OT2 'reservoirs'

pylabrobot/liquid_handling/backends/opentrons_backend_tests.py

@@ -19,7 +19,7 @@ def _is_python_3_10():
 def _mock_define(lw):
   return {
     "data": {
-      "definitionUri": f"lw['namespace']/{lw['metadata']['displayName']}/1"
+      "definitionUri": f'lw["namespace"]/{lw["metadata"]["displayName"]}/1'
     }
   }
 

pylabrobot/machines/backends/machine.py

@@ -20,8 +20,8 @@ def deserialize(cls, data: dict):
     class_name = data.pop("type")
     subclass = find_subclass(class_name, cls=cls)
     if subclass is None:
-      raise ValueError(f"Could not find subclass with name '{data['type']}'")
+      raise ValueError(f'Could not find subclass with name "{data["type"]}"')
     if issubclass(subclass, ABCMeta):
-      raise ValueError(f"Subclass with name '{data['type']}' is abstract")
+      raise ValueError(f'Subclass with name "{data["type"]}" is abstract')
     assert issubclass(subclass, cls)
     return subclass(**data)

pylabrobot/plate_reading/backend.py

@@ -76,7 +76,7 @@ def find_subclass(cls: Type[PlateReaderBackend], name: str) -> \
 
     subclass = find_subclass(cls, data["type"])
     if subclass is None:
-      raise ValueError(f"Could not find subclass with name {data['type']}")
+      raise ValueError(f'Could not find subclass with name {data["type"]}')
 
     del data["type"]
     return subclass(**data)

pylabrobot/resources/__init__.py

@@ -16,9 +16,11 @@
 from .petri_dish import PetriDish, PetriDishHolder
 from .plate import Plate, Lid, Well
 from .powder import Powder
+from .reservoir import Reservoir
 from .resource import Resource
 from .tip_rack import TipRack, TipSpot
 from .trash import Trash
+from .trough import Trough
 from .tube import Tube
 from .tube_rack import TubeRack
 

pylabrobot/resources/ml_star/mfx_carriers.py

@@ -1,56 +1,56 @@
-""" ML Star MultiFleX (MFX) carriers """
-
-# pylint: disable=empty-docstring
-# pylint: disable=invalid-name
-# pylint: disable=line-too-long
-
-from pylabrobot.resources.carrier import (
-  MFXCarrier,
-  Coordinate,
-  create_homogeneous_carrier_sites
-)
-
-
-def MFX_CAR_L5_base(name: str) -> MFXCarrier:
-  """ Hamilton cat. no.: 188039
-  Labware carrier base for up to 5 Multiflex Modules
-  """
-  return MFXCarrier(
-    name=name,
-    size_x=135.0,
-    size_y=497.0,
-    size_z=18.195,
-    sites=create_homogeneous_carrier_sites([
-        Coordinate(0.0, 5.0, 18.195),
-        Coordinate(0.0, 101.0, 18.195),
-        Coordinate(0.0, 197.0, 18.195),
-        Coordinate(0.0, 293.0, 18.195),
-        Coordinate(0.0, 389.0, 18.195)
-      ],
-      site_size_x=135.0,
-      site_size_y=94.0,
-    ),
-    model="MFX_CAR_L5_base"
-  )
-
-def PLT_CAR_L4_SHAKER(name: str) -> MFXCarrier:
-  """ Hamilton cat. no.: 187001
-  Template carrier with 4 positions for Hamilton Heater Shaker.
-  Occupies 7 tracks (7T). Can be screwed onto the deck.
-  """
-  return MFXCarrier(
-    name=name,
-    size_x=157.5,
-    size_y=497.0,
-    size_z=8.0,
-    sites=create_homogeneous_carrier_sites([
-        Coordinate(6.0, 2, 8.0), # not tested, interpolated Coordinate
-        Coordinate(6.0, 123, 8.0), # not tested, interpolated Coordinate
-        Coordinate(6.0, 244.0, 8.0), # tested using Hamilton_HC
-        Coordinate(6.0, 365.0, 8.0), # tested using Hamilton_HS
-      ],
-      site_size_x=145.5,
-      site_size_y=104.0,
-    ),
-    model="PLT_CAR_L4_SHAKER"
-  )
+""" ML Star MultiFleX (MFX) carriers """
+
+# pylint: disable=empty-docstring
+# pylint: disable=invalid-name
+# pylint: disable=line-too-long
+
+from pylabrobot.resources.carrier import (
+  MFXCarrier,
+  Coordinate,
+  create_homogeneous_carrier_sites
+)
+
+
+def MFX_CAR_L5_base(name: str) -> MFXCarrier:
+  """ Hamilton cat. no.: 188039
+  Labware carrier base for up to 5 Multiflex Modules
+  """
+  return MFXCarrier(
+    name=name,
+    size_x=135.0,
+    size_y=497.0,
+    size_z=18.195,
+    sites=create_homogeneous_carrier_sites([
+        Coordinate(0.0, 5.0, 18.195),
+        Coordinate(0.0, 101.0, 18.195),
+        Coordinate(0.0, 197.0, 18.195),
+        Coordinate(0.0, 293.0, 18.195),
+        Coordinate(0.0, 389.0, 18.195)
+      ],
+      site_size_x=135.0,
+      site_size_y=94.0,
+    ),
+    model="MFX_CAR_L5_base"
+  )
+
+def PLT_CAR_L4_SHAKER(name: str) -> MFXCarrier:
+  """ Hamilton cat. no.: 187001
+  Template carrier with 4 positions for Hamilton Heater Shaker.
+  Occupies 7 tracks (7T). Can be screwed onto the deck.
+  """
+  return MFXCarrier(
+    name=name,
+    size_x=157.5,
+    size_y=497.0,
+    size_z=8.0,
+    sites=create_homogeneous_carrier_sites([
+        Coordinate(6.0, 2, 8.0), # not tested, interpolated Coordinate
+        Coordinate(6.0, 123, 8.0), # not tested, interpolated Coordinate
+        Coordinate(6.0, 244.0, 8.0), # tested using Hamilton_HC
+        Coordinate(6.0, 365.0, 8.0), # tested using Hamilton_HS
+      ],
+      site_size_x=145.5,
+      site_size_y=104.0,
+    ),
+    model="PLT_CAR_L4_SHAKER"
+  )

pylabrobot/resources/opentrons/__init__.py

@@ -1,6 +1,7 @@
 from .deck import OTDeck
 from .load import load_opentrons_resource, load_shared_opentrons_resource
 from .plates import *
+from .reservoirs import *
 from .tip_racks import *
 from .tube_racks import *
 from .module import OTModule

pylabrobot/resources/opentrons/load.py

@@ -10,11 +10,12 @@
 
 from pylabrobot.resources.coordinate import Coordinate
 from pylabrobot.resources.plate import Plate
+from pylabrobot.resources.reservoir import Reservoir
 from pylabrobot.resources.tip import Tip, TipCreator
 from pylabrobot.resources.tip_rack import TipRack, TipSpot
 from pylabrobot.resources.tube import Tube
 from pylabrobot.resources.tube_rack import TubeRack
-from pylabrobot.resources.well import Well
+from pylabrobot.resources.well import Well, CrossSectionType
 
 
 if TYPE_CHECKING:
@@ -27,7 +28,7 @@ class UnknownResourceType(Exception):
 
 def ot_definition_to_resource(
   data: "LabwareDefinition",
-  name: str) -> Union[Plate, TipRack, TubeRack]:
+  name: str) -> Union[Plate, TipRack, TubeRack, Reservoir]:
   """ Convert an Opentrons definition file to a PyLabRobot resource file. """
 
   if not USE_OT:
@@ -42,7 +43,8 @@ def ot_definition_to_resource(
 
   tube_rack_display_cats = {"adapter", "aluminumBlock", "tubeRack"}
 
-  if display_category in ["wellPlate", "tipRack", "tubeRack", "adapter", "aluminumBlock"]:
+  if display_category in ["wellPlate", "tipRack", "tubeRack", "adapter", "aluminumBlock",
+                          "reservoir"]:
     items = data["ordering"]
     wells: List[List[Union[TipSpot, Well, Tube]]] = [] # TODO: can we use TypeGuard?
 
@@ -72,13 +74,21 @@ def volume_from_name(name: str) -> float:
         well_size_z = well_data["depth"]
 
         location=Coordinate(x=well_data["x"], y=well_data["y"], z=well_data["z"])
+
         if display_category == "wellPlate":
+
+          if well_data["shape"] == "rectangular":
+            cross_section_type = CrossSectionType.RECTANGLE
+          else:
+            cross_section_type = CrossSectionType.CIRCLE
+
           well = Well(
             name=item,
             size_x=well_size_x,
             size_y=well_size_y,
             size_z=well_size_z,
-            max_volume=well_data["totalLiquidVolume"]
+            max_volume=well_data["totalLiquidVolume"],
+            cross_section_type=cross_section_type
           )
           well.location = location
           wells[i].append(well)
@@ -113,6 +123,23 @@ def make_tip() -> Tip:
           )
           tube.location = location
           wells[i].append(tube)
+        elif display_category == "reservoir":
+
+          if well_data["shape"] == "rectangular":
+            cross_section_type = CrossSectionType.RECTANGLE
+          else:
+            cross_section_type = CrossSectionType.CIRCLE
+
+          well = Well(
+            name=item,
+            size_x=well_size_x,
+            size_y=well_size_y,
+            size_z=well_size_z,
+            max_volume=well_data["totalLiquidVolume"],
+            cross_section_type=cross_section_type
+          )
+          well.location = location
+          wells[i].append(well)
 
     if display_category == "wellPlate":
       return Plate(
@@ -143,11 +170,20 @@ def make_tip() -> Tip:
         items=cast(List[List[Tube]], wells),
         model=data["metadata"]["displayName"]
       )
+    if display_category == "reservoir":
+      return Reservoir(
+        name=name,
+        size_x=size_x,
+        size_y=size_y,
+        size_z=size_z,
+        items=cast(List[List[Well]], wells),
+        model=data["metadata"]["displayName"]
+      )
 
   raise UnknownResourceType(f"Unknown resource type '{display_category}'.")
 
 
-def load_opentrons_resource(fn: str, name: str) -> Union[Plate, TipRack, TubeRack]:
+def load_opentrons_resource(fn: str, name: str) -> Union[Plate, TipRack, TubeRack, Reservoir]:
   """ Load an Opentrons resource from a file.
 
   Args:
@@ -180,7 +216,7 @@ def load_shared_opentrons_resource(
   definition: str,
   name: str,
   version: int = 1
-) -> Union[Plate, TipRack, TubeRack]:
+) -> Union[Plate, TipRack, TubeRack, Reservoir]:
   """ Load an Opentrons resource from the shared Opentrons resource library.
 
   See https://github.com/Opentrons/opentrons/tree/edge/shared-data.

pylabrobot/resources/opentrons/plates.py

@@ -3,7 +3,6 @@
 from pylabrobot.resources.opentrons.load import load_shared_opentrons_resource
 from pylabrobot.resources.plate import Plate
 
-
 def corning_384_wellplate_112ul_flat(name: str) -> Plate:
   return cast(Plate, load_shared_opentrons_resource(
     definition="corning_384_wellplate_112ul_flat",

pylabrobot/resources/opentrons/reservoirs.py

@@ -0,0 +1,46 @@
+from typing import cast
+
+from pylabrobot.resources.opentrons.load import load_shared_opentrons_resource
+from pylabrobot.resources.reservoir import Reservoir
+
+def agilent_1_reservoir_290ml(name: str) -> Reservoir:
+  return cast(Reservoir, load_shared_opentrons_resource(
+    definition="agilent_1_reservoir_290ml",
+    name=name,
+    version=1
+  ))
+
+def axygen_1_reservoir_90ml(name: str) -> Reservoir:
+  return cast(Reservoir, load_shared_opentrons_resource(
+    definition="axygen_1_reservoir_90ml",
+    name=name,
+    version=1
+  ))
+
+def nest_12_reservoir_15ml(name: str) -> Reservoir:
+  return cast(Reservoir, load_shared_opentrons_resource(
+    definition="nest_12_reservoir_15ml",
+    name=name,
+    version=1
+  ))
+
+def nest_1_reservoir_195ml(name: str) -> Reservoir:
+  return cast(Reservoir, load_shared_opentrons_resource(
+    definition="nest_1_reservoir_195ml",
+    name=name,
+    version=1
+  ))
+
+def nest_1_reservoir_290ml(name: str) -> Reservoir:
+  return cast(Reservoir, load_shared_opentrons_resource(
+    definition="nest_1_reservoir_290ml",
+    name=name,
+    version=1
+  ))
+
+def usascientific_12_reservoir_22ml(name: str) -> Reservoir:
+  return cast(Reservoir, load_shared_opentrons_resource(
+    definition="usascientific_12_reservoir_22ml",
+    name=name,
+    version=1
+  ))