feat(shared-data): add custom & default thermocycler overlap offsets …

…for labware (#13630) (#13750)

* added TC overlaps for nest & biorad pcr plates
* added a backwards-compatible default overlap for TC labware on OT2
* fix pd e2e migration fixture
---------

Co-authored-by: Sanniti Pimpley <[email protected]>

api/src/opentrons/protocol_engine/state/labware.py

@@ -560,12 +560,27 @@ def get_module_overlap_offsets(
         """Get the labware's overlap with requested module model."""
         definition = self.get_definition(labware_id)
         stacking_overlap = definition.stackingOffsetWithModule.get(
-            str(module_model.value), OverlapOffset(x=0, y=0, z=0)
+            str(module_model.value)
         )
+        if not stacking_overlap:
+            if self._is_thermocycler_on_ot2(module_model):
+                return OverlapOffset(x=0, y=0, z=10.7)
+            else:
+                return OverlapOffset(x=0, y=0, z=0)
+
         return OverlapOffset(
             x=stacking_overlap.x, y=stacking_overlap.y, z=stacking_overlap.z
         )
 
+    def _is_thermocycler_on_ot2(self, module_model: ModuleModel) -> bool:
+        """Whether the given module is a thermocycler with the current deck being an OT2 deck."""
+        robot_model = self.get_deck_definition()["robot"]["model"]
+        return (
+            module_model
+            in [ModuleModel.THERMOCYCLER_MODULE_V1, ModuleModel.THERMOCYCLER_MODULE_V2]
+            and robot_model == "OT-2 Standard"
+        )
+
     def get_default_magnet_height(self, module_id: str, offset: float) -> float:
         """Return a labware's default Magnetic Module engage height with added offset, if supplied.
 

api/tests/opentrons/protocol_engine/state/test_labware_view.py

@@ -1,9 +1,10 @@
 """Labware state store tests."""
 import pytest
 from datetime import datetime
-from typing import Dict, Optional, cast, ContextManager, Any, Union
+from typing import Dict, Optional, cast, ContextManager, Any, Union, NamedTuple, List
 from contextlib import nullcontext as does_not_raise
 
+from opentrons_shared_data.deck import load as load_deck
 from opentrons_shared_data.deck.dev_types import DeckDefinitionV3
 from opentrons_shared_data.pipette.dev_types import LabwareUri
 from opentrons_shared_data.labware.labware_definition import (
@@ -13,6 +14,11 @@
     GripperOffsets,
     OffsetVector,
 )
+
+from opentrons.protocols.api_support.deck_type import (
+    STANDARD_OT2_DECK,
+    STANDARD_OT3_DECK,
+)
 from opentrons.protocols.models import LabwareDefinition
 from opentrons.types import DeckSlotName, Point, MountType
 
@@ -39,7 +45,6 @@
     LabwareLoadParams,
 )
 
-
 plate = LoadedLabware(
     id="plate-id",
     loadName="plate-load-name",
@@ -686,26 +691,91 @@ def test_get_labware_overlap_offsets() -> None:
     assert result == OverlapOffset(x=1, y=2, z=3)
 
 
-def test_get_module_overlap_offsets() -> None:
+class ModuleOverlapSpec(NamedTuple):
+    """Spec data to test LabwareView.get_module_overlap_offsets."""
+
+    spec_deck_definition: DeckDefinitionV3
+    module_model: ModuleModel
+    stacking_offset_with_module: Dict[str, SharedDataOverlapOffset]
+    expected_offset: OverlapOffset
+
+
+module_overlap_specs: List[ModuleOverlapSpec] = [
+    ModuleOverlapSpec(
+        # Labware on temp module on OT2, with stacking overlap for temp module
+        spec_deck_definition=load_deck(STANDARD_OT2_DECK, 3),
+        module_model=ModuleModel.TEMPERATURE_MODULE_V2,
+        stacking_offset_with_module={
+            str(ModuleModel.TEMPERATURE_MODULE_V2.value): SharedDataOverlapOffset(
+                x=1, y=2, z=3
+            ),
+        },
+        expected_offset=OverlapOffset(x=1, y=2, z=3),
+    ),
+    ModuleOverlapSpec(
+        # Labware on TC Gen1 on OT2, with stacking overlap for TC Gen1
+        spec_deck_definition=load_deck(STANDARD_OT2_DECK, 3),
+        module_model=ModuleModel.THERMOCYCLER_MODULE_V1,
+        stacking_offset_with_module={
+            str(ModuleModel.THERMOCYCLER_MODULE_V1.value): SharedDataOverlapOffset(
+                x=11, y=22, z=33
+            ),
+        },
+        expected_offset=OverlapOffset(x=11, y=22, z=33),
+    ),
+    ModuleOverlapSpec(
+        # Labware on TC Gen2 on OT2, with no stacking overlap
+        spec_deck_definition=load_deck(STANDARD_OT2_DECK, 3),
+        module_model=ModuleModel.THERMOCYCLER_MODULE_V2,
+        stacking_offset_with_module={},
+        expected_offset=OverlapOffset(x=0, y=0, z=10.7),
+    ),
+    ModuleOverlapSpec(
+        # Labware on TC Gen2 on Flex, with no stacking overlap
+        spec_deck_definition=load_deck(STANDARD_OT3_DECK, 3),
+        module_model=ModuleModel.THERMOCYCLER_MODULE_V2,
+        stacking_offset_with_module={},
+        expected_offset=OverlapOffset(x=0, y=0, z=0),
+    ),
+    ModuleOverlapSpec(
+        # Labware on TC Gen2 on Flex, with stacking overlap for TC Gen2
+        spec_deck_definition=load_deck(STANDARD_OT3_DECK, 3),
+        module_model=ModuleModel.THERMOCYCLER_MODULE_V2,
+        stacking_offset_with_module={
+            str(ModuleModel.THERMOCYCLER_MODULE_V2.value): SharedDataOverlapOffset(
+                x=111, y=222, z=333
+            ),
+        },
+        expected_offset=OverlapOffset(x=111, y=222, z=333),
+    ),
+]
+
+
+@pytest.mark.parametrize(
+    argnames=ModuleOverlapSpec._fields,
+    argvalues=module_overlap_specs,
+)
+def test_get_module_overlap_offsets(
+    spec_deck_definition: DeckDefinitionV3,
+    module_model: ModuleModel,
+    stacking_offset_with_module: Dict[str, SharedDataOverlapOffset],
+    expected_offset: OverlapOffset,
+) -> None:
     """It should get the labware overlap offsets."""
     subject = get_labware_view(
+        deck_definition=spec_deck_definition,
         labware_by_id={"plate-id": plate},
         definitions_by_uri={
             "some-plate-uri": LabwareDefinition.construct(  # type: ignore[call-arg]
-                stackingOffsetWithModule={
-                    str(
-                        ModuleModel.TEMPERATURE_MODULE_V2.value
-                    ): SharedDataOverlapOffset(x=1, y=2, z=3)
-                }
+                stackingOffsetWithModule=stacking_offset_with_module
             )
         },
     )
-
     result = subject.get_module_overlap_offsets(
-        labware_id="plate-id", module_model=ModuleModel.TEMPERATURE_MODULE_V2
+        labware_id="plate-id", module_model=module_model
     )
 
-    assert result == OverlapOffset(x=1, y=2, z=3)
+    assert result == expected_offset
 
 
 def test_get_default_magnet_height(

protocol-designer/fixtures/protocol/7/doItAllV7.json

@@ -2415,6 +2415,13 @@
       "stackingOffsetWithLabware": {
         "opentrons_96_pcr_adapter": { "x": 0, "y": 0, "z": 10.2 },
         "opentrons_96_well_aluminum_block": { "x": 0, "y": 0, "z": 12.66 }
+      },
+      "stackingOffsetWithModule": {
+        "thermocyclerModuleV2": {
+          "x": 0,
+          "y": 0,
+          "z": 10.8
+        }
       }
     },
     "opentrons/opentrons_24_aluminumblock_nest_1.5ml_snapcap/1": {

shared-data/labware/definitions/2/biorad_96_wellplate_200ul_pcr/2.json

@@ -1025,5 +1025,12 @@
       "y": 0,
       "z": 15.41
     }
+  },
+  "stackingOffsetWithModule": {
+    "thermocyclerModuleV2": {
+      "x": 0,
+      "y": 0,
+      "z": 10.75
+    }
   }
 }

shared-data/labware/definitions/2/nest_96_wellplate_100ul_pcr_full_skirt/2.json

@@ -1028,5 +1028,12 @@
       "y": 0,
       "z": 12.66
     }
+  },
+  "stackingOffsetWithModule": {
+    "thermocyclerModuleV2": {
+      "x": 0,
+      "y": 0,
+      "z": 10.8
+    }
   }
 }