single container aspirate/dispense (#377)

Author: rickwierenga

pylabrobot/liquid_handling/backends/backend.py

@@ -8,7 +8,7 @@
   DropTipRack,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -123,7 +123,7 @@ async def aspirate96(
     """Aspirate from all wells in 96 well plate."""
 
   @abstractmethod
-  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr]):
+  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer]):
     """Dispense to all wells in 96 well plate."""
 
   @abstractmethod

pylabrobot/liquid_handling/backends/chatterbox.py

@@ -8,7 +8,7 @@
   DropTipRack,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -221,7 +221,7 @@ async def aspirate96(
       resource = aspiration.container
     print(f"Aspirating {aspiration.volume} from {resource}.")
 
-  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr]):
+  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer]):
     if isinstance(dispense, MultiHeadDispensePlate):
       resource = dispense.wells[0].parent
     else:

pylabrobot/liquid_handling/backends/hamilton/STAR.py

@@ -32,7 +32,7 @@
   GripDirection,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -2375,7 +2375,7 @@ async def aspirate96(
 
   async def dispense96(
     self,
-    dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr],
+    dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer],
     jet: bool = False,
     empty: bool = False,
     blow_out: bool = False,

pylabrobot/liquid_handling/backends/hamilton/vantage.py

@@ -16,7 +16,7 @@
   DropTipRack,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -1135,7 +1135,7 @@ async def aspirate96(
 
   async def dispense96(
     self,
-    dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr],
+    dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer],
     jet: bool = False,
     blow_out: bool = False,  # "empty" in the VENUS liquid editor
     empty: bool = False,  # truly "empty", does not exist in liquid editor, dm4

pylabrobot/liquid_handling/backends/opentrons_backend.py

@@ -11,7 +11,7 @@
   DropTipRack,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -584,7 +584,7 @@ async def aspirate96(
   ):
     raise NotImplementedError("The Opentrons backend does not support the 96 head.")
 
-  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr]):
+  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer]):
     raise NotImplementedError("The Opentrons backend does not support the 96 head.")
 
   async def pick_up_resource(self, pickup: ResourcePickup):

pylabrobot/liquid_handling/backends/serializing_backend.py

@@ -10,7 +10,7 @@
   DropTipRack,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -173,7 +173,7 @@ async def aspirate96(
       data["aspiration"]["trough"] = aspiration.container.name
     await self.send_command(command="aspirate96", data=data)
 
-  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr]):
+  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer]):
     data = {
       "dispense": {
         "offset": serialize(dispense.offset),

pylabrobot/liquid_handling/backends/tecan/EVO.py

@@ -29,7 +29,7 @@
   DropTipRack,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -516,7 +516,7 @@ async def aspirate96(
   ):
     raise NotImplementedError()
 
-  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr]):
+  async def dispense96(self, dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer]):
     raise NotImplementedError()
 
   async def pick_up_resource(self, pickup: ResourcePickup):

pylabrobot/liquid_handling/liquid_handler.py

@@ -65,7 +65,7 @@
   GripDirection,
   MultiHeadAspirationContainer,
   MultiHeadAspirationPlate,
-  MultiHeadDispenseContainr,
+  MultiHeadDispenseContainer,
   MultiHeadDispensePlate,
   Pickup,
   PickupTipRack,
@@ -1568,6 +1568,7 @@ async def aspirate96(
     flow_rate = float(flow_rate) if flow_rate is not None else None
     blow_out_air_volume = float(blow_out_air_volume) if blow_out_air_volume is not None else None
 
+    containers: Sequence[Container]
     if isinstance(resource, Container):
       if (
         resource.get_absolute_size_x() < 108.0 or resource.get_absolute_size_y() < 70.0
@@ -1598,24 +1599,26 @@ async def aspirate96(
         blow_out_air_volume=blow_out_air_volume,
         liquids=cast(List[List[Tuple[Optional[Liquid], float]]], all_liquids),  # stupid
       )
+
+      containers = [resource]
     else:
       if isinstance(resource, Plate):
         if resource.has_lid():
           raise ValueError("Aspirating from plate with lid")
-        wells = resource.get_all_items()
+        containers = resource.get_all_items()
       else:
-        wells = resource
+        containers = resource
 
         # ensure that wells are all in the same plate
-        plate = wells[0].parent
-        for well in wells:
+        plate = containers[0].parent
+        for well in containers:
           if well.parent != plate:
             raise ValueError("All wells must be in the same plate")
 
-      if not len(wells) == 96:
-        raise ValueError(f"aspirate96 expects 96 wells, got {len(wells)}")
+      if not len(containers) == 96:
+        raise ValueError(f"aspirate96 expects 96 wells, got {len(containers)}")
 
-      for well, channel in zip(wells, self.head96.values()):
+      for well, channel in zip(containers, self.head96.values()):
         # superfluous to have append in two places but the type checker is very angry and does not
         # understand that Optional[Liquid] (remove_liquid) is the same as None from the first case
         if well.tracker.is_disabled or not does_volume_tracking():
@@ -1629,7 +1632,7 @@ async def aspirate96(
           channel.get_tip().tracker.add_liquid(liquid=liquid, volume=vol)
 
       aspiration = MultiHeadAspirationPlate(
-        wells=wells,
+        wells=cast(List[Well], containers),
         volume=volume,
         offset=offset,
         flow_rate=flow_rate,
@@ -1642,9 +1645,9 @@ async def aspirate96(
     try:
       await self.backend.aspirate96(aspiration=aspiration, **backend_kwargs)
     except Exception as error:
-      for channel, well in zip(self.head96.values(), wells):
-        if does_volume_tracking() and not well.tracker.is_disabled:
-          well.tracker.rollback()
+      for channel, container in zip(self.head96.values(), containers):
+        if does_volume_tracking() and not container.tracker.is_disabled:
+          container.tracker.rollback()
         channel.get_tip().tracker.rollback()
       self._trigger_callback(
         "aspirate96",
@@ -1654,10 +1657,11 @@ async def aspirate96(
         **backend_kwargs,
       )
     else:
-      for channel, well in zip(self.head96.values(), wells):
-        if does_volume_tracking() and not well.tracker.is_disabled:
-          well.tracker.commit()
-        channel.get_tip().tracker.commit()
+      for channel, container in zip(self.head96.values(), containers):
+        if does_volume_tracking() and not container.tracker.is_disabled:
+          container.tracker.commit()
+      channel.get_tip().tracker.commit()
+
       self._trigger_callback(
         "aspirate96",
         liquid_handler=self,
@@ -1708,13 +1712,14 @@ async def dispense96(
 
     tips = [channel.get_tip() for channel in self.head96.values()]
     all_liquids: List[List[Tuple[Optional[Liquid], float]]] = []
-    dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainr]
+    dispense: Union[MultiHeadDispensePlate, MultiHeadDispenseContainer]
 
     # Convert everything to floats to handle exotic number types
     volume = float(volume)
     flow_rate = float(flow_rate) if flow_rate is not None else None
     blow_out_air_volume = float(blow_out_air_volume) if blow_out_air_volume is not None else None
 
+    containers: Sequence[Container]
     if isinstance(resource, Container):
       if (
         resource.get_absolute_size_x() < 108.0 or resource.get_absolute_size_y() < 70.0
@@ -1735,7 +1740,7 @@ async def dispense96(
         for liquid, vol in reversed(reversed_liquids):
           channel.get_tip().tracker.add_liquid(liquid=liquid, volume=vol)
 
-      dispense = MultiHeadDispenseContainr(
+      dispense = MultiHeadDispenseContainer(
         container=resource,
         volume=volume,
         offset=offset,
@@ -1745,24 +1750,26 @@ async def dispense96(
         blow_out_air_volume=blow_out_air_volume,
         liquids=cast(List[List[Tuple[Optional[Liquid], float]]], all_liquids),  # stupid
       )
+
+      containers = [resource]
     else:
       if isinstance(resource, Plate):
         if resource.has_lid():
           raise ValueError("Aspirating from plate with lid")
-        wells = resource.get_all_items()
-      else:
-        wells = resource
+        containers = resource.get_all_items()
+      else:  # List[Well]
+        containers = resource
 
         # ensure that wells are all in the same plate
-        plate = wells[0].parent
-        for well in wells:
+        plate = containers[0].parent
+        for well in containers:
           if well.parent != plate:
             raise ValueError("All wells must be in the same plate")
 
-      if not len(wells) == 96:
-        raise ValueError(f"dispense96 expects 96 wells, got {len(wells)}")
+      if not len(containers) == 96:
+        raise ValueError(f"dispense96 expects 96 wells, got {len(containers)}")
 
-      for channel, well in zip(self.head96.values(), wells):
+      for channel, well in zip(self.head96.values(), containers):
         # even if the volume tracker is disabled, a liquid (None, volume) is added to the list
         # during the aspiration command
         liquids = channel.get_tip().tracker.remove_liquid(volume=volume)
@@ -1773,7 +1780,7 @@ async def dispense96(
           well.tracker.add_liquid(liquid=liquid, volume=vol)
 
       dispense = MultiHeadDispensePlate(
-        wells=wells,
+        wells=cast(List[Well], containers),
         volume=volume,
         offset=offset,
         flow_rate=flow_rate,
@@ -1786,9 +1793,9 @@ async def dispense96(
     try:
       await self.backend.dispense96(dispense=dispense, **backend_kwargs)
     except Exception as error:
-      for channel, well in zip(self.head96.values(), wells):
+      for channel, container in zip(self.head96.values(), containers):
         if does_volume_tracking() and not well.tracker.is_disabled:
-          well.tracker.rollback()
+          container.tracker.rollback()
         channel.get_tip().tracker.rollback()
 
       self._trigger_callback(
@@ -1799,9 +1806,9 @@ async def dispense96(
         **backend_kwargs,
       )
     else:
-      for channel, well in zip(self.head96.values(), wells):
+      for channel, container in zip(self.head96.values(), containers):
         if does_volume_tracking() and not well.tracker.is_disabled:
-          well.tracker.commit()
+          container.tracker.commit()
         channel.get_tip().tracker.commit()
 
       self._trigger_callback(

pylabrobot/liquid_handling/liquid_handler_tests.py

@@ -35,6 +35,7 @@
   NoTipError,
 )
 from pylabrobot.resources.hamilton import HTF, STF, STARLetDeck
+from pylabrobot.resources.opentrons.reservoirs import agilent_1_reservoir_290ml
 from pylabrobot.resources.utils import create_ordered_items_2d
 from pylabrobot.resources.volume_tracker import (
   set_cross_contamination_tracking,
@@ -1009,6 +1010,11 @@ async def test_save_state(self):
 
     set_volume_tracking(enabled=False)
 
+  async def test_aspirate_single_reservoir(self):
+    reagent_reservoir = agilent_1_reservoir_290ml(name="reservoir")
+    await self.lh.pick_up_tips96(self.tip_rack)
+    await self.lh.aspirate96(reagent_reservoir.get_item("A1"), volume=100)
+
 
 class TestLiquidHandlerVolumeTracking(unittest.IsolatedAsyncioTestCase):
   async def asyncSetUp(self):

pylabrobot/liquid_handling/standard.py

@@ -109,7 +109,7 @@ class MultiHeadAspirationContainer:
 
 
 @dataclass(frozen=True)
-class MultiHeadDispenseContainr:
+class MultiHeadDispenseContainer:
   container: Container
   offset: Coordinate
   tips: List[Tip]