opentrons 8.5.0a8__tar.gz → 8.5.0a10__tar.gz

{opentrons-8.5.0a8 → opentrons-8.5.0a10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.5.0a8
+Version: 8.5.0a10
 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==8.5.0a8
+Requires-Dist: opentrons-shared-data==8.5.0a10
 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==8.5.0a8; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.5.0a10; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.5.0a8; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.5.0a10; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.5.0a8 → opentrons-8.5.0a10}/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,
@@ -1698,15 +1701,15 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
                 conditioning_volume=conditioning_vol,
             )
 
-            # If the tip has volumes correspoinding to multiple destinations, then
+            # If the tip has volumes corresponding to multiple destinations, then
             # 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 next_vol, next_dest in vol_dest_combo:
+            for dispense_vol, dispense_dest in vol_dest_combo:
                 if use_single_dispense:
                     tip_contents = self.dispense_liquid_class(
-                        volume=next_vol,
-                        dest=next_dest,
+                        volume=dispense_vol,
+                        dest=dispense_dest,
                         source=source,
                         transfer_properties=transfer_props,
                         transfer_type=tx_comps_executor.TransferType.ONE_TO_MANY,
@@ -1718,8 +1721,8 @@ class InstrumentCore(AbstractInstrument[WellCore, LabwareCore]):
                     )
                 else:
                     tip_contents = self.dispense_liquid_class_during_multi_dispense(
-                        volume=next_vol,
-                        dest=next_dest,
+                        volume=dispense_vol,
+                        dest=dispense_dest,
                         source=source,
                         transfer_properties=transfer_props,
                         transfer_type=tx_comps_executor.TransferType.ONE_TO_MANY,
@@ -2143,9 +2146,12 @@ 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(
-            last_air_gap
+            current_vol - last_air_gap
         )
         # The minimum flow rate should be air_gap_volume per second
         flow_rate = max(

{opentrons-8.5.0a8 → opentrons-8.5.0a10}/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,
@@ -229,7 +230,9 @@ class TransferComponentsExecutor:
             and self._target_well is not None
         )
         aspirate_props = self._transfer_properties.aspirate
-        correction_volume = aspirate_props.correction_by_volume.get_for_volume(volume)
+        correction_volume = aspirate_props.correction_by_volume.get_for_volume(
+            self._instrument.get_current_volume() + volume
+        )
         self._instrument.aspirate(
             location=self._target_location,
             well_core=None,
@@ -251,8 +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(
-            volume
+            current_vol - volume
         )
         self._instrument.dispense(
             location=self._target_location,
@@ -895,7 +902,7 @@ class TransferComponentsExecutor:
             return
         aspirate_props = self._transfer_properties.aspirate
         correction_volume = aspirate_props.correction_by_volume.get_for_volume(
-            air_gap_volume
+            self._instrument.get_current_volume() + air_gap_volume
         )
         # The minimum flow rate should be air_gap_volume per second
         flow_rate = max(

{opentrons-8.5.0a8 → opentrons-8.5.0a10}/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
@@ -1829,6 +1828,7 @@ 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 +1838,6 @@ 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(
@@ -1962,13 +1961,14 @@ 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 +1978,6 @@ 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(
@@ -2111,13 +2110,14 @@ 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 +2127,6 @@ 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-8.5.0a8 → opentrons-8.5.0a10}/src/opentrons/protocol_api/protocol_context.py

@@ -1377,10 +1377,13 @@ 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.
         """
@@ -1394,28 +1397,14 @@ 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, Opentrons-verified liquid class, or to 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 the Flex pipette and tips 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 in the format returned by :py:meth:`.LiquidClass.get_for`. See also the `liquid class JSON schema <https://github.com/Opentrons/opentrons/tree/edge/shared-data/liquid-class/schemas>`_.
 
-                        # TransferPropertiesDict is a dictionary representation of the
-                        # transfer properties returned by the `LiquidClass.get_for(..)` function.
-                    }}
+        :param base_liquid_class: An Opentrons-verified liquid class to base the newly defined liquid class on. The specified ``transfer_properties`` will override any existing properties for the Flex pipette and tips. 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.
 
         """
         if definition_exists(name, DEFAULT_LC_VERSION):

{opentrons-8.5.0a8 → opentrons-8.5.0a10}/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-8.5.0a8 → opentrons-8.5.0a10}/src/opentrons.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.5.0a8
+Version: 8.5.0a10
 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==8.5.0a8
+Requires-Dist: opentrons-shared-data==8.5.0a10
 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==8.5.0a8; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.5.0a10; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.5.0a8; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.5.0a10; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.5.0a8 → opentrons-8.5.0a10}/src/opentrons.egg-info/requires.txt

@@ -1,4 +1,4 @@
-opentrons-shared-data==8.5.0a8
+opentrons-shared-data==8.5.0a10
 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]==8.5.0a8
+opentrons-hardware[FLEX]==8.5.0a10
 
 [ot2-hardware]
-opentrons-hardware==8.5.0a8
+opentrons-hardware==8.5.0a10