feat(abr-testing): add deck riser parameter to protocols

abr-testing/abr_testing/protocols/active_protocols/12_KAPA HyperPlus Library Prep.py

@@ -50,6 +50,7 @@ def add_parameters(parameters: ParameterContext) -> None:
         default=False,
     )
     helpers.create_disposable_lid_parameter(parameters)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
     helpers.create_two_pipette_mount_parameters(parameters)
     parameters.add_int(
         variable_name="num_samples",
@@ -85,6 +86,7 @@ def run(ctx: ProtocolContext) -> None:
     dry_run = ctx.params.dry_run  # type: ignore[attr-defined]
     pipette_1000_mount = ctx.params.pipette_mount_1  # type: ignore[attr-defined]
     pipette_50_mount = ctx.params.pipette_mount_2  # type: ignore[attr-defined]
+    deck_riser = ctx.params.deck_riser  # type: ignore[attr-defined]
     REUSE_ETOH_TIPS = True
     REUSE_RSB_TIPS = (
         True  # Reuse tips for RSB buffer (adding RSB, mixing, and transferring)
@@ -158,7 +160,7 @@ def run(ctx: ProtocolContext) -> None:
     unused_lids: List[Labware] = []
     # Load TC Lids
     if disposable_lid:
-        unused_lids = helpers.load_disposable_lids(ctx, 5, ["C3"])
+        unused_lids = helpers.load_disposable_lids(ctx, 5, ["C3"], deck_riser)
     # Import Global Variables
 
     global tip50

abr-testing/abr_testing/protocols/active_protocols/2_BMS_PCR_Protocol.py

@@ -22,13 +22,16 @@ def add_parameters(parameters: ParameterContext) -> None:
     helpers.create_single_pipette_mount_parameter(parameters)
     helpers.create_disposable_lid_parameter(parameters)
     helpers.create_csv_parameter(parameters)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
 
 
 def run(ctx: ProtocolContext) -> None:
     """Protocol."""
     pipette_mount = ctx.params.pipette_mount  # type: ignore[attr-defined]
     disposable_lid = ctx.params.disposable_lid  # type: ignore[attr-defined]
     parsed_csv = ctx.params.parameters_csv.parse_as_csv()  # type: ignore[attr-defined]
+    deck_riser = ctx.params.deck_riser  # type: ignore[attr-defined]
+
     rxn_vol = 50
     real_mode = True
     # DECK SETUP AND LABWARE
@@ -60,7 +63,7 @@ def run(ctx: ProtocolContext) -> None:
 
     # Opentrons tough pcr auto sealing lids
     if disposable_lid:
-        unused_lids = helpers.load_disposable_lids(ctx, 3, ["C3"])
+        unused_lids = helpers.load_disposable_lids(ctx, 3, ["C3"], deck_riser)
     used_lids: List[Labware] = []
 
     # LOAD PIPETTES
@@ -205,4 +208,6 @@ def run(ctx: ProtocolContext) -> None:
                 ctx.move_labware(lid_on_plate, "C2", use_gripper=True)
             else:
                 ctx.move_labware(lid_on_plate, used_lids[-2], use_gripper=True)
+        p50.drop_tip()
+        p50.configure_nozzle_layout(style=SINGLE, start="A1", tip_racks=tiprack_50)
         helpers.find_liquid_height_of_all_wells(ctx, p50, wells_to_probe_flattened)

abr-testing/abr_testing/protocols/active_protocols/3_OT3 ABR Normalize with Tubes.py

@@ -340,5 +340,4 @@ def run(ctx: ProtocolContext) -> None:
         )
 
         current += 1
-    print(wells_with_liquids)
     helpers.find_liquid_height_of_all_wells(ctx, p50, wells_with_liquids)

abr-testing/abr_testing/protocols/active_protocols/5_96ch complex protocol with single tip Pick Up.py

@@ -44,13 +44,15 @@ def add_parameters(parameters: ParameterContext) -> None:
     helpers.create_tip_size_parameter(parameters)
     helpers.create_dot_bottom_parameter(parameters)
     helpers.create_disposable_lid_parameter(parameters)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
 
 
 def run(ctx: ProtocolContext) -> None:
     """Protocol."""
     b = ctx.params.dot_bottom  # type: ignore[attr-defined]
     TIPRACK_96_NAME = ctx.params.tip_size  # type: ignore[attr-defined]
     disposable_lid = ctx.params.disposable_lid  # type: ignore[attr-defined]
+    deck_riser = ctx.params.deck_riser  # type: ignore[attr-defined]
 
     waste_chute = ctx.load_waste_chute()
 
@@ -61,7 +63,7 @@ def run(ctx: ProtocolContext) -> None:
         helpers.temp_str, "C1"
     )  # type: ignore[assignment]
     if disposable_lid:
-        unused_lids = helpers.load_disposable_lids(ctx, 3, ["A4"])
+        unused_lids = helpers.load_disposable_lids(ctx, 3, ["A4"], deck_riser)
     used_lids: List[Labware] = []
     thermocycler.open_lid()
     h_s.open_labware_latch()

abr-testing/abr_testing/protocols/helpers.py

@@ -39,12 +39,24 @@ def load_common_liquid_setup_labware_and_instruments(
 
 
 def load_disposable_lids(
-    protocol: ProtocolContext, num_of_lids: int, deck_slot: List[str]
+    protocol: ProtocolContext,
+    num_of_lids: int,
+    deck_slot: List[str],
+    deck_riser: bool = False,
 ) -> List[Labware]:
     """Load Stack of Disposable lids."""
-    unused_lids = [
-        protocol.load_labware("opentrons_tough_pcr_auto_sealing_lid", deck_slot[0])
-    ]
+    if deck_riser:
+        deck_riser_adapter = protocol.load_adapter(
+            "opentrons_flex_deck_riser", deck_slot[0]
+        )
+        unused_lids = [
+            deck_riser_adapter.load_labware("opentrons_tough_pcr_auto_sealing_lid")
+        ]
+    else:
+        unused_lids = [
+            protocol.load_labware("opentrons_tough_pcr_auto_sealing_lid", deck_slot[0])
+        ]
+
     if len(deck_slot) == 1:
         for i in range(num_of_lids - 1):
             unused_lids.append(
@@ -152,6 +164,16 @@ def create_disposable_lid_parameter(parameters: ParameterContext) -> None:
     )
 
 
+def create_tc_lid_deck_riser_parameter(parameters: ParameterContext) -> None:
+    """Create parameter for tc lid deck riser."""
+    parameters.add_bool(
+        variable_name="deck_riser",
+        display_name="Deck Riser",
+        description="True means use deck riser.",
+        default=False,
+    )
+
+
 def create_tip_size_parameter(parameters: ParameterContext) -> None:
     """Create parameter for tip size."""
     parameters.add_str(
@@ -334,10 +356,10 @@ def find_liquid_height_of_all_wells(
     """Find the liquid height of all wells in protocol."""
     dict_of_labware_heights = {}
     pipette.pick_up_tip()
+    pip_channels = pipette.active_channels
     for well in wells:
         labware_name = well.parent.load_name
         total_number_of_wells_in_plate = len(well.parent.wells())
-        pip_channels = pipette.active_channels
         # if pip_channels is > 1 and total_wells > 12 - only probe 1st row.
         if (
             pip_channels > 1
@@ -349,11 +371,11 @@ def find_liquid_height_of_all_wells(
         elif total_number_of_wells_in_plate <= 12:
             liquid_height_of_well = find_liquid_height(pipette, well)
             dict_of_labware_heights[labware_name, well] = liquid_height_of_well
-    if pip_channels == pipette.channels:
+    if pip_channels != pipette.channels:
+        pipette.drop_tip()
+    else:
         pipette.return_tip()
         pipette.reset_tipracks()
-    else:
-        pipette.drop_tip()
     msg = f"result: {dict_of_labware_heights}"
     protocol.comment(msg=msg)
     return dict_of_labware_heights