feat(abr-testing): Flex stacker protocol edits

abr-testing/abr_testing/protocols/active_protocols/11_Dynabeads_IP_Flex_96well_RIT.py

@@ -57,43 +57,41 @@ def run(protocol: ProtocolContext) -> None:
     single_channel_mount = protocol.params.pipette_mount_1  # type: ignore[attr-defined]
     eight_channel_mount = protocol.params.pipette_mount_2  # type: ignore[attr-defined]
     deactivate_modules_bool = protocol.params.deactivate_modules  # type: ignore[attr-defined]
-    helpers.comment_protocol_version(protocol, "01")
+    helpers.comment_protocol_version(protocol, "02")
 
     MIX_SPEED = heater_shaker_speed
     MIX_SEC = 10
 
     # if on deck:
     INCUBATION_SPEED = heater_shaker_speed * 0.5
     INCUBATION_MIN = 60
-    # load labware
-
-    sample_plate_1 = protocol.load_labware(
-        "nest_96_wellplate_2ml_deep", "B2", "sample plate 1"
+    # load labware stacker
+    stacker_deep_wells = helpers.load_stacker_module(
+        protocol, "PS241204SZEVT22", "C4", "nest_96_wellplate_2ml_deep"
     )
-    sample_plate_2 = protocol.load_labware(
-        "nest_96_wellplate_2ml_deep", "C4", "sample plate 2"
-    )
-
+    # load labware
+    sample_plate_1 = stacker_deep_wells.unload_and_move_labware("B2")
     wash_res = protocol.load_labware("nest_12_reservoir_15ml", "B1", "wash")
     reagent_res = protocol.load_labware(
         "opentrons_15_tuberack_nest_15ml_conical", "C3", "reagents"
     )
     waste_res = protocol.load_labware("nest_1_reservoir_290ml", "D2", "Liquid Waste")
-
-    tips = protocol.load_labware("opentrons_flex_96_tiprack_1000ul", "B3")
-    tips_sample = protocol.load_labware(
-        "opentrons_flex_96_tiprack_1000ul", "A2", "sample tips"
+    # stacker 1: 1000 ul tips
+    tip_stacker_1000 = helpers.load_stacker_module(
+        protocol, "PS241204SZEVT25", "B4", "opentrons_flex_96_tiprack_1000ul"
     )
+    # Unload tip racks
+    tips = tip_stacker_1000.unload_and_move_labware("B3")
+    tips_sample = tip_stacker_1000.unload_and_move_labware("A2")
     tips_sample_loc = tips_sample.wells()[:95]
+    tips_reused = tip_stacker_1000.unload_and_move_labware("C2")
+    tips_reused_loc = tips_reused.wells()[:95]
+    tip_rack_list: List[Labware] = [tips, tips_sample, tips_reused]
     if READY_FOR_SDSPAGE == 0:
-        tips_elu = protocol.load_labware(
-            "opentrons_flex_96_tiprack_1000ul", "A1", "elution tips"
-        )
+        tips_elu = tip_stacker_1000.unload_and_move_labware("A1")
         tips_elu_loc = tips_elu.wells()[:95]
-    tips_reused = protocol.load_labware(
-        "opentrons_flex_96_tiprack_1000ul", "C2", "reused tips"
-    )
-    tips_reused_loc = tips_reused.wells()[:95]
+        tip_rack_list.append(tips_elu)
+
     p1000 = protocol.load_instrument(
         "flex_8channel_1000", eight_channel_mount, tip_racks=[tips]
     )
@@ -103,24 +101,21 @@ def run(protocol: ProtocolContext) -> None:
     h_s: HeaterShakerContext = protocol.load_module(
         helpers.hs_str, "D1"
     )  # type: ignore[assignment]
-    working_plate, h_s_adapter = helpers.load_hs_adapter_and_labware(
-        "nest_96_wellplate_2ml_deep", h_s, "Working Plate"
-    )
+    h_s_adapter = h_s.load_adapter("opentrons_96_deep_well_adapter")
+    h_s.open_labware_latch()
+    working_plate = stacker_deep_wells.unload_and_move_labware(h_s_adapter)
 
     if READY_FOR_SDSPAGE == 0:
         temp: TemperatureModuleContext = protocol.load_module(
             helpers.temp_str, "D3"
         )  # type: ignore[assignment]
-        final_plate, temp_adapter = helpers.load_temp_adapter_and_labware(
-            "nest_96_wellplate_2ml_deep", temp, "Final Plate"
-        )
+        temp_adapter = temp.load_adapter("opentrons_96_deep_well_adapter")
+        final_plate = stacker_deep_wells.unload_and_move_labware(temp_adapter)
     mag: MagneticBlockContext = protocol.load_module(
         helpers.mag_str, "C1"
     )  # type: ignore[assignment]
-
     # liquids
     samples1 = sample_plate_1.rows()[0][:NUM_COL]  # 1
-    samples2 = sample_plate_2.rows()[0][:NUM_COL]  # 1
     beads = reagent_res.wells()[0]  # 2
     ab = reagent_res.wells()[1]  # 3
     elu = reagent_res.wells()[2]  # 4
@@ -139,7 +134,6 @@ def run(protocol: ProtocolContext) -> None:
         "Elution": [{"well": elu, "volume": 9800.0}],
         "Wash": [{"well": wash, "volume": 1500.0}],
         "Samples 1": [{"well": samples1, "volume": 250.0}],
-        "Samples 2": [{"well": samples2, "volume": 250.0}],
     }
     helpers.find_liquid_height_of_loaded_liquids(
         protocol, liquid_vols_and_wells, p1000_single
@@ -289,11 +283,21 @@ def run(sample_plate: Labware) -> None:
 
     run(sample_plate_1)
     # swap plates
-    protocol.move_labware(sample_plate_1, "B4", True)
-    protocol.move_labware(sample_plate_2, "B2", True)
+    helpers.move_labware_to_destination(
+        protocol=protocol,
+        labware=sample_plate_1,
+        dest="B4",
+        use_gripper=True,
+        flex_stacker=True,
+    )
+    sample_plate_2 = stacker_deep_wells.unload_and_move_labware("B2")
+    stacker_deep_wells.move_and_store_labware(sample_plate_1)
+
     run(sample_plate_2)
 
     helpers.clean_up_plates(p1000_single, [wash_res], waste, 1000)
     helpers.find_liquid_height_of_all_wells(protocol, p1000_single, [waste_res["A1"]])
+    # reload tip racks and labware
+    helpers.move_to_stacker_and_store(tip_stacker_1000, tip_rack_list)
     if deactivate_modules_bool:
         helpers.deactivate_modules(protocol)

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

@@ -14,7 +14,7 @@
     MagneticBlockContext,
     ThermocyclerContext,
 )
-from typing import List, Tuple, Dict
+from typing import List, Dict, Tuple
 
 metadata = {
     "protocolName": "KAPA HyperPlus Library Preparation",
@@ -39,8 +39,8 @@ 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)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
     helpers.create_deactivate_modules_parameter(parameters)
     parameters.add_int(
         variable_name="num_samples",
@@ -78,7 +78,7 @@ def run(protocol: ProtocolContext) -> None:
     pipette_1000_mount = protocol.params.pipette_mount_1  # type: ignore[attr-defined]
     pipette_50_mount = protocol.params.pipette_mount_2  # type: ignore[attr-defined]
     deck_riser = protocol.params.deck_riser  # type: ignore[attr-defined]
-    helpers.comment_protocol_version(protocol, "01")
+    helpers.comment_protocol_version(protocol, "02")
 
     REUSE_ETOH_TIPS = True
     REUSE_RSB_TIPS = (
@@ -95,6 +95,10 @@ def run(protocol: ProtocolContext) -> None:
         trash_tips = False
 
     num_cols = math.ceil(num_samples / 8)
+    unused_lids: List[Labware] = []
+    # Load TC Lids
+    if disposable_lid:
+        unused_lids = helpers.load_disposable_lids(protocol, 5, ["D3"], deck_riser)
 
     # Pre-set parameters
     # sample_vol = 35.0
@@ -121,49 +125,52 @@ def run(protocol: ProtocolContext) -> None:
     temp_mod: TemperatureModuleContext = protocol.load_module(
         helpers.temp_str, "B3"
     )  # type: ignore[assignment]
-    temp_plate, temp_adapter = helpers.load_temp_adapter_and_labware(
-        "armadillo_96_wellplate_200ul_pcr_full_skirt",
-        temp_mod,
-        "Temp Module Reservoir Plate",
+    temp_adapter = temp_mod.load_adapter("opentrons_96_well_aluminum_block")
+    tip_stacker_200 = helpers.load_stacker_module(
+        protocol, "PS241204SZEVT24", "D4", "opentrons_flex_96_tiprack_200ul"
+    )
+    tip_stacker_50 = helpers.load_stacker_module(
+        protocol, "PS241204SZEVT26", "A4", "opentrons_flex_96_tiprack_50ul"
+    )
+    tip_stacker_plates = helpers.load_stacker_module(
+        protocol, "PS241204SZEVT18", "C4", "armadillo_96_wellplate_200ul_pcr_full_skirt"
     )
 
     if not dry_run:
         temp_mod.set_temperature(4)
     tc_mod: ThermocyclerContext = protocol.load_module(helpers.tc_str)  # type: ignore[assignment]
     # Just in case
     tc_mod.open_lid()
+    # Unload Armadillo plates
+    FLP_plate = tip_stacker_plates.unload_and_move_labware(magblock)
 
-    FLP_plate = magblock.load_labware(
-        "armadillo_96_wellplate_200ul_pcr_full_skirt", "FLP Plate"
-    )
     samples_flp = FLP_plate.rows()[0][:num_cols]
-
-    sample_plate = protocol.load_labware(
-        "armadillo_96_wellplate_200ul_pcr_full_skirt", "D1", "Sample Plate 1"
-    )
-
-    sample_plate_2 = protocol.load_labware(
-        "armadillo_96_wellplate_200ul_pcr_full_skirt", "B2", "Sample Plate 2"
-    )
+    sample_plate = tip_stacker_plates.unload_and_move_labware("D1")
+    sample_plate_2 = tip_stacker_plates.unload_and_move_labware("B2")
+    temp_plate = tip_stacker_plates.unload_and_move_labware(temp_adapter)
     samples_2 = sample_plate_2.rows()[0][:num_cols]
     samples = sample_plate.rows()[0][:num_cols]
     reservoir = protocol.load_labware(
         "nest_96_wellplate_2ml_deep", "C2", "Beads + Buffer + Ethanol"
     )
-    # Load tipracks
-    tiprack_50_1 = protocol.load_labware("opentrons_flex_96_tiprack_50ul", "A3")
-    tiprack_50_2 = protocol.load_labware("opentrons_flex_96_tiprack_50ul", "A2")
-
-    tiprack_200_1 = protocol.load_labware("opentrons_flex_96_tiprack_200ul", "C1")
-    tiprack_200_2 = protocol.load_labware("opentrons_flex_96_tiprack_200ul", "C3")
+    # Unload tipracks
+    tiprack_50_locations = ["A2", "A3"]
+    tiprack_200_locations = ["C1", "C3"]
+    tipracks_50 = []
+    tipracks_200 = []
+
+    # Unload 50 ul tips
+    for tip_rack_destination_50 in tiprack_50_locations:
+        tip_rack_50 = tip_stacker_50.unload_and_move_labware(tip_rack_destination_50)
+        tipracks_50.append(tip_rack_50)
+    # Unload 200 ul tips
+    for tip_rack_destination_200 in tiprack_200_locations:
+        tip_rack_200 = tip_stacker_200.unload_and_move_labware(tip_rack_destination_200)
+        tipracks_200.append(tip_rack_200)
 
     if trash_tips:
         protocol.load_waste_chute()
 
-    unused_lids: List[Labware] = []
-    # Load TC Lids
-    if disposable_lid:
-        unused_lids = helpers.load_disposable_lids(protocol, 5, ["C4"], deck_riser)
     # Import Global Variables
 
     global tip50
@@ -175,10 +182,10 @@ def run(protocol: ProtocolContext) -> None:
     p200 = protocol.load_instrument(
         "flex_8channel_1000",
         pipette_1000_mount,
-        tip_racks=[tiprack_200_1, tiprack_200_2],
+        tip_racks=tipracks_200,
     )
     p50 = protocol.load_instrument(
-        "flex_8channel_50", pipette_50_mount, tip_racks=[tiprack_50_1, tiprack_50_2]
+        "flex_8channel_50", pipette_50_mount, tip_racks=tipracks_50
     )
 
     # Load Reagent Locations in Reservoirs

abr-testing/abr_testing/protocols/active_protocols/4_Illumina DNA Enrichment.py

@@ -75,7 +75,7 @@ def run(protocol: ProtocolContext) -> None:
     deck_riser = protocol.params.deck_riser  # type: ignore[attr-defined]
     trash_lid = protocol.params.trash_lid  # type: ignore[attr-defined]
     deactivate_modules_bool = protocol.params.deactivate_modules  # type: ignore[attr-defined]
-    helpers.comment_protocol_version(protocol, "01")
+    helpers.comment_protocol_version(protocol, "02")
 
     unused_lids: List[Labware] = []
     used_lids: List[Labware] = []
@@ -333,7 +333,12 @@ def tipcheck() -> None:
                         unused_lids,
                         used_lids,
                     ) = helpers.use_disposable_lid_with_tc(
-                        protocol, unused_lids, used_lids, sample_plate_1, thermocycler
+                        protocol,
+                        unused_lids,
+                        used_lids,
+                        sample_plate_1,
+                        thermocycler,
+                        flex_stacker=True,
                     )
                 else:
                     thermocycler.close_lid()
@@ -417,6 +422,7 @@ def tipcheck() -> None:
                     used_lids,
                     sample_plate_1,
                     thermocycler,
+                    flex_stacker=True,
                 )
             else:
                 thermocycler.close_lid()
@@ -736,6 +742,7 @@ def tipcheck() -> None:
                             used_lids,
                             sample_plate_1,
                             thermocycler,
+                            flex_stacker=True,
                         )
                     else:
                         thermocycler.close_lid()

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

@@ -130,21 +130,42 @@ def move_to_locations(
 
             def reset_labware() -> None:
                 """Reset the labware to the reset location."""
-                protocol.move_labware(
-                    labware_to_move, reset_location, use_gripper=use_gripper
-                )
+                if reset_location in ["C4"] or helpers.get_parent(labware_to_move) in [
+                    "C4"
+                ]:
+                    helpers.move_labware_to_destination(
+                        protocol=protocol,
+                        labware=labware_to_move,
+                        dest=reset_location,
+                        use_gripper=True,
+                        flex_stacker=True,
+                    )
+                else:
+                    protocol.move_labware(
+                        labware_to_move, reset_location, use_gripper=use_gripper
+                    )
 
             if len(move_locations) == 0:
                 return
 
             for location in move_locations:
-                protocol.move_labware(
-                    labware_to_move, location, use_gripper=use_gripper
-                )
+                if location in ["C4"] or helpers.get_parent(labware_to_move) in [
+                    "C4",
+                ]:
+                    helpers.move_labware_to_destination(
+                        protocol=protocol,
+                        labware=labware_to_move,
+                        dest=location,
+                        use_gripper=True,
+                        flex_stacker=True,
+                    )
+                else:
+                    protocol.move_labware(
+                        labware_to_move, location, use_gripper=use_gripper
+                    )
 
                 if reset_after_each_move:
                     reset_labware()
-
             if not reset_after_each_move:
                 reset_labware()
 
@@ -214,7 +235,6 @@ def staging_area_slot_4_moves(labware: Labware, reset_location: str) -> None:
                     h_s_adapter,
                 ],  # Module Moves
             ]
-
             run_moves(
                 labware,
                 staging_area_slot_4_move_sequence,
@@ -255,20 +275,28 @@ def module_moves(labware: Labware, module_locations: List) -> None:
         )
         staging_area_slot_3_moves(dest_pcr_plate, STAGING_AREA_SLOT_3_RESET_LOCATION)
 
-        protocol.move_labware(
-            dest_pcr_plate,
-            STAGING_AREA_SLOT_4_RESET_LOCATION,
+        helpers.move_labware_to_destination(
+            protocol=protocol,
+            labware=dest_pcr_plate,
+            dest=STAGING_AREA_SLOT_4_RESET_LOCATION,
             use_gripper=USING_GRIPPER,
+            flex_stacker=True,
         )
         staging_area_slot_4_moves(dest_pcr_plate, STAGING_AREA_SLOT_4_RESET_LOCATION)
-
         module_locations = [thermocycler] + adapters
         module_moves(dest_pcr_plate, module_locations)
+
         protocol.move_labware(dest_pcr_plate, thermocycler, use_gripper=USING_GRIPPER)
 
     def test_manual_moves() -> None:
         """Test manual moves."""
-        protocol.move_labware(source_reservoir, "D4", use_gripper=USING_GRIPPER)
+        helpers.move_labware_to_destination(
+            protocol=protocol,
+            labware=source_reservoir,
+            dest="D4",
+            use_gripper=USING_GRIPPER,
+            flex_stacker=True,
+        )
 
     def test_pipetting() -> None:
         """Test pipetting."""
@@ -306,7 +334,13 @@ def test_column_tip_rack_usage() -> None:
             )
             protocol.comment("------------------------------")
             protocol.comment(f"channels {pipette_96_channel.active_channels}")
-            protocol.move_labware(tip_rack_3, "C3", use_gripper=USING_GRIPPER)
+            helpers.move_labware_to_destination(
+                protocol=protocol,
+                labware=tip_rack_3,
+                dest="C3",
+                use_gripper=USING_GRIPPER,
+                flex_stacker=True,
+            )
             for well in list_of_columns:
                 tiprack_well = "A" + str(well)
                 well_name = "A" + str(well)