Merge back 'chore_release-8.5.0' into 'chore_release-pd-8.5.0'

Resolved conflicts in `api/tests/opentrons/protocol_api_integration/test_transfer_with_liquid_classes.py`.

Author: ddcc4

.github/workflows/api-test-lint-deploy.yaml

@@ -67,7 +67,7 @@ jobs:
       - name: Lint with opentrons_hardware
         run: make -C api lint
   test:
-    name: 'opentrons package tests on ${{ matrix.os }}, python ${{ matrix.python }}'
+    name: 'opentrons package tests on ${{ matrix.os }}, python ${{ matrix.python }}, ot-hardware ${{ matrix.with-ot-hardware }}'
     timeout-minutes: 30
     needs: [lint]
     strategy:

api/release-notes.md

@@ -10,7 +10,20 @@ By installing and using Opentrons software, you agree to the Opentrons End-User
 
 ## Opentrons Robot Software Changes in 8.5.0
 
-### TODO
+Welcome to the v8.5.0 release of the Opentrons robot software! This release features the ability to pipette more accurately by using liquid classes in your protocols.
+
+### New Features
+
+- Use Opentrons-verified liquid classes (aqueous, viscous, and volatile) in the Python Protocol API to automatically adjust submerge speed, flow rate, touch tip, air gap, and more.
+- Customize and create your own liquid classes for even more control.
+
+### Improvements
+
+- Several Python API methods have new parameters that add capabilities available in Protocol Designer.
+
+### Bug Fixes
+
+- The Absorbance Plate Reader no longer reports measurements below 0.
 
 ---
 
@@ -51,13 +64,12 @@ The 8.3.2 hotfix release fixes a bug where protocol commands could time out, esp
 
 The 8.3.1 hotfix release contains two bug fixes:
 
-- Exported data from the Absorbance Plate Reader no longer contains invalid values. 
-- A small fix allows all robots to properly reboot after an upgrade to v8.3.0. 
+- Exported data from the Absorbance Plate Reader no longer contains invalid values.
+- A small fix allows all robots to properly reboot after an upgrade to v8.3.0.
 
 ## Opentrons Robot Software Changes in 8.3.0
 
-Welcome to the v8.3.0 release of the Opentrons robot software! This release includes improvements to error recovery on the Flex, as well as beta features for our commercial partners. 
-
+Welcome to the v8.3.0 release of the Opentrons robot software! This release includes improvements to error recovery on the Flex, as well as beta features for our commercial partners.
 
 ### Improved Features
 
@@ -172,7 +184,7 @@ Welcome to the v7.3.0 release of the Opentrons robot software!
 ### Bug Fixes
 
 - Fixed an edge case where capitalizing part of a labware load name could cause unexpected behavior or collisions.
-- Fixed Python packages installed  on the OT-2 with `pip` not being found by `import` statements.
+- Fixed Python packages installed on the OT-2 with `pip` not being found by `import` statements.
 
 ---
 
@@ -208,7 +220,7 @@ Welcome to the v7.2.1 release of the Opentrons robot software!
 
 Welcome to the v7.2.0 release of the Opentrons robot software!
 
-This update may take longer than usual if your robot has a lot of long protocols and runs stored on it. Allow *approximately 20 minutes* for your robot to restart. This delay will only happen once.
+This update may take longer than usual if your robot has a lot of long protocols and runs stored on it. Allow _approximately 20 minutes_ for your robot to restart. This delay will only happen once.
 
 If you don't care about preserving your labware offsets and run history, you can avoid the delay by clearing your runs and protocols before starting this update. Go to **Robot Settings** > **Device Reset** and select **Clear protocol run history**.
 
@@ -343,12 +355,12 @@ Some protocols can't be simulated with the `opentrons_simulate` command-line too
 Welcome to the v6.3.1 release of the OT-2 software! This hotfix release addresses a few problems.
 
 ### Improved Features
+
 - Changed the Thermocycler GEN2 plate ejection behavior to prevent plates from getting stuck after PCR cycles or being ejected too forcefully.
 
 ### Bug Fixes
 
-- Specifying Python API version 2.14 no longer prevents ``set_block_temperature`` from executing a hold time.
-
+- Specifying Python API version 2.14 no longer prevents `set_block_temperature` from executing a hold time.
 
 ---
 
@@ -374,6 +386,7 @@ Some protocols can't be simulated with the `opentrons_simulate` command-line too
 - Python protocols specifying an `apiLevel` of 2.14
 
 ---
+
 ## OT-2 Software Changes in 6.2.1
 
 Welcome to the v6.2.1 release of the OT-2 software! This hotfix release addresses a few problems.

api/src/opentrons/protocol_api/_transfer_liquid_validation.py

@@ -47,10 +47,10 @@ def verify_and_normalize_transfer_args(
         flat_dests_list = []
     if group_wells_for_multi_channel and nozzle_map.tip_count > 1:
         flat_sources_list = tx_liquid_utils.group_wells_for_multi_channel_transfer(
-            flat_sources_list, nozzle_map
+            flat_sources_list, nozzle_map, "source"
         )
         flat_dests_list = tx_liquid_utils.group_wells_for_multi_channel_transfer(
-            flat_dests_list, nozzle_map
+            flat_dests_list, nozzle_map, "destination"
         )
     for well in flat_sources_list + flat_dests_list:
         instrument.validate_takes_liquid(

api/src/opentrons/protocol_api/core/engine/instrument.py

@@ -1,7 +1,6 @@
 """ProtocolEngine-based InstrumentContext core implementation."""
 
 from __future__ import annotations
-from contextlib import contextmanager
 from itertools import dropwhile
 from copy import deepcopy
 from typing import (
@@ -13,7 +12,6 @@
     Sequence,
     Tuple,
     NamedTuple,
-    Generator,
     Literal,
 )
 from opentrons.types import (
@@ -1384,43 +1382,25 @@ def _pick_up_tip() -> Tuple[Location, WellCore]:
                         air_gap=0,
                     )
                 ]
-                # Enable LPD only if all of these apply:
-                # - LPD is globally enabled for this pipette
-                # - it is the first time visiting this well
-                # - pipette tip is unused
-                enable_lpd = (
-                    self.get_liquid_presence_detection() and step_source != prev_src
-                )
-            elif new_tip == TransferTipPolicyV2.ONCE:
-                # Enable LPD only if:
-                # - LPD is globally enabled for this pipette
-                # - this is the first source well of the entire transfer, which means
-                #   that the current tip is unused
-                enable_lpd = self.get_liquid_presence_detection() and prev_src is None
-            else:
-                enable_lpd = False
 
-            with self.lpd_for_transfer(enable_lpd):
-                post_asp_tip_contents = self.aspirate_liquid_class(
-                    volume=step_volume,
-                    source=step_source,
-                    transfer_properties=transfer_props,
-                    transfer_type=tx_comps_executor.TransferType.ONE_TO_ONE,
-                    tip_contents=post_disp_tip_contents,
-                    volume_for_pipette_mode_configuration=step_volume,
-                )
-                post_disp_tip_contents = self.dispense_liquid_class(
-                    volume=step_volume,
-                    dest=step_destination,
-                    source=step_source,
-                    transfer_properties=transfer_props,
-                    transfer_type=tx_comps_executor.TransferType.ONE_TO_ONE,
-                    tip_contents=post_asp_tip_contents,
-                    add_final_air_gap=(
-                        False if is_last_step and keep_last_tip else True
-                    ),
-                    trash_location=trash_location,
-                )
+            post_asp_tip_contents = self.aspirate_liquid_class(
+                volume=step_volume,
+                source=step_source,
+                transfer_properties=transfer_props,
+                transfer_type=tx_comps_executor.TransferType.ONE_TO_ONE,
+                tip_contents=post_disp_tip_contents,
+                volume_for_pipette_mode_configuration=step_volume,
+            )
+            post_disp_tip_contents = self.dispense_liquid_class(
+                volume=step_volume,
+                dest=step_destination,
+                source=step_source,
+                transfer_properties=transfer_props,
+                transfer_type=tx_comps_executor.TransferType.ONE_TO_ONE,
+                tip_contents=post_asp_tip_contents,
+                add_final_air_gap=(False if is_last_step and keep_last_tip else True),
+                trash_location=trash_location,
+            )
             prev_src = step_source
             prev_dest = step_destination
 
@@ -1695,17 +1675,6 @@ def _pick_up_tip() -> Tuple[Location, WellCore]:
                     " Specify a blowout location and enable blowout when using a disposal volume."
                 )
 
-            if (
-                self.get_liquid_presence_detection()
-                and new_tip != TransferTipPolicyV2.NEVER
-                and is_first_step
-            ):
-                # Do probing only once, regardless of whether you are coming back to refill
-                # with a fresh tip since there's only one source well
-                enable_lpd = True
-            else:
-                enable_lpd = False
-
             if not is_first_step and new_tip == TransferTipPolicyV2.ALWAYS:
                 _drop_tip()
                 last_tip = _pick_up_tip()
@@ -1715,20 +1684,19 @@ def _pick_up_tip() -> Tuple[Location, WellCore]:
                         air_gap=0,
                     )
                 ]
-            with self.lpd_for_transfer(enable=enable_lpd):
-                # Aspirate the total volume determined by the loop above
-                tip_contents = self.aspirate_liquid_class(
-                    volume=total_aspirate_volume + conditioning_vol + disposal_vol,
-                    source=source,
-                    transfer_properties=transfer_props,
-                    transfer_type=tx_comps_executor.TransferType.ONE_TO_MANY,
-                    tip_contents=tip_contents,
-                    # We configure the mode based on the last dispense volume and disposal volume
-                    # since the mode is only used to determine the dispense push out volume
-                    # and we can do a push out only at the last dispense, that too if there is no disposal volume.
-                    volume_for_pipette_mode_configuration=vol_dest_combo[-1][0],
-                    conditioning_volume=conditioning_vol,
-                )
+            # Aspirate the total volume determined by the loop above
+            tip_contents = self.aspirate_liquid_class(
+                volume=total_aspirate_volume + conditioning_vol + disposal_vol,
+                source=source,
+                transfer_properties=transfer_props,
+                transfer_type=tx_comps_executor.TransferType.ONE_TO_MANY,
+                tip_contents=tip_contents,
+                # We configure the mode based on the last dispense volume and disposal volume
+                # since the mode is only used to determine the dispense push out volume
+                # and we can do a push out only at the last dispense, that too if there is no disposal volume.
+                volume_for_pipette_mode_configuration=vol_dest_combo[-1][0],
+                conditioning_volume=conditioning_vol,
+            )
 
             # If the tip has volumes correspoinding to multiple destinations, then
             # multi-dispense in those destinations.
@@ -1963,7 +1931,6 @@ def _pick_up_tip() -> Tuple[Location, WellCore]:
         next_step_volume, next_source = next(source_per_volume_step)
         is_first_step = True
         is_last_step = False
-        prev_src: Optional[tuple[Location, WellCore]] = None
         while not is_last_step:
             total_dispense_volume = 0.0
             vol_aspirate_combo = []
@@ -1981,13 +1948,7 @@ def _pick_up_tip() -> Tuple[Location, WellCore]:
                     is_last_step = True
                     break
 
-            if (
-                self.get_liquid_presence_detection()
-                and new_tip != TransferTipPolicyV2.NEVER
-                and is_first_step
-            ):
-                enable_lpd = True
-            elif not is_first_step and new_tip == TransferTipPolicyV2.ALWAYS:
+            if not is_first_step and new_tip == TransferTipPolicyV2.ALWAYS:
                 _drop_tip()
                 last_tip = _pick_up_tip()
                 tip_contents = [
@@ -1996,33 +1957,22 @@ def _pick_up_tip() -> Tuple[Location, WellCore]:
                         air_gap=0,
                     )
                 ]
-                # Enable LPD if it's globally enabled, as long as
-                # the next source is different from previous source
-                enable_lpd = (
-                    self.get_liquid_presence_detection()
-                    and prev_src != vol_aspirate_combo[0][1]
-                )
-            else:
-                enable_lpd = False
 
             total_aspirated_volume = 0.0
             for step_num, (step_volume, step_source) in enumerate(vol_aspirate_combo):
-                with self.lpd_for_transfer(enable=enable_lpd):
-                    tip_contents = self.aspirate_liquid_class(
-                        volume=step_volume,
-                        source=step_source,
-                        transfer_properties=transfer_props,
-                        transfer_type=tx_comps_executor.TransferType.MANY_TO_ONE,
-                        tip_contents=tip_contents,
-                        volume_for_pipette_mode_configuration=(
-                            total_dispense_volume if step_num == 0 else None
-                        ),
-                        current_volume=total_aspirated_volume,
-                    )
-                prev_src = step_source
+                tip_contents = self.aspirate_liquid_class(
+                    volume=step_volume,
+                    source=step_source,
+                    transfer_properties=transfer_props,
+                    transfer_type=tx_comps_executor.TransferType.MANY_TO_ONE,
+                    tip_contents=tip_contents,
+                    volume_for_pipette_mode_configuration=(
+                        total_dispense_volume if step_num == 0 else None
+                    ),
+                    current_volume=total_aspirated_volume,
+                )
                 total_aspirated_volume += step_volume
                 is_first_step = False
-                enable_lpd = False
             tip_contents = self.dispense_liquid_class(
                 volume=total_dispense_volume,
                 dest=dest,
@@ -2119,10 +2069,6 @@ def aspirate_liquid_class(
                 location=prep_location,
             )
             last_liquid_and_airgap_in_tip.air_gap = 0
-            if self.get_liquid_presence_detection():
-                self.liquid_probe_with_recovery(
-                    well_core=source_well, loc=prep_location
-                )
             # TODO: do volume configuration + prepare for aspirate only if the mode needs to be changed
             self.configure_for_volume(volume_for_pipette_mode_configuration)
             self.prepare_to_aspirate()
@@ -2541,14 +2487,6 @@ def delay(self, seconds: float) -> None:
         """Call a protocol delay."""
         self._protocol_core.delay(seconds=seconds, msg=None)
 
-    @contextmanager
-    def lpd_for_transfer(self, enable: bool) -> Generator[None, None, None]:
-        """Context manager for the instrument's LPD state during a transfer."""
-        global_lpd_enabled = self.get_liquid_presence_detection()
-        self.set_liquid_presence_detection(enable=enable)
-        yield
-        self.set_liquid_presence_detection(enable=global_lpd_enabled)
-
 
 class _TipInfo(NamedTuple):
     tiprack_location: Location

api/src/opentrons/protocols/advanced_control/transfers/transfer_liquid_utils.py

@@ -72,6 +72,7 @@ def raise_if_location_inside_liquid(
 def group_wells_for_multi_channel_transfer(
     targets: Sequence[Well],
     nozzle_map: NozzleMapInterface,
+    target_name: Literal["source", "destination"],
 ) -> List[Well]:
     """Takes a list of wells and a nozzle map and returns a list of target wells to address every well given
 
@@ -94,13 +95,20 @@ def group_wells_for_multi_channel_transfer(
         or (configuration == NozzleConfigurationType.ROW and active_nozzles == 12)
         or active_nozzles == 96
     ):
-        return _group_wells_for_nozzle_configuration(list(targets), nozzle_map)
+        return _group_wells_for_nozzle_configuration(
+            list(targets), nozzle_map, target_name
+        )
     else:
-        raise ValueError("Unsupported tip configuration for well grouping")
+        raise ValueError(
+            "Unsupported nozzle configuration for well grouping. Set group_wells to False"
+            " to only target wells with the primary nozzle for this configuration."
+        )
 
 
 def _group_wells_for_nozzle_configuration(  # noqa: C901
-    targets: List[Well], nozzle_map: NozzleMapInterface
+    targets: List[Well],
+    nozzle_map: NozzleMapInterface,
+    target_name: Literal["source", "destination"],
 ) -> List[Well]:
     """Groups wells together for a column, row, or full 96 configuration and returns a reduced list of target wells."""
     grouped_wells = []
@@ -132,8 +140,9 @@ def _group_wells_for_nozzle_configuration(  # noqa: C901
         if active_wells_covered:
             if well.parent != active_labware:
                 raise ValueError(
-                    "Could not resolve wells provided to pipette's nozzle configuration. "
-                    "Please ensure wells are ordered to match pipette's nozzle layout."
+                    f"Could not group {target_name} wells to match pipette's nozzle configuration. Ensure that the"
+                    " wells are ordered correctly (e.g. rows() for a row layout or columns() for a column layout), or"
+                    " set group_wells to False to only target wells with the primary nozzle."
                 )
 
             if well.well_name in active_wells_covered:
@@ -165,8 +174,9 @@ def _group_wells_for_nozzle_configuration(  # noqa: C901
                 alternate_384_well_coverage_count += 1
             else:
                 raise ValueError(
-                    "Could not resolve wells provided to pipette's nozzle configuration. "
-                    "Please ensure wells are ordered to match pipette's nozzle layout."
+                    f"Could not group {target_name} wells to match pipette's nozzle configuration. Ensure that the"
+                    " wells are ordered correctly (e.g. rows() for a row layout or columns() for a column layout), or"
+                    " set group_wells to False to only target wells with the primary nozzle."
                 )
         # If we have no active wells covered to account for, add a new target well and list of covered wells to check
         else:
@@ -193,8 +203,8 @@ def _group_wells_for_nozzle_configuration(  # noqa: C901
 
     if active_wells_covered:
         raise ValueError(
-            "Could not target all wells provided without aspirating or dispensing from other wells. "
-            f"Other wells that would be targeted: {active_wells_covered}"
+            f"Pipette will access {target_name} wells not provided in the liquid handling command."
+            f" Set group_wells to False or include these wells: {active_wells_covered}"
         )
 
     # If we reversed the lookup of wells, reverse the grouped wells we will return