opentrons 8.5.0a9__tar.gz → 8.5.1__tar.gz

{opentrons-8.5.0a9 → opentrons-8.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.5.0a9
+Version: 8.5.1
 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==8.5.0a9
+Requires-Dist: opentrons-shared-data==8.5.1
 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: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.5.0a9; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.5.1; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.5.0a9; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.5.1; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.5.0a9 → opentrons-8.5.1}/src/opentrons/protocol_api/core/engine/instrument.py

@@ -30,6 +30,9 @@ from opentrons.protocols.advanced_control.transfers.common import (
     NoLiquidClassPropertyError,
 )
 from opentrons.protocols.advanced_control.transfers import common as tx_commons
+from opentrons.protocols.advanced_control.transfers.transfer_liquid_utils import (
+    check_current_volume_before_dispensing,
+)
 from opentrons.protocol_engine import commands as cmd
 from opentrons.protocol_engine import (
     DeckPoint,
@@ -1702,7 +1705,7 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
             # multi-dispense in those destinations.
             # If the tip has a volume corresponding to a single destination, then
             # do a single-dispense into that destination.
-            for dispense_vol, dispense_dest in vol_dest_combo:
+            for idx, (dispense_vol, dispense_dest) in enumerate(vol_dest_combo):
                 if use_single_dispense:
                     tip_contents = self.dispense_liquid_class(
                         volume=dispense_vol,
@@ -1730,6 +1733,7 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
                         trash_location=trash_location,
                         conditioning_volume=conditioning_vol,
                         disposal_volume=disposal_vol,
+                        is_last_dispense_in_tip=(idx == len(vol_dest_combo) - 1),
                     )
                 is_first_step = False
 
@@ -2143,9 +2147,12 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
         """Remove an air gap that was previously added during a transfer."""
         if last_air_gap == 0:
             return
-
+        current_vol = self.get_current_volume()
+        check_current_volume_before_dispensing(
+            current_volume=current_vol, dispense_volume=last_air_gap
+        )
         correction_volume = dispense_props.correction_by_volume.get_for_volume(
-            self.get_current_volume() - last_air_gap
+            current_vol - last_air_gap
         )
         # The minimum flow rate should be air_gap_volume per second
         flow_rate = max(
@@ -2280,6 +2287,7 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
         trash_location: Union[Location, TrashBin, WasteChute],
         conditioning_volume: float,
         disposal_volume: float,
+        is_last_dispense_in_tip: bool,
     ) -> List[tx_comps_executor.LiquidAndAirGapPair]:
         """Execute a dispense step that's part of a multi-dispense.
 
@@ -2326,9 +2334,8 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
         components_executor.submerge(
             submerge_properties=dispense_props.submerge, post_submerge_action="dispense"
         )
-        tip_starting_volume = self.get_current_volume()
         is_last_dispense_without_disposal_vol = (
-            disposal_volume == 0 and tip_starting_volume == volume
+            disposal_volume == 0 and is_last_dispense_in_tip
         )
         push_out_vol = (
             # TODO (spp): verify if it's okay to use push_out_by_volume of single dispense
@@ -2348,7 +2355,7 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
             source_well=source[1] if source else None,
             conditioning_volume=conditioning_volume,
             add_final_air_gap=add_final_air_gap,
-            is_last_retract=tip_starting_volume - volume == disposal_volume,
+            is_last_retract=is_last_dispense_in_tip,
         )
         last_contents = components_executor.tip_state.last_liquid_and_air_gap_in_tip
         new_tip_contents = tip_contents[0:-1] + [last_contents]

{opentrons-8.5.0a9 → opentrons-8.5.1}/src/opentrons/protocol_api/core/engine/transfer_components_executor.py

@@ -25,6 +25,7 @@ from opentrons.protocol_engine.errors import TouchTipDisabledError
 from opentrons.types import Location, Point, Mount
 from opentrons.protocols.advanced_control.transfers.transfer_liquid_utils import (
     LocationCheckDescriptors,
+    check_current_volume_before_dispensing,
 )
 from opentrons.protocols.advanced_control.transfers import (
     transfer_liquid_utils as tx_utils,
@@ -253,8 +254,12 @@ class TransferComponentsExecutor:
         push_out_override: Optional[float],
     ) -> None:
         """Dispense according to dispense properties and wait if enabled."""
+        current_vol = self._instrument.get_current_volume()
+        check_current_volume_before_dispensing(
+            current_volume=current_vol, dispense_volume=volume
+        )
         correction_volume = dispense_properties.correction_by_volume.get_for_volume(
-            self._instrument.get_current_volume() - volume
+            current_vol - volume
         )
         self._instrument.dispense(
             location=self._target_location,
@@ -538,6 +543,11 @@ class TransferComponentsExecutor:
             blowout_props.enabled
             and blowout_props.location == BlowoutLocation.DESTINATION
         ) or not blowout_props.enabled
+
+        if is_final_air_gap and not add_final_air_gap:
+            air_gap_volume = 0.0
+        else:
+            air_gap_volume = retract_props.air_gap_by_volume.get_for_volume(0)
         # Regardless of the blowout location, do touch tip and air gap
         # when leaving the dispense well. If this will be the final air gap, i.e,
         # we won't be moving to a Trash or a Source for Blowout after this air gap,
@@ -546,7 +556,7 @@ class TransferComponentsExecutor:
             touch_tip_properties=retract_props.touch_tip,
             location=retract_location,
             well=self._target_well,
-            add_air_gap=False if is_final_air_gap and not add_final_air_gap else True,
+            air_gap_volume=air_gap_volume,
         )
 
         if (
@@ -594,15 +604,21 @@ class TransferComponentsExecutor:
             last_air_gap = self._tip_state.last_liquid_and_air_gap_in_tip.air_gap
             self._tip_state.delete_air_gap(last_air_gap)
             self._tip_state.ready_to_aspirate = False
+
+            air_gap_volume = (
+                retract_props.air_gap_by_volume.get_for_volume(0)
+                if add_final_air_gap
+                else 0.0
+            )
             # Do touch tip and air gap again after blowing out into source well or trash
             self._do_touch_tip_and_air_gap_after_dispense(
                 touch_tip_properties=retract_props.touch_tip,
                 location=touch_tip_and_air_gap_location,
                 well=touch_tip_and_air_gap_well,
-                add_air_gap=add_final_air_gap,
+                air_gap_volume=air_gap_volume,
             )
 
-    def retract_during_multi_dispensing(
+    def retract_during_multi_dispensing(  # noqa: C901
         self,
         trash_location: Union[Location, TrashBin, WasteChute],
         source_location: Optional[Location],
@@ -715,6 +731,14 @@ class TransferComponentsExecutor:
             else:
                 add_air_gap = True
 
+        air_gap_volume = (
+            retract_props.air_gap_by_volume.get_for_volume(
+                self.tip_state.last_liquid_and_air_gap_in_tip.liquid
+            )
+            if add_air_gap
+            else 0.0
+        )
+
         # Regardless of the blowout location, do touch tip
         # when leaving the dispense well.
         # Add an air gap depending on conditioning volume + whether this is
@@ -724,7 +748,7 @@ class TransferComponentsExecutor:
             touch_tip_properties=retract_props.touch_tip,
             location=retract_location,
             well=self._target_well,
-            add_air_gap=add_air_gap,
+            air_gap_volume=air_gap_volume,
         )
 
         if (
@@ -771,17 +795,22 @@ class TransferComponentsExecutor:
             self._tip_state.delete_last_air_gap_and_liquid()
             self._tip_state.ready_to_aspirate = False
 
+            if (
+                # Same check as before for when it's the final air gap of current retract
+                conditioning_volume > 0
+                and is_last_retract
+                and add_final_air_gap
+            ):
+                # The volume in tip at this point should be 0uL
+                air_gap_volume = retract_props.air_gap_by_volume.get_for_volume(0)
+            else:
+                air_gap_volume = 0
             # Do touch tip and air gap again after blowing out into source well or trash
             self._do_touch_tip_and_air_gap_after_dispense(
                 touch_tip_properties=retract_props.touch_tip,
                 location=touch_tip_and_air_gap_location,
                 well=touch_tip_and_air_gap_well,
-                add_air_gap=(
-                    # Same check as before for when it's the final air gap of current retract
-                    conditioning_volume > 0
-                    and is_last_retract
-                    and add_final_air_gap
-                ),
+                air_gap_volume=air_gap_volume,
             )
 
     def _do_touch_tip_and_air_gap_after_dispense(  # noqa: C901
@@ -789,7 +818,7 @@ class TransferComponentsExecutor:
         touch_tip_properties: TouchTipProperties,
         location: Union[Location, TrashBin, WasteChute],
         well: Optional[WellCore],
-        add_air_gap: bool,
+        air_gap_volume: float,
     ) -> None:
         """Perform touch tip and air gap as part of post-dispense retract.
 
@@ -835,7 +864,7 @@ class TransferComponentsExecutor:
                     # Full speed because the tip will already be out of the liquid
                     speed=None,
                 )
-        if add_air_gap or not self._tip_state.ready_to_aspirate:
+        if air_gap_volume > 0 or not self._tip_state.ready_to_aspirate:
             # If we need to move the plunger up either to prepare for aspirate or to add air gap,
             # move to a safe location above the well if the retract location is not already
             # at or above this safe location
@@ -881,12 +910,8 @@ class TransferComponentsExecutor:
             if not self._tip_state.ready_to_aspirate:
                 self._instrument.prepare_to_aspirate()
                 self._tip_state.ready_to_aspirate = True
-            if add_air_gap:
-                self._add_air_gap(
-                    air_gap_volume=self._transfer_properties.aspirate.retract.air_gap_by_volume.get_for_volume(
-                        0
-                    )
-                )
+            if air_gap_volume > 0:
+                self._add_air_gap(air_gap_volume=air_gap_volume)
 
     def _add_air_gap(
         self,

{opentrons-8.5.0a9 → opentrons-8.5.1}/src/opentrons/protocol_api/instrument_context.py

@@ -840,10 +840,9 @@ class InstrumentContext(publisher.CommandPublisher):
         :type speed: float
         :param mm_from_edge: How far to move inside the well, as a distance from the
                              well's edge.
-                             When ``mm_from_edge=0``, the pipette tip will move all the
-                             way to the edge of the target well. When ``mm_from_edge=1``,
-                             the pipette tip will move to 1 mm from the well's edge.
-                             Lower values will press the tip harder into the well's
+                             When ``mm_from_edge=0``, the pipette will move to the target well's edge to touch the tip. When ``mm_from_edge=1``,
+                             the pipette will move to 1 mm from the target well's edge to touch the tip.
+                             Values lower than 0 will press the tip harder into the target well's
                              walls; higher values will touch the well more lightly, or
                              not at all.
                              ``mm_from_edge`` and ``radius`` are mutually exclusive: to
@@ -1802,9 +1801,6 @@ class InstrumentContext(publisher.CommandPublisher):
     ) -> InstrumentContext:
         """Move a particular type of liquid from one well or group of wells to another.
 
-        ..
-            This is intended for Opentrons internal use only and is not a guaranteed API.
-
         :param liquid_class: The type of liquid to move. You must specify the liquid class,
             even if you have used :py:meth:`.Labware.load_liquid` to indicate what liquid the
             source contains.
@@ -1829,6 +1825,7 @@ class InstrumentContext(publisher.CommandPublisher):
 
         :param trash_location: A trash container, well, or other location to dispose of
             tips. Depending on the liquid class, the pipette may also blow out liquid here.
+            If not specified, the pipette will dispose of tips in its :py:obj:`~.InstrumentContext.trash_container`.
         :param return_tip: Whether to drop used tips in their original locations
             in the tip rack, instead of the trash.
         :param group_wells: For multi-channel transfers only. If set to ``True``, group together contiguous wells
@@ -1838,7 +1835,6 @@ class InstrumentContext(publisher.CommandPublisher):
             ``False``, the last tip will be dropped or returned. If not set, behavior depends on the value of
             ``new_tip``. ``new_tip="never"`` keeps the tip, and all other values of ``new_tip`` drop or return the tip.
 
-        :meta private:
         """
         if volume == 0.0:
             _log.info(
@@ -1945,16 +1941,12 @@ class InstrumentContext(publisher.CommandPublisher):
         """
         Distribute a particular type of liquid from one well to a group of wells.
 
-        ..
-            This is intended for Opentrons internal use only and is not a guaranteed API.
-
         :param liquid_class: The type of liquid to move. You must specify the liquid class,
             even if you have used :py:meth:`.Labware.load_liquid` to indicate what liquid the
             source contains.
         :type liquid_class: :py:class:`.LiquidClass`
 
-        :param volume: The amount, in µL, to aspirate from the source and dispense to
-                       each destination.
+        :param volume: The amount, in µL, to dispense to each destination.
         :param source: A single well for the pipette to target, or a group of wells to
                        target in a single aspirate for a multi-channel pipette.
         :param dest: A list of wells to dispense liquid into.
@@ -1962,13 +1954,14 @@ class InstrumentContext(publisher.CommandPublisher):
             Defaults to ``"once"``.
 
               - ``"once"``: Use one tip for the entire command.
+              - ``"always"``: Use a new tip before each aspirate.
               - ``"never"``: Do not pick up or drop tips at all.
-              - ``"always"``: Pick up a new tip before every aspirate.
 
             See :ref:`param-tip-handling` for details.
 
         :param trash_location: A trash container, well, or other location to dispose of
             tips. Depending on the liquid class, the pipette may also blow out liquid here.
+            If not specified, the pipette will dispose of tips in its :py:obj:`~.InstrumentContext.trash_container`.
         :param return_tip: Whether to drop used tips in their original locations
             in the tip rack, instead of the trash.
         :param group_wells: For multi-channel transfers only. If set to ``True``, group together contiguous wells
@@ -1978,7 +1971,6 @@ class InstrumentContext(publisher.CommandPublisher):
             ``False``, the last tip will be dropped or returned. If not set, behavior depends on the value of
             ``new_tip``. ``new_tip="never"`` keeps the tip, and all other values of ``new_tip`` drop or return the tip.
 
-        :meta private:
         """
         if volume == 0.0:
             _log.info(
@@ -2093,16 +2085,12 @@ class InstrumentContext(publisher.CommandPublisher):
         """
         Consolidate a particular type of liquid from a group of wells to one well.
 
-        ..
-            This is intended for Opentrons internal use only and is not a guaranteed API.
-
         :param liquid_class: The type of liquid to move. You must specify the liquid class,
             even if you have used :py:meth:`.Labware.load_liquid` to indicate what liquid the
             source contains.
         :type liquid_class: :py:class:`.LiquidClass`
 
-        :param volume: The amount, in µL, to aspirate from the source and dispense to
-                       each destination.
+        :param volume: The amount, in µL, to aspirate from each source well.
         :param source: A list of wells to aspirate liquid from.
         :param dest: A single well, list of wells, trash bin, or waste chute to dispense liquid into.
                      Multiple wells can only be given for multi-channel pipette configurations, and
@@ -2111,13 +2099,14 @@ class InstrumentContext(publisher.CommandPublisher):
             Defaults to ``"once"``.
 
               - ``"once"``: Use one tip for the entire command.
+              - ``"always"``: Use a new tip after each aspirate and dispense, even when visiting the same source again.
               - ``"never"``: Do not pick up or drop tips at all.
-              - ``"always"``: Pick up a new tip before going back to source for refilling after a dispense.
 
             See :ref:`param-tip-handling` for details.
 
         :param trash_location: A trash container, well, or other location to dispose of
             tips. Depending on the liquid class, the pipette may also blow out liquid here.
+            If not specified, the pipette will dispose of tips in its :py:obj:`~.InstrumentContext.trash_container`.
         :param return_tip: Whether to drop used tips in their original locations
             in the tip rack, instead of the trash.
         :param group_wells: For multi-channel transfers only. If set to ``True``, group together contiguous wells
@@ -2127,7 +2116,6 @@ class InstrumentContext(publisher.CommandPublisher):
             ``False``, the last tip will be dropped or returned. If not set, behavior depends on the value of
             ``new_tip``. ``new_tip="never"`` keeps the tip, and all other values of ``new_tip`` drop or return the tip.
 
-        :meta private:
         """
         if volume == 0.0:
             _log.info(

{opentrons-8.5.0a9 → opentrons-8.5.1}/src/opentrons/protocol_api/protocol_context.py

@@ -1377,12 +1377,17 @@ class ProtocolContext(CommandPublisher):
         name: str,
     ) -> LiquidClass:
         """
-        Get an instance of a built-in liquid class for use in the protocol.
+        Get an instance of an Opentrons-verified liquid class for use in a Flex protocol.
 
-        Args:
-            name: Name of an Opentrons-defined liquid class.
+        :param name: Name of an Opentrons-verified liquid class. Must be one of:
+
+            - ``"water"``: an Opentrons-verified liquid class based on deionized water.
+            - ``"glycerol_50"``: an Opentrons-verified liquid class for viscous liquid. Based on 50% glycerol.
+            - ``"ethanol_80"``: an Opentrons-verified liquid class for volatile liquid. Based on 80% ethanol.
 
         :raises: ``LiquidClassDefinitionDoesNotExist``: if the specified liquid class does not exist.
+
+        :returns: A new LiquidClass object.
         """
         return self._core.get_liquid_class(name=name, version=DEFAULT_LC_VERSION)
 
@@ -1394,29 +1399,16 @@ class ProtocolContext(CommandPublisher):
         base_liquid_class: Optional[LiquidClass] = None,
         display_name: Optional[str] = None,
     ) -> LiquidClass:
-        """Define a custom liquid class, either a completely new one or based on an existing one.
-
-        Args:
-            name: The name to give to the new liquid class. Cannot use names of existing in-built liquid classes.
-            properties: A dict of transfer properties per tip per pipette.
-                Accepts a nested dictionary in the following format:
-
-                .. code-block:: python
+        """Define a custom liquid class, either based on an existing liquid class, or create a completely new one.
 
-                    {
-                    <pipette_name>: {
-                        <tiprack_uri>: <properties in the shape of TransferPropertiesDict>
+        :param name: The name to give to the new liquid class. Cannot use the name of an Opentrons-verified liquid class.
+        :param properties: A dict of transfer properties for pipette and tip combinations to use for liquid class transfers. The nested dictionary must have top-level keys corresponding to pipette load names and second-level keys corresponding to compatible tip rack load names. Further nested key–value pairs should be as specified in ``TransferPropertiesDict``. See the  `liquid class type definitions <https://github.com/Opentrons/opentrons/blob/edge/shared-data/python/opentrons_shared_data/liquid_classes/types.py>`_.
 
-                        # TransferPropertiesDict is a dictionary representation of the
-                        # transfer properties returned by the `LiquidClass.get_for(..)` function.
-                    }}
+        :param base_liquid_class: An existing liquid class object to base the newly defined liquid class on. The specified ``transfer_properties`` will override any existing properties for the specified pipette and tip combinations. All other properties will remain the same as those in the base class.
 
-            base_liquid_class: A LiquidClass to base this liquid class on. The properties
-                specified in transfer_properties will override any existing ones
-                for the specified pipettes & tips.
-            display_name: An optional human-readable name for the liquid. If not provided,
-                will default to title-cased name.
+        :param display_name: An optional name for the liquid class. Defaults to the title-case ``name`` if a display name isn't provided.
 
+        :returns: A new LiquidClass object.
         """
         if definition_exists(name, DEFAULT_LC_VERSION):
             raise ValueError(

{opentrons-8.5.0a9 → opentrons-8.5.1}/src/opentrons/protocols/advanced_control/transfers/transfer_liquid_utils.py

@@ -212,3 +212,20 @@ def _group_wells_for_nozzle_configuration(  # noqa: C901
         grouped_wells.reverse()
 
     return grouped_wells
+
+
+def check_current_volume_before_dispensing(
+    current_volume: float,
+    dispense_volume: float,
+) -> None:
+    """Check if the current volume is valid for dispensing the dispense volume."""
+    if current_volume < dispense_volume:
+        # Although this should never happen, we can get into an unexpected state
+        # following error recovery and not have the expected amount of liquid in the tip.
+        # If this happens, we want to raise a useful error so the user can understand
+        # the cause of the problem. If we don't make this check for current volume,
+        # an unhelpful error might get raised when a '..byVolume' property encounters
+        # a negative volume (current_volume - dispense_volume).
+        raise RuntimeError(
+            f"Cannot dispense {dispense_volume}uL when the tip has only {current_volume}uL."
+        )

{opentrons-8.5.0a9 → opentrons-8.5.1}/src/opentrons.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.5.0a9
+Version: 8.5.1
 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==8.5.0a9
+Requires-Dist: opentrons-shared-data==8.5.1
 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: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.5.0a9; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.5.1; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.5.0a9; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.5.1; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.5.0a9 → opentrons-8.5.1}/src/opentrons.egg-info/requires.txt

@@ -1,4 +1,4 @@
-opentrons-shared-data==8.5.0a9
+opentrons-shared-data==8.5.1
 aionotify==0.3.1
 anyio<4.0.0,>=3.6.1
 jsonschema<4.18.0,>=3.0.1
@@ -15,7 +15,7 @@ packaging>=21.0
 importlib-metadata>=1.0
 
 [flex-hardware]
-opentrons-hardware[FLEX]==8.5.0a9
+opentrons-hardware[FLEX]==8.5.1
 
 [ot2-hardware]
-opentrons-hardware==8.5.0a9
+opentrons-hardware==8.5.1