Merge branch 'edge' into stacker-labware-offsets

Author: rclarke0

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

@@ -120,6 +120,8 @@ jobs:
         run: make -C api test-cov
       - name: Ensure assets build
         run: make -C api sdist wheel
+      - name: Check stacking regression tests
+        run: make -C api test-integration
       - name: Upload coverage report
         uses: 'codecov/codecov-action@v3'
         with:

abr-testing/abr_testing/protocols/custom_labware/millimore_magnet/1.json

@@ -0,0 +1,55 @@
+{
+  "ordering": [],
+  "brand": {
+    "brand": "Millipore",
+    "brandId": []
+  },
+  "metadata": {
+    "displayName": "Millipore 24 Ball Magnet",
+    "displayCategory": "adapter",
+    "displayVolumeUnits": "µL",
+    "tags": []
+  },
+  "dimensions": {
+    "xDimension": 127.8,
+    "yDimension": 85.6,
+    "zDimension": 11.15
+  },
+  "wells": {},
+  "groups": [
+    {
+      "metadata": {},
+      "wells": []
+    }
+  ],
+  "parameters": {
+    "format": "96Standard",
+    "quirks": [],
+    "isTiprack": false,
+    "isMagneticModuleCompatible": false,
+    "loadName": "millipore_24_ball_magnet"
+  },
+  "namespace": "custom_beta",
+  "version": 2,
+  "schemaVersion": 2,
+  "allowedRoles": ["adapter"],
+  "cornerOffsetFromSlot": {
+    "x": 0,
+    "y": 0,
+    "z": 0
+  },
+  "gripperOffsets": {
+    "default": {
+      "pickUpOffset": {
+        "x": 0,
+        "y": 0,
+        "z": 0
+      },
+      "dropOffset": {
+        "x": 0,
+        "y": 0,
+        "z": 0.5
+      }
+    }
+  }
+}

abr-testing/abr_testing/protocols/millipore_protocols/DuolinkPLA_Day1_Multiwell_RoundWell.py

@@ -0,0 +1,304 @@
+"""Duolink Day 1 Multiwell Round Well Protocol."""
+from opentrons.types import Point
+from opentrons.protocol_api import ProtocolContext, ParameterContext, Well
+from typing import List
+from opentrons.protocol_api.module_contexts import HeaterShakerContext
+
+
+metadata = {
+    "protocolName": """Duolink PLA for Microscopy (Multiwell Plate Assay with
+    96 Round Well Culture Plate) - Day 1""",
+    "author": "Opentrons Science Team",
+}
+
+requirements = {
+    "robotType": "Flex",
+    "apiLevel": "2.23",
+}
+
+VOL_BLOCK = 40
+VOL_AB = 40
+
+MIN_BLOCK = 60
+
+H_DISCARD = 0.7
+D_1K = -2.3
+D_200 = -2.1
+
+DEFAULT_RATE = 700
+SLOW = 100  # speed up
+
+
+def add_parameters(parameters: ParameterContext) -> None:
+    """Add parameters to the protocol context."""
+    parameters.add_int(
+        variable_name="num_sample",
+        display_name="Number of Samples",
+        description="Number of samples to be processed (up to 96)",
+        default=96,
+        minimum=1,
+        maximum=96,
+    )
+    parameters.add_bool(
+        variable_name="dry_run",
+        display_name="Dry Run",
+        description="All incubation steps skipped and tips returned to tipracks",
+        default=False,
+    )
+    parameters.add_bool(
+        variable_name="heat_on_deck",
+        display_name="Incubation on Deck",
+        description="Use Heater-Shaker Module for 37 degree C incubation?",
+        default=True,
+    )
+    parameters.add_bool(
+        variable_name="use_lid",
+        display_name="Use Plate Lid",
+        description="Use a lid to cover assay plate during incubation?",
+        default=True,
+    )
+
+
+def run(ctx: ProtocolContext) -> None:
+    """Run the protocol."""
+    num_sample = ctx.params.num_sample  # type: ignore[attr-defined]
+    dry_run = ctx.params.dry_run  # type: ignore[attr-defined]
+    heat_on_deck = ctx.params.heat_on_deck  # type: ignore[attr-defined]
+    use_lid = ctx.params.use_lid  # type: ignore[attr-defined]
+
+    num_col_full = int(num_sample // 8)
+    num_well_last_col = num_sample % 8
+    if num_well_last_col > 0:
+        num_col_total = num_col_full + 1
+    else:
+        num_col_total = num_col_full
+
+    # deck layout
+    if heat_on_deck:
+        hs: HeaterShakerContext = ctx.load_module(
+            "heaterShakerModuleV1", "D1"
+        )  # type: ignore[assignment]
+        hs_adapter = hs.load_adapter("opentrons_universal_flat_adapter")
+
+    working_plate = ctx.load_labware(
+        "corning_96_wellplate_360ul_flat", "C2", "ASSAY PLATE"
+    )
+
+    reagent_plate = ctx.load_labware("nest_96_wellplate_2ml_deep", "C1", "REAGENTS")
+    waste_res = ctx.load_labware("nest_1_reservoir_290ml", "D2", "LIQUID WASTE")
+    waste = waste_res.wells()[0]
+
+    ctx.load_trash_bin("A3")
+
+    tips_1k = ctx.load_labware("opentrons_flex_96_tiprack_1000ul", "B3", "1000uL TIPS")
+    tips_200 = ctx.load_labware("opentrons_flex_96_tiprack_200ul", "B2", "200uL TIPS")
+
+    p1k_8 = ctx.load_instrument("flex_8channel_1000", "left")
+    p1k_1 = ctx.load_instrument("flex_1channel_1000", "right")
+
+    p1k_8.flow_rate.aspirate = DEFAULT_RATE
+    p1k_8.flow_rate.dispense = DEFAULT_RATE
+    p1k_1.flow_rate.aspirate = DEFAULT_RATE
+    p1k_1.flow_rate.dispense = DEFAULT_RATE
+
+    # liquid location
+    rxn_total = working_plate.rows()[0][:num_col_total]
+    rxn_full = working_plate.rows()[0][:num_col_full]
+    if num_well_last_col > 0:
+        rxn_remainder = working_plate.wells()[
+            num_col_full * 8 : num_col_full * 8 + num_well_last_col
+        ]
+
+    ab = reagent_plate.rows()[0][0]
+    ab_remainder = reagent_plate.wells()[:num_well_last_col]
+    block = reagent_plate.rows()[0][1]
+    block_remainder = reagent_plate.wells()[8 : 8 + num_well_last_col]
+
+    # volume info
+    vol_ab = 40 * num_col_full + 40
+    vol_ab_plus_one = 40 * (num_col_full + 1) + 40
+    def_ab = ctx.define_liquid(
+        name="ANTIBODY SOLUTION", description="", display_color="#98FB98"
+    )  # green
+    if num_well_last_col > 0:
+        [
+            reagent_plate.rows()[row][0].load_liquid(
+                liquid=def_ab, volume=vol_ab_plus_one
+            )
+            for row in range(num_well_last_col)
+        ]
+    [
+        reagent_plate.rows()[row][0].load_liquid(liquid=def_ab, volume=vol_ab)
+        for row in range(num_well_last_col, 8)
+    ]
+
+    vol_re = 40 * num_col_total + 40
+    def_block = ctx.define_liquid(
+        name="BLOCKING SOLUTION", description="", display_color="#FFC300"
+    )  # yellow
+    [
+        reagent_plate.rows()[row][1].load_liquid(liquid=def_block, volume=vol_re)
+        for row in range(8)
+    ]
+
+    if use_lid:
+
+        ctx.load_lid_stack("corning_96_wellplate_360ul_lid", "C4", 1)
+
+        def cover_plate() -> None:
+            """Cover the plate with a lid."""
+            ctx.move_lid(
+                "C4",
+                working_plate,
+                use_gripper=True,
+                pick_up_offset={"x": 0, "y": 0, "z": 0},
+                drop_offset={"x": 0, "y": 0, "z": 0},
+            )
+
+        def remove_lid() -> None:
+            """Remove the lid from the plate."""
+            ctx.move_lid(
+                working_plate,
+                "C4",
+                use_gripper=True,
+                pick_up_offset={"x": 0, "y": 0, "z": 0},
+                drop_offset={"x": 0, "y": 0, "z": 0},
+            )
+
+    def heat(min: float) -> None:
+        """Heat the plate on the Heater-Shaker."""
+        hs.set_and_wait_for_temperature(37)
+        hs.open_labware_latch()
+        ctx.move_labware(
+            labware=working_plate,
+            new_location=hs_adapter,
+            use_gripper=True,
+            pick_up_offset={"x": 0, "y": 0, "z": -7},
+            drop_offset={"x": 0, "y": 0, "z": -7},
+        )
+
+        hs.close_labware_latch()
+        hs.open_labware_latch()
+
+        ctx.delay(minutes=min)
+
+        ctx.move_labware(
+            labware=working_plate,
+            new_location="C2",
+            use_gripper=True,
+            pick_up_offset={"x": 0, "y": 0, "z": -7},
+            drop_offset={"x": 0, "y": 0, "z": -7},
+        )
+
+    def transfer(start: Well, vol: float) -> None:
+        """Transfer liquid from start wells to reaction wells."""
+        p1k_8.tip_racks = [tips_1k]
+        p1k_8.pick_up_tip()
+        p1k_8.aspirate(vol * len(rxn_full), start)
+        p1k_8.air_gap(10)
+        p1k_8.dispense(10, rxn_full[0].top(z=0))
+        p1k_8.flow_rate.dispense = SLOW
+        for col in rxn_full:
+            p1k_8.move_to(col.top(z=0))
+            p1k_8.dispense(vol, col.top(z=-2).move(Point(x=D_1K, y=D_1K)))
+            p1k_8.move_to(col.top(z=0))
+        p1k_8.blow_out()
+        if dry_run:
+            p1k_8.return_tip()
+        else:
+            p1k_8.drop_tip()
+        p1k_8.flow_rate.dispense = DEFAULT_RATE
+
+    def transfer_remainder(start: List[Well], vol: float) -> None:
+        """Transfer remaining liquid from start wells to reaction wells."""
+        p1k_1.tip_racks = [tips_1k]
+        p1k_1.pick_up_tip()
+        for well_start in start:
+            p1k_1.aspirate(vol, well_start)
+        p1k_1.air_gap(10)
+        p1k_1.dispense(10, rxn_remainder[0].top(z=0))
+        p1k_1.flow_rate.dispense = SLOW
+        for well_end in rxn_remainder:
+            p1k_1.move_to(well_end.top(z=0))
+            p1k_1.dispense(vol, well_end.top(z=-2).move(Point(x=D_1K, y=D_1K)))
+            p1k_1.move_to(well_end.top(z=0))
+        p1k_1.blow_out()
+        if dry_run:
+            p1k_1.return_tip()
+        else:
+            p1k_1.drop_tip()
+        p1k_1.flow_rate.dispense = DEFAULT_RATE
+
+    def discard(vol: float) -> None:
+        """Discard liquid from reaction wells."""
+        for col in rxn_total:
+            p1k_8.tip_racks = [tips_200]
+            p1k_8.pick_up_tip()
+            p1k_8.flow_rate.aspirate = SLOW
+            p1k_8.move_to(col.top(z=0))
+            p1k_8.aspirate(
+                vol + 20, col.bottom(z=H_DISCARD).move(Point(x=D_200, y=D_200))
+            )
+            ctx.delay(seconds=2)
+            p1k_8.move_to(col.top(z=0))
+            p1k_8.flow_rate.aspirate = DEFAULT_RATE
+            p1k_8.dispense(vol + 20, waste.top(z=-5))
+            p1k_8.blow_out()
+            if dry_run:
+                p1k_8.return_tip()
+            else:
+                p1k_8.drop_tip()
+
+    ctx.comment("                                   ")
+    ctx.comment("***********************************")
+    ctx.comment("  Transferring Blocking Solution   ")
+    ctx.comment("***********************************")
+    ctx.comment("                                   ")
+
+    transfer(block, VOL_BLOCK)
+    if num_well_last_col > 0:
+        transfer_remainder(block_remainder, VOL_BLOCK)
+
+    ctx.comment("                                   ")
+    ctx.comment("***********************************")
+    ctx.comment("  Incubating on the Heater-Shaker  ")
+    ctx.comment("***********************************")
+    ctx.comment("                                   ")
+
+    if use_lid:
+        cover_plate()
+    else:
+        ctx.pause("Please place seal on plate.")
+
+    if heat_on_deck:
+        heat(MIN_BLOCK if not dry_run else 0.1)
+    else:
+        ctx.pause(
+            "Incubation at 37 degree C for 1 hour - remove seal and return plate to slot C2"
+        )
+
+    if use_lid:
+        remove_lid()
+
+    ctx.comment("                                   ")
+    ctx.comment("***********************************")
+    ctx.comment("    Removing Blocking Solution     ")
+    ctx.comment("***********************************")
+    ctx.comment("                                   ")
+
+    discard(VOL_BLOCK)
+
+    ctx.comment("                                   ")
+    ctx.comment("***********************************")
+    ctx.comment("  Transferring Primary Antibody    ")
+    ctx.comment("***********************************")
+    ctx.comment("                                   ")
+
+    transfer(ab, VOL_AB)
+    if num_well_last_col > 0:
+        transfer_remainder(ab_remainder, VOL_AB)
+
+    if use_lid:
+        cover_plate()
+    else:
+        ctx.pause("Please place seal on plate and incubate at 4 degree C overnight")