opentrons 8.4.0a9__py2.py3-none-any.whl → 8.4.0a11__py2.py3-none-any.whl

opentrons/protocol_api/core/engine/instrument.py

@@ -2283,6 +2283,13 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
         well_location = WellLocation(
             origin=WellOrigin.TOP, offset=WellOffset(x=offset.x, y=offset.y, z=offset.z)
         )
+        pipette_movement_conflict.check_safe_for_pipette_movement(
+            engine_state=self._engine_client.state,
+            pipette_id=self._pipette_id,
+            labware_id=labware_id,
+            well_name=well_name,
+            well_location=well_location,
+        )
         self._engine_client.execute_command(
             cmd.LiquidProbeParams(
                 labwareId=labware_id,
@@ -2303,6 +2310,13 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
         well_location = WellLocation(
             origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=2)
         )
+        pipette_movement_conflict.check_safe_for_pipette_movement(
+            engine_state=self._engine_client.state,
+            pipette_id=self._pipette_id,
+            labware_id=labware_id,
+            well_name=well_name,
+            well_location=well_location,
+        )
         result = self._engine_client.execute_command_without_recovery(
             cmd.LiquidProbeParams(
                 labwareId=labware_id,

opentrons/protocol_api/core/engine/well.py

@@ -197,12 +197,14 @@ class WellCore(AbstractWellCore):
             raise PipetteNotAttachedError(f"No pipette present on mount {mount}")
         pipette_id = pipette_from_mount.id
         starting_liquid_height = self.current_liquid_height()
-        projected_final_height = self._engine_client.state.geometry.get_well_height_after_liquid_handling_no_error(
-            labware_id=labware_id,
-            well_name=well_name,
-            pipette_id=pipette_id,
-            initial_height=starting_liquid_height,
-            volume=operation_volume,
+        projected_final_height = (
+            self._engine_client.state.geometry.get_well_height_after_liquid_handling(
+                labware_id=labware_id,
+                well_name=well_name,
+                pipette_id=pipette_id,
+                initial_height=starting_liquid_height,
+                volume=operation_volume,
+            )
         )
         return projected_final_height
 

opentrons/protocol_api/instrument_context.py

@@ -2085,12 +2085,10 @@ class InstrumentContext(publisher.CommandPublisher):
                        to the volume of liquid that will be dispensed.
         :type volume: float
 
-        :param rate: How quickly the plunger moves to displace the commanded volume. The plunger speed
-                     in µL/s is calculated as ``rate`` multiplied by
-                     :py:attr:`flow_rate.dispense<flow_rate>`. This rate does not directly relate to
+        :param rate: How quickly the plunger moves to displace the commanded volume, in µL/s. This rate does not directly relate to
                      the flow rate of liquid out of the resin tip.
 
-                     The default value of ``10.0`` is recommended.
+                     Defaults to ``10.0`` µL/s.
         :type rate: float
         """
         well: Optional[labware.Well] = None

opentrons/protocol_engine/state/frustum_helpers.py

@@ -423,7 +423,8 @@ def _find_height_in_partial_frustum(
     # if we finish looping through the whole well, bottom_section will be the well's volume
     total_well_volume = bottom_section_volume
     # if we've looked through all sections and can't find the target volume, raise an error
-    # also this code should never be reached bc an error should be raised by find_height_at_well_volume
+    # also this code should never be reached bc an invalid target volume should be changed
+    # by find_height_at_well_volume
     raise InvalidLiquidHeightFound(
         f"Target volume {target_volume} uL exceeds the well volume {total_well_volume} uL."
     )
@@ -432,7 +433,6 @@ def _find_height_in_partial_frustum(
 def find_height_at_well_volume(
     target_volume: LiquidTrackingType,
     well_geometry: InnerWellGeometry,
-    raise_error_if_result_invalid: bool = True,
 ) -> LiquidTrackingType:
     """Find the height within a well, at a known volume."""
     # comparisons with SimulatedProbeResult objects aren't meaningful, just
@@ -443,12 +443,10 @@ def find_height_at_well_volume(
     volumetric_capacity = get_well_volumetric_capacity(well_geometry)
     max_volume = sum(row[1] for row in volumetric_capacity)
 
-    if raise_error_if_result_invalid:
-        if target_volume < 0 or target_volume > max_volume:
-            raise InvalidLiquidHeightFound(
-                f"Invalid target volume {target_volume} uL; max volume is {max_volume} uL"
-            )
-
+    if target_volume < 0:
+        target_volume = 0
+    elif target_volume > max_volume:
+        target_volume = max_volume
     sorted_well = sorted(well_geometry.sections, key=lambda section: section.topHeight)
     # find the section the target volume is in and compute the height
     return _find_height_in_partial_frustum(

opentrons/protocol_engine/state/geometry.py

@@ -7,7 +7,6 @@ from numpy.typing import NDArray
 from typing import Optional, List, Tuple, Union, cast, TypeVar, Dict, Set
 from dataclasses import dataclass
 from functools import cached_property
-from math import isclose
 
 from opentrons.types import (
     Point,
@@ -33,7 +32,6 @@ from ..errors import (
     LabwareNotLoadedOnLabwareError,
     LabwareNotLoadedOnModuleError,
     LabwareMovementNotAllowedError,
-    OperationLocationNotInWellError,
     InvalidLabwarePositionError,
     LabwareNotOnDeckError,
 )
@@ -522,39 +520,23 @@ class GeometryView:
             z=origin_pos.z + cal_offset.z,
         )
 
-    def validate_well_position(
+    def _validate_well_position(
         self,
-        well_location: WellLocationType,
-        z_offset: float,
-        pipette_id: Optional[str] = None,
-    ) -> None:
-        """Raise exception if operation location is not within well.
-
-        Primarily this checks if there is not enough liquid in a well to do meniscus-relative static aspiration.
-        """
-        if well_location.origin == WellOrigin.MENISCUS:
-            assert pipette_id is not None, "pipette id is None"
-            lld_min_height = self._pipettes.get_current_tip_lld_settings(
-                pipette_id=pipette_id
-            )
-            if z_offset < lld_min_height:
-                if isinstance(well_location, LiquidHandlingWellLocation):
-                    raise OperationLocationNotInWellError(
-                        f"Specifying {well_location.origin} with a height offset of {well_location.offset.z} results in a height of {z_offset} mm; the minimum allowed height for liquid tracking is {lld_min_height} mm"
-                    )
-                else:
-                    raise OperationLocationNotInWellError(
-                        f"Specifying {well_location.origin} with an offset of {well_location.offset} results in an operation location that could be below the bottom of the well"
-                    )
-        elif z_offset < 0 and not isclose(z_offset, 0, abs_tol=0.0000001):
-            if isinstance(well_location, LiquidHandlingWellLocation):
-                raise OperationLocationNotInWellError(
-                    f"Specifying {well_location.origin} with an offset of {well_location.offset} and a volume offset of {well_location.volumeOffset} results in an operation location below the bottom of the well"
-                )
-            else:
-                raise OperationLocationNotInWellError(
-                    f"Specifying {well_location.origin} with an offset of {well_location.offset} results in an operation location below the bottom of the well"
-                )
+        target_height: LiquidTrackingType,  # height in mm inside a well relative to the bottom
+        well_max_height: float,
+        pipette_id: str,
+    ) -> LiquidTrackingType:
+        """If well offset would be outside the bounds of a well, silently bring it back to the boundary."""
+        if isinstance(target_height, SimulatedProbeResult):
+            return target_height
+        lld_min_height = self._pipettes.get_current_tip_lld_settings(
+            pipette_id=pipette_id
+        )
+        if target_height < lld_min_height:
+            target_height = lld_min_height
+        elif target_height > well_max_height:
+            target_height = well_max_height
+        return target_height
 
     def validate_probed_height(
         self,
@@ -595,7 +577,7 @@ class GeometryView:
 
         offset = WellOffset(x=0, y=0, z=well_depth)
         if well_location is not None:
-            offset = well_location.offset
+            offset = well_location.offset  # location of the bottom of the well
             offset_adjustment = self.get_well_offset_adjustment(
                 labware_id=labware_id,
                 well_name=well_name,
@@ -606,11 +588,6 @@ class GeometryView:
             )
             if not isinstance(offset_adjustment, SimulatedProbeResult):
                 offset = offset.model_copy(update={"z": offset.z + offset_adjustment})
-                self.validate_well_position(
-                    well_location=well_location,
-                    z_offset=offset.z,
-                    pipette_id=pipette_id,
-                )
         return Point(
             x=labware_pos.x + offset.x + well_def.x,
             y=labware_pos.y + offset.y + well_def.y,
@@ -2107,6 +2084,8 @@ class GeometryView:
 
         This is given an initial handling height, with reference to the well bottom.
         """
+        well_def = self._labware.get_well_definition(labware_id, well_name)
+        well_depth = well_def.depth
         well_geometry = self._labware.get_well_geometry(
             labware_id=labware_id, well_name=well_name
         )
@@ -2122,49 +2101,17 @@ class GeometryView:
                     pipette_id=pipette_id,
                 )
             )
-            return find_height_at_well_volume(
+            # NOTE(cm): if final_volume is outside the bounds of the well, it will get
+            # adjusted inside find_height_at_well_volume to accomodate well the height
+            # calculation.
+            height_inside_well = find_height_at_well_volume(
                 target_volume=final_volume, well_geometry=well_geometry
             )
-        except InvalidLiquidHeightFound as _exception:
-            raise InvalidLiquidHeightFound(
-                message=_exception.message
-                + f"for well {well_name} of {self._labware.get_display_name(labware_id)} on slot {self.get_ancestor_slot_name(labware_id)}"
-            )
-
-    def get_well_height_after_liquid_handling_no_error(
-        self,
-        labware_id: str,
-        well_name: str,
-        pipette_id: str,
-        initial_height: LiquidTrackingType,
-        volume: float,
-    ) -> LiquidTrackingType:
-        """Return what the height of liquid in a labware well after liquid handling will be.
-
-        This raises no error if the value returned is an invalid physical location, so it should never be
-        used for navigation, only for a pre-emptive estimate.
-        """
-        well_geometry = self._labware.get_well_geometry(
-            labware_id=labware_id, well_name=well_name
-        )
-        try:
-            initial_volume = find_volume_at_well_height(
-                target_height=initial_height, well_geometry=well_geometry
-            )
-            final_volume = initial_volume + (
-                volume
-                * self.get_nozzles_per_well(
-                    labware_id=labware_id,
-                    target_well_name=well_name,
-                    pipette_id=pipette_id,
-                )
-            )
-            well_volume = find_height_at_well_volume(
-                target_volume=final_volume,
-                well_geometry=well_geometry,
-                raise_error_if_result_invalid=False,
+            return self._validate_well_position(
+                target_height=height_inside_well,
+                well_max_height=well_depth,
+                pipette_id=pipette_id,
             )
-            return well_volume
         except InvalidLiquidHeightFound as _exception:
             raise InvalidLiquidHeightFound(
                 message=_exception.message

{opentrons-8.4.0a9.dist-info → opentrons-8.4.0a11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.4.0a9
+Version: 8.4.0a11
 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 (==8.4.0a9)
+Requires-Dist: opentrons-shared-data (==8.4.0a11)
 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] (==8.4.0a9) ; extra == 'flex-hardware'
+Requires-Dist: opentrons-hardware[flex] (==8.4.0a11) ; extra == 'flex-hardware'
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware (==8.4.0a9) ; extra == 'ot2-hardware'
+Requires-Dist: opentrons-hardware (==8.4.0a11) ; extra == 'ot2-hardware'
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.4.0a9.dist-info → opentrons-8.4.0a11.dist-info}/RECORD

@@ -228,7 +228,7 @@ opentrons/protocol_api/config.py,sha256=r9lyvXjagTX_g3q5FGURPpcz2IA9sSF7Oa_1mKx-
 opentrons/protocol_api/create_protocol_context.py,sha256=wwsZje0L__oDnu1Yrihau320_f-ASloR9eL1QCtkOh8,7612
 opentrons/protocol_api/deck.py,sha256=94vFceg1SC1bAGd7TvC1ZpYwnJR-VlzurEZ6jkacYeg,8910
 opentrons/protocol_api/disposal_locations.py,sha256=NRiSGmDR0LnbyEkWSOM-o64uR2fUoB1NWJG7Y7SsJSs,7920
-opentrons/protocol_api/instrument_context.py,sha256=wqQ_un5E_sLjhwwNsp2qF_GTD0lajlrBG68JE7WgbPY,120913
+opentrons/protocol_api/instrument_context.py,sha256=6KW5cQ-G0HOrYTMH7835dEqMJZ2F2yPH48sl0Eu9eW8,120754
 opentrons/protocol_api/labware.py,sha256=KRt91dOzmCX6l8LQ5Wny7kIk_L0Y69Uzpolp-geE0MY,60458
 opentrons/protocol_api/module_contexts.py,sha256=3tVXj6Q7n-WuTJPU_dvIQLzzGv1P-jsMuDtMVpuhAf8,48291
 opentrons/protocol_api/module_validation_and_errors.py,sha256=XL_m72P8rcvGO2fynY7UzXLcpGuI6X4s0V6Xf735Iyc,1464
@@ -248,7 +248,7 @@ opentrons/protocol_api/core/well_grid.py,sha256=BU28DKaBgEU_JdZ6pEzrwNxmuh6TkO4z
 opentrons/protocol_api/core/engine/__init__.py,sha256=B_5T7zgkWDb1mXPg4NbT-wBkQaK-WVokMMnJRNu7xiM,582
 opentrons/protocol_api/core/engine/deck_conflict.py,sha256=q3JViIAHDthIqq6ce7h2gxw3CHRfYsm5kkwzuXB-Gnc,12334
 opentrons/protocol_api/core/engine/exceptions.py,sha256=aZgNrmYEeuPZm21nX_KZYtvyjv5h_zPjxxgPkEV7_bw,725
-opentrons/protocol_api/core/engine/instrument.py,sha256=jh3QIqGYDFMoJIrgZLq-IR2liqEhq5aCQgh5xomW3P8,95884
+opentrons/protocol_api/core/engine/instrument.py,sha256=A6ku8gzJBUGpi9qcLSsuJxZavtzUVhWxw8RHCasY5a8,96442
 opentrons/protocol_api/core/engine/labware.py,sha256=1xvzguNnK7aecFLiJK0gtRrZ5kpwtzLS73HnKvdJ5lc,8413
 opentrons/protocol_api/core/engine/load_labware_params.py,sha256=I4Cb8rqpBhmykQuZE8QRG802APrdCy_TYS88rm_9oGA,7159
 opentrons/protocol_api/core/engine/module_core.py,sha256=MLPgYSRJHUZPZ9rTLvsg3GlpL5b6-Pjk5UBgXCGrL6U,30994
@@ -259,7 +259,7 @@ opentrons/protocol_api/core/engine/protocol.py,sha256=_1gdg4lq2B21LWV9Tqb924E39H
 opentrons/protocol_api/core/engine/robot.py,sha256=o252HrC11tmZ5LRKT6NwXCoTeqcQFXHeNjszfxbJHjo,5366
 opentrons/protocol_api/core/engine/stringify.py,sha256=GwFgEhFMk-uPfFQhQG_2mkaf4cxaItiY8RW7rZwiooQ,2794
 opentrons/protocol_api/core/engine/transfer_components_executor.py,sha256=96SsftBRPB5WCeChLokXkdPJcmjP8FqlXEZXhNAlZKA,37582
-opentrons/protocol_api/core/engine/well.py,sha256=o4Qm25AvZwd4ytR3IpK4wH-BwAmzt_7fVIKQsbHMsgg,8122
+opentrons/protocol_api/core/engine/well.py,sha256=9_BgB8O7gE4Y3XgoyJMNtcZasgxSPqDEyAzrQjI60qU,8161
 opentrons/protocol_api/core/legacy/__init__.py,sha256=_9jCJNKG3SlS_vljVu8HHkZmtLf4F-f-JHALLF5d5go,401
 opentrons/protocol_api/core/legacy/deck.py,sha256=qHqcGo-Kdkl9L1aOE0pwrm9tsAnwkXbt4rIOr_VEP-s,13955
 opentrons/protocol_api/core/legacy/labware_offset_provider.py,sha256=2DLIby9xmUrwLb2ht8hZbvNTxqPhNzWijd7yCb2cqP8,3783
@@ -449,8 +449,8 @@ opentrons/protocol_engine/state/commands.py,sha256=aoON_C5DbiIEPxOGATvwCsSG9eHsF
 opentrons/protocol_engine/state/config.py,sha256=7jSGxC6Vqj1eA8fqZ2I3zjlxVXg8pxvcBYMztRIx9Mg,1515
 opentrons/protocol_engine/state/files.py,sha256=w8xxxg8HY0RqKKEGSfHWfrjV54Gb02O3dwtisJ-9j8E,1753
 opentrons/protocol_engine/state/fluid_stack.py,sha256=uwkf0qYk1UX5iU52xmk-e3yLPK8OG-TtMCcBqrkVFpM,5932
-opentrons/protocol_engine/state/frustum_helpers.py,sha256=uRBLLR75Z_PnfVd-U7gPF3NeOALR3TgLNCojgxB4z0o,17343
-opentrons/protocol_engine/state/geometry.py,sha256=v5saIiG6nwMSq_bWXcZUsmOabmHJjG80s7RdxaX-DUg,101235
+opentrons/protocol_engine/state/frustum_helpers.py,sha256=0xWDgYV_FyGKRmae3_5dKY6OJbRgvjC-veEFuZj_0-4,17194
+opentrons/protocol_engine/state/geometry.py,sha256=dDCrhiyYUn-0KxEVHrIoN0V_jBDV1DFJ5f3XIjp_ZLk,98690
 opentrons/protocol_engine/state/labware.py,sha256=rehy7R1HIhxx3DTtTHIKxqHoBQJ_1tDhhiculMJeIy8,57556
 opentrons/protocol_engine/state/liquid_classes.py,sha256=u_z75UYdiFAKG0yB3mr1il4T3qaS0Sotq8sL7KLODP8,2990
 opentrons/protocol_engine/state/liquids.py,sha256=NoesktcQdJUjIVmet1uqqJPf-rzbo4SGemXwQC295W0,2338
@@ -583,9 +583,9 @@ opentrons/util/linal.py,sha256=IlKAP9HkNBBgULeSf4YVwSKHdx9jnCjSr7nvDvlRALg,5753
 opentrons/util/logging_config.py,sha256=7et4YYuQdWdq_e50U-8vFS_QyNBRgdnqPGAQJm8qrIo,9954
 opentrons/util/logging_queue_handler.py,sha256=ZsSJwy-oV8DXwpYiZisQ1PbYwmK2cOslD46AcyJ1E4I,2484
 opentrons/util/performance_helpers.py,sha256=ew7H8XD20iS6-2TJAzbQeyzStZkkE6PzHt_Adx3wbZQ,5172
-opentrons-8.4.0a9.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
-opentrons-8.4.0a9.dist-info/METADATA,sha256=q9nO7VyTyS_ehqIVeJ9SkKhqiDo32Qgai3bDc7n2nxw,5084
-opentrons-8.4.0a9.dist-info/WHEEL,sha256=qUzzGenXXuJTzyjFah76kDVqDvnk-YDzY00svnrl84w,109
-opentrons-8.4.0a9.dist-info/entry_points.txt,sha256=fTa6eGCYkvOtv0ov-KVE8LLGetgb35LQLF9x85OWPVw,106
-opentrons-8.4.0a9.dist-info/top_level.txt,sha256=wk6whpbMZdBQpcK0Fg0YVfUGrAgVOFON7oQAhOMGMW8,10
-opentrons-8.4.0a9.dist-info/RECORD,,
+opentrons-8.4.0a11.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+opentrons-8.4.0a11.dist-info/METADATA,sha256=GLuvrxBIEKihFmoBZK_O5IRINPswDRTAhdzM0IJcuFg,5088
+opentrons-8.4.0a11.dist-info/WHEEL,sha256=qUzzGenXXuJTzyjFah76kDVqDvnk-YDzY00svnrl84w,109
+opentrons-8.4.0a11.dist-info/entry_points.txt,sha256=fTa6eGCYkvOtv0ov-KVE8LLGetgb35LQLF9x85OWPVw,106
+opentrons-8.4.0a11.dist-info/top_level.txt,sha256=wk6whpbMZdBQpcK0Fg0YVfUGrAgVOFON7oQAhOMGMW8,10
+opentrons-8.4.0a11.dist-info/RECORD,,