISENGAGE,
         )
         if drop_tips_after_run:
-            await self._drop_tip()
-            await self._hardware_api.stop(home_after=home_after_stop)
-        else:
-            await self._hardware_api.stop(home_after=False)
-            if home_after_stop:
-                await self._home_everything_except_plungers()
+            await self._try_to_drop_tips()
+
+        await self._hardware_api.stop(home_after=False)
+
+        if home_after_stop:
+            await self._home_everything_except_plungers()

opentrons/protocol_engine/execution/tip_handler.py

@@ -62,6 +62,7 @@ class TipHandler(TypingProtocol):
         pipette_id: str,
         labware_id: str,
         well_name: str,
+        do_not_ignore_tip_presence: bool = True,
     ) -> TipGeometry:
         """Pick up the named tip.
 
@@ -75,7 +76,13 @@ class TipHandler(TypingProtocol):
         """
         ...
 
-    async def drop_tip(self, pipette_id: str, home_after: Optional[bool]) -> None:
+    async def drop_tip(
+        self,
+        pipette_id: str,
+        home_after: Optional[bool],
+        do_not_ignore_tip_presence: bool = True,
+        ignore_plunger: bool = False,
+    ) -> None:
         """Drop the attached tip into the current location.
 
         Pipette should be in place over the destination prior to calling this method.
@@ -230,6 +237,7 @@ class HardwareTipHandler(TipHandler):
         pipette_id: str,
         labware_id: str,
         well_name: str,
+        do_not_ignore_tip_presence: bool = True,
     ) -> TipGeometry:
         """See documentation on abstract base class."""
         hw_mount = self._get_hw_mount(pipette_id)
@@ -253,10 +261,11 @@ class HardwareTipHandler(TipHandler):
         await self._hardware_api.tip_pickup_moves(
             mount=hw_mount, presses=None, increment=None
         )
-        try:
-            await self.verify_tip_presence(pipette_id, TipPresenceStatus.PRESENT)
-        except TipNotAttachedError as e:
-            raise PickUpTipTipNotAttachedError(tip_geometry=tip_geometry) from e
+        if do_not_ignore_tip_presence:
+            try:
+                await self.verify_tip_presence(pipette_id, TipPresenceStatus.PRESENT)
+            except TipNotAttachedError as e:
+                raise PickUpTipTipNotAttachedError(tip_geometry=tip_geometry) from e
 
         self.cache_tip(pipette_id, tip_geometry)
 
@@ -264,7 +273,13 @@ class HardwareTipHandler(TipHandler):
 
         return tip_geometry
 
-    async def drop_tip(self, pipette_id: str, home_after: Optional[bool]) -> None:
+    async def drop_tip(
+        self,
+        pipette_id: str,
+        home_after: Optional[bool],
+        do_not_ignore_tip_presence: bool = True,
+        ignore_plunger: bool = False,
+    ) -> None:
         """See documentation on abstract base class."""
         hw_mount = self._get_hw_mount(pipette_id)
 
@@ -275,10 +290,13 @@ class HardwareTipHandler(TipHandler):
         else:
             kwargs = {}
 
-        await self._hardware_api.tip_drop_moves(mount=hw_mount, **kwargs)
+        await self._hardware_api.tip_drop_moves(
+            mount=hw_mount, ignore_plunger=ignore_plunger, **kwargs
+        )
 
-        # Allow TipNotAttachedError to propagate.
-        await self.verify_tip_presence(pipette_id, TipPresenceStatus.ABSENT)
+        if do_not_ignore_tip_presence:
+            # Allow TipNotAttachedError to propagate.
+            await self.verify_tip_presence(pipette_id, TipPresenceStatus.ABSENT)
 
         self.remove_tip(pipette_id)
 
@@ -383,6 +401,7 @@ class VirtualTipHandler(TipHandler):
         pipette_id: str,
         labware_id: str,
         well_name: str,
+        do_not_ignore_tip_presence: bool = True,
     ) -> TipGeometry:
         """Pick up a tip at the current location using a virtual pipette.
 
@@ -424,6 +443,8 @@ class VirtualTipHandler(TipHandler):
         self,
         pipette_id: str,
         home_after: Optional[bool],
+        do_not_ignore_tip_presence: bool = True,
+        ignore_plunger: bool = False,
     ) -> None:
         """Pick up a tip at the current location using a virtual pipette.
 

opentrons/protocol_engine/resources/labware_validation.py

@@ -14,6 +14,11 @@ def is_absorbance_reader_lid(load_name: str) -> bool:
     return load_name == "opentrons_flex_lid_absorbance_plate_reader_module"
 
 
+def is_evotips(load_name: str) -> bool:
+    """Check if a labware is an evotips tiprack."""
+    return load_name == "evotips_opentrons_96_labware"
+
+
 def validate_definition_is_labware(definition: LabwareDefinition) -> bool:
     """Validate that one of the definition's allowed roles is `labware`.
 
@@ -44,6 +49,14 @@ def validate_labware_can_be_stacked(
     return below_labware_load_name in top_labware_definition.stackingOffsetWithLabware
 
 
+def validate_labware_can_be_ondeck(definition: LabwareDefinition) -> bool:
+    """Validate that the labware being loaded onto the deck can sit in a slot."""
+    return (
+        definition.parameters.quirks is None
+        or "stackingOnly" not in definition.parameters.quirks
+    )
+
+
 def validate_gripper_compatible(definition: LabwareDefinition) -> bool:
     """Validate that the labware definition does not have a quirk disallowing movement with gripper."""
     return (

opentrons/protocol_engine/state/commands.py

@@ -1,4 +1,5 @@
 """Protocol engine commands sub-state."""
+
 from __future__ import annotations
 
 import enum
@@ -304,7 +305,7 @@ class CommandStore(HasState[CommandState], HandlesActions):
         # TODO(mc, 2021-06-22): mypy has trouble with this automatic
         # request > command mapping, figure out how to type precisely
         # (or wait for a future mypy version that can figure it out).
-        queued_command = action.request._CommandCls.model_construct(  # type: ignore[call-arg]
+        queued_command = action.request._CommandCls.model_construct(
             id=action.command_id,
             key=(
                 action.request.key
@@ -506,7 +507,10 @@ class CommandStore(HasState[CommandState], HandlesActions):
                         pass
                     case QueueStatus.RUNNING | QueueStatus.PAUSED:
                         self._state.queue_status = QueueStatus.PAUSED
-                    case QueueStatus.AWAITING_RECOVERY | QueueStatus.AWAITING_RECOVERY_PAUSED:
+                    case (
+                        QueueStatus.AWAITING_RECOVERY
+                        | QueueStatus.AWAITING_RECOVERY_PAUSED
+                    ):
                         self._state.queue_status = QueueStatus.AWAITING_RECOVERY_PAUSED
             elif action.door_state == DoorState.CLOSED:
                 self._state.is_door_blocking = False

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

opentrons/protocol_engine/state/labware.py

@@ -524,7 +524,6 @@ class LabwareView:
         will be used.
         """
         definition = self.get_definition(labware_id)
-
         if well_name is None:
             well_name = definition.ordering[0][0]
 
@@ -887,6 +886,19 @@ class LabwareView:
                     f"Labware {labware.loadName} is already present at {location}."
                 )
 
+    def raise_if_labware_cannot_be_ondeck(
+        self,
+        location: LabwareLocation,
+        labware_definition: LabwareDefinition,
+    ) -> None:
+        """Raise an error if the labware cannot be in the specified location."""
+        if isinstance(
+            location, (DeckSlotLocation, AddressableAreaLocation)
+        ) and not labware_validation.validate_labware_can_be_ondeck(labware_definition):
+            raise errors.LabwareCannotSitOnDeckError(
+                f"{labware_definition.parameters.loadName} cannot sit in a slot by itself."
+            )
+
     def raise_if_labware_incompatible_with_plate_reader(
         self,
         labware_definition: LabwareDefinition,

opentrons/protocol_engine/state/pipettes.py

@@ -331,6 +331,11 @@ class PipetteStore(HasState[PipetteState], HandlesActions):
     def _update_aspirated(
         self, update: update_types.PipetteAspiratedFluidUpdate
     ) -> None:
+        if self._state.pipette_contents_by_id[update.pipette_id] is None:
+            self._state.pipette_contents_by_id[
+                update.pipette_id
+            ] = fluid_stack.FluidStack()
+
         self._fluid_stack_log_if_empty(update.pipette_id).add_fluid(update.fluid)
 
     def _update_ejected(self, update: update_types.PipetteEjectedFluidUpdate) -> None:

opentrons/protocols/labware.py

@@ -4,7 +4,7 @@ import logging
 import json
 import os
 from pathlib import Path
-from typing import Any, AnyStr, Dict, Optional, Union, List
+from typing import Any, AnyStr, Dict, Optional, Union, List, Sequence, Literal
 
 import jsonschema  # type: ignore
 
@@ -17,10 +17,30 @@ from opentrons.protocols.api_support.constants import (
     USER_DEFS_PATH,
 )
 from opentrons_shared_data.labware.types import LabwareDefinition
+from opentrons_shared_data.errors.exceptions import InvalidProtocolData
 
 
 MODULE_LOG = logging.getLogger(__name__)
 
+LabwareProblem = Literal[
+    "no-schema-id", "bad-schema-id", "schema-mismatch", "invalid-json"
+]
+
+
+class NotALabwareError(InvalidProtocolData):
+    def __init__(
+        self, problem: LabwareProblem, wrapping: Sequence[BaseException]
+    ) -> None:
+        messages: dict[LabwareProblem, str] = {
+            "no-schema-id": "No schema ID present in file",
+            "bad-schema-id": "Bad schema ID in file",
+            "invalid-json": "File does not contain valid JSON",
+            "schema-mismatch": "File does not match labware schema",
+        }
+        super().__init__(
+            message=messages[problem], detail={"kind": problem}, wrapping=wrapping
+        )
+
 
 def get_labware_definition(
     load_name: str,
@@ -126,7 +146,7 @@ def save_definition(
         json.dump(labware_def, f)
 
 
-def verify_definition(
+def verify_definition(  # noqa: C901
     contents: Union[AnyStr, LabwareDefinition, Dict[str, Any]]
 ) -> LabwareDefinition:
     """Verify that an input string is a labware definition and return it.
@@ -146,15 +166,24 @@ def verify_definition(
     if isinstance(contents, dict):
         to_return = contents
     else:
-        to_return = json.loads(contents)
+        try:
+            to_return = json.loads(contents)
+        except json.JSONDecodeError as e:
+            raise NotALabwareError("invalid-json", [e]) from e
     try:
         schema_version = to_return["schemaVersion"]
+    except KeyError as e:
+        raise NotALabwareError("no-schema-id", [e]) from e
+
+    try:
         schema = schemata_by_version[schema_version]
-    except KeyError:
-        raise RuntimeError(
-            f'Invalid or unknown labware schema version {to_return.get("schemaVersion", None)}'
-        )
-    jsonschema.validate(to_return, schema)
+    except KeyError as e:
+        raise NotALabwareError("bad-schema-id", [e]) from e
+
+    try:
+        jsonschema.validate(to_return, schema)
+    except jsonschema.ValidationError as e:
+        raise NotALabwareError("schema-mismatch", [e]) from e
 
     # we can type ignore this because if it passes the jsonschema it has
     # the correct structure

opentrons/util/entrypoint_util.py

@@ -6,7 +6,6 @@ import contextlib
 from dataclasses import dataclass
 import json
 import logging
-from json import JSONDecodeError
 import pathlib
 import subprocess
 import sys
@@ -21,8 +20,6 @@ from typing import (
     TYPE_CHECKING,
 )
 
-from jsonschema import ValidationError  # type: ignore
-
 from opentrons.calibration_storage.deck_configuration import (
     deserialize_deck_configuration,
 )
@@ -32,7 +29,7 @@ from opentrons.config import (
     JUPYTER_NOTEBOOK_LABWARE_DIR,
     SystemArchitecture,
 )
-from opentrons.protocol_api import labware
+from opentrons.protocols import labware
 from opentrons.calibration_storage import helpers
 from opentrons.protocol_engine.errors.error_occurrence import (
     ErrorOccurrence as ProtocolEngineErrorOccurrence,
@@ -79,7 +76,7 @@ def labware_from_paths(
             if child.is_file() and child.suffix.endswith("json"):
                 try:
                     defn = labware.verify_definition(child.read_bytes())
-                except (ValidationError, JSONDecodeError):
+                except labware.NotALabwareError:
                     log.info(f"{child}: invalid labware, ignoring")
                     log.debug(
                         f"{child}: labware invalid because of this exception.",

{opentrons-8.3.0a1.dist-info → opentrons-8.3.0a4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.3.0a1
+Version: 8.3.0a4
 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 (==8.3.0a1)
+Requires-Dist: opentrons-shared-data (==8.3.0a4)
 Requires-Dist: aionotify (==0.3.1)
 Requires-Dist: anyio (<4.0.0,>=3.6.1)
 Requires-Dist: jsonschema (<4.18.0,>=3.0.1)
@@ -35,9 +35,9 @@ 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] (==8.3.0a1) ; extra == 'flex-hardware'
+Requires-Dist: opentrons-hardware[flex] (==8.3.0a4) ; extra == 'flex-hardware'
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware (==8.3.0a1) ; extra == 'ot2-hardware'
+Requires-Dist: opentrons-hardware (==8.3.0a4) ; extra == 'ot2-hardware'
 
 .. _Full API Documentation: http://docs.opentrons.com