freeze the ops classes and remove doc strings

Author: rickwierenga

Diff for: pylabrobot/liquid_handling/backends/hamilton/STAR.py

@@ -1577,8 +1577,8 @@ async def aspirate(
     self._assert_valid_resources([op.resource for op in ops])
 
     # correct volumes using the liquid class
-    for op, hlc in zip(ops, hamilton_liquid_classes):
-      op.volume = hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+    volumes = [hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+               for op, hlc in zip(ops, hamilton_liquid_classes)]
 
     well_bottoms = [op.resource.get_absolute_location().z + op.offset.z + \
                     op.resource.material_z_thickness for op in ops]
@@ -1657,7 +1657,7 @@ async def aspirate(
         x_positions=x_positions,
         y_positions=y_positions,
 
-        aspiration_volumes=[round(op.volume * 10) for op in ops],
+        aspiration_volumes=[round(vol * 10) for vol in volumes],
         lld_search_height=[round(lsh * 10) for lsh in lld_search_height],
         clot_detection_height=[round(cd * 10) for cd in clot_detection_height],
         liquid_surface_no_lld=[round(ls * 10) for ls in liquid_surfaces_no_lld],
@@ -1839,8 +1839,8 @@ async def dispense(
         ))
 
     # correct volumes using the liquid class
-    for op, hlc in zip(ops, hamilton_liquid_classes):
-      op.volume = hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+    volumes = [hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+               for op, hlc in zip(ops, hamilton_liquid_classes)]
 
     well_bottoms = [op.resource.get_absolute_location().z + op.offset.z + \
                     op.resource.material_z_thickness for op in ops]
@@ -1858,7 +1858,6 @@ async def dispense(
       [_dispensing_mode_for_op(empty=empty[i], jet=jet[i], blow_out=blow_out[i])
        for i in range(len(ops))]
 
-    dispense_volumes = [op.volume for op in ops]
     pull_out_distance_transport_air = _fill_in_defaults(pull_out_distance_transport_air, [10.0]*n)
     second_section_height = _fill_in_defaults(second_section_height, [3.2]*n)
     second_section_ratio = _fill_in_defaults(second_section_ratio, [618.0]*n)
@@ -1907,7 +1906,7 @@ async def dispense(
         y_positions=y_positions,
 
         dispensing_mode=dispensing_modes,
-        dispense_volumes=[round(dv*10) for dv in dispense_volumes],
+        dispense_volumes=[round(vol*10) for vol in volumes],
         lld_search_height=[round(lsh*10) for lsh in lld_search_height],
         liquid_surface_no_lld=[round(ls*10) for ls in liquid_surfaces_no_lld],
         pull_out_distance_transport_air=[round(po*10) for po in pull_out_distance_transport_air],

Diff for: pylabrobot/liquid_handling/backends/hamilton/vantage.py

@@ -620,8 +620,8 @@ async def aspirate(
     self._assert_valid_resources([op.resource for op in ops])
 
     # correct volumes using the liquid class
-    for op, hlc in zip(ops, hlcs):
-      op.volume = hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+    volumes = [hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+               for op, hlc in zip(ops, hlcs)]
 
     well_bottoms = [op.resource.get_absolute_location().z + op.offset.z + \
                     op.resource.material_z_thickness for op in ops]
@@ -663,7 +663,7 @@ async def aspirate(
       immersion_depth=[round(id_*10) for id_ in immersion_depth or [0]*len(ops)],
       surface_following_distance=[round(sfd*10) for sfd in surface_following_distance or
                                   [0]*len(ops)],
-      aspiration_volume=[round(op.volume*100) for op in ops],
+      aspiration_volume=[round(vol*100) for vol in volumes],
       aspiration_speed=[round(fr * 10) for fr in flow_rates],
       transport_air_volume=[round(tav*10) for tav in
         transport_air_volume or [hlc.aspiration_air_transport_volume if hlc is not None else 0
@@ -785,8 +785,8 @@ async def dispense(
     self._assert_valid_resources([op.resource for op in ops])
 
     # correct volumes using the liquid class
-    for op, hlc in zip(ops, hlcs):
-      op.volume = hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+    volumes = [hlc.compute_corrected_volume(op.volume) if hlc is not None else op.volume
+               for op, hlc in zip(ops, hlcs)]
 
     well_bottoms = [op.resource.get_absolute_location().z + op.offset.z + \
                     op.resource.material_z_thickness for op in ops]
@@ -831,7 +831,7 @@ async def dispense(
           minimal_traverse_height_at_begin_of_command or [self._traversal_height]*len(ops)],
       minimal_height_at_command_end=
         [round(mh*10) for mh in minimal_height_at_command_end or [self._traversal_height]*len(ops)],
-      dispense_volume=[round(op.volume * 100) for op in ops],
+      dispense_volume=[round(vol*100) for vol in volumes],
       dispense_speed=[round(fr*10) for fr in flow_rates],
       cut_off_speed=[round(cs*10) for cs in cut_off_speed or [250]*len(ops)],
       stop_back_volume=[round(sbv*100) for sbv in stop_back_volume or [0]*len(ops)],

Diff for: pylabrobot/liquid_handling/backends/tecan/EVO.py

@@ -317,9 +317,6 @@ async def aspirate(
         tip_type=op.tip.tip_type
       ) if isinstance(op.tip, TecanTip) else None for op in ops]
 
-    for op, tlc in zip(ops, tecan_liquid_classes):
-      op.volume = tlc.compute_corrected_volume(op.volume) if tlc is not None else op.volume
-
     ys = int(ops[0].resource.get_absolute_size_y() * 10)
     zadd: List[Optional[int]] = [0] * self.num_channels
     for i, channel in enumerate(use_channels):
@@ -406,11 +403,6 @@ async def dispense(
         tip_type=op.tip.tip_type
       ) if isinstance(op.tip, TecanTip) else None for op in ops]
 
-    for op, tlc in zip(ops, tecan_liquid_classes):
-      op.volume = tlc.compute_corrected_volume(op.volume) + \
-        tlc.aspirate_lag_volume + tlc.aspirate_tag_volume \
-        if tlc is not None else op.volume
-
     x, _ = self._first_valid(x_positions)
     y, yi = self._first_valid(y_positions)
     assert x is not None and y is not None
@@ -724,7 +716,8 @@ def _aspirate_action(
       assert tlc is not None and z is not None
       sep[channel] = int(tlc.aspirate_speed * 12) # 6?
       ssz[channel] = round(z * tlc.aspirate_speed / ops[i].volume)
-      mtr[channel] = round(ops[i].volume * 6) # 3?
+      volume = tlc.compute_corrected_volume(ops[i].volume)
+      mtr[channel] = round(volume * 6) # 3?
       ssz_r[channel] = int(tlc.aspirate_retract_speed * 10)
 
     return ssz, sep, stz, mtr, ssz_r
@@ -755,7 +748,9 @@ def _dispense_action(
       sep[channel] = int(tlc.dispense_speed * 12) # 6?
       spp[channel] = int(tlc.dispense_breakoff * 12) # 6?
       stz[channel] = 0
-      mtr[channel] = -round(ops[i].volume * 6) # 3?
+      volume = tlc.compute_corrected_volume(ops[i].volume) + tlc.aspirate_lag_volume + \
+        tlc.aspirate_tag_volume
+      mtr[channel] = -round(volume * 6) # 3?
 
     return sep, spp, stz, mtr
 

Diff for: pylabrobot/liquid_handling/backends/tecan/EVO_tests.py

@@ -122,11 +122,11 @@ async def test_aspirate(self):
       call(module="C5", command="SML", params=[985, 2000, 2000, 2000, 2000, 2000, 2000, 2000]),
       call(module="C5", command="SBL", params=[20, None, None, None, None, None, None, None]),
       call(module="C5", command="SHZ", params=[1455, 1455, 1455, 1455, 1455, 1455, 1455, 1455]),
-      call(module="C5", command="MDT", params=[1, None, None, None, 31, 0, 0, 0, 0, 0, 0, 0]),
+      call(module="C5", command="MDT", params=[1, None, None, None, 30, 0, 0, 0, 0, 0, 0, 0]),
       call(module="C5", command="SHZ", params=[2000, 2000, 2000, 2000, 2000, 2000, 2000, 2000]),
       call(module="C5", command="SSZ", params=[30, None, None, None, None, None, None, None]),
       call(module="C5", command="SEP", params=[1200, None, None, None, None, None, None, None]),
-      call(module="C5", command="STZ", params=[-31, None, None, None, None, None, None, None]),
+      call(module="C5", command="STZ", params=[-30, None, None, None, None, None, None, None]),
       call(module="C5", command="MTR", params=[626, None, None, None, None, None, None, None]),
       call(module="C5", command="SSZ", params=[200, None, None, None, None, None, None, None]),
       call(module="C5", command="MAZ", params=[1375, None, None, None, None, None, None, None]),

Diff for: pylabrobot/liquid_handling/standard.py

@@ -14,42 +14,34 @@
   from pylabrobot.resources.tip_rack import TipSpot
 
 
-@dataclass
+@dataclass(frozen=True)
 class Pickup:
-  """ A pickup operation. """
   resource: TipSpot
   offset: Coordinate
   tip: Tip # TODO: perhaps we can remove this, because the tip spot has the tip?
 
 
-@dataclass
+@dataclass(frozen=True)
 class Drop:
-  """ A drop operation. """
   resource: Resource
   offset: Coordinate
   tip: Tip
 
 
-@dataclass
+@dataclass(frozen=True)
 class PickupTipRack:
-  """ A pickup operation for an entire tip rack. """
-
   resource: TipRack
   offset: Coordinate
 
 
-@dataclass
+@dataclass(frozen=True)
 class DropTipRack:
-  """ A drop operation for an entire tip rack. """
-
   resource: Union[TipRack, Trash]
   offset: Coordinate
 
 
-@dataclass
+@dataclass(frozen=True)
 class Aspiration:
-  """ Aspiration contains information about an aspiration. """
-
   resource: Container
   offset: Coordinate
   tip: Tip
@@ -60,10 +52,8 @@ class Aspiration:
   liquids: List[Tuple[Optional[Liquid], float]]
 
 
-@dataclass
+@dataclass(frozen=True)
 class Dispense:
-  """ Dispense contains information about an dispense. """
-
   resource: Container
   offset: Coordinate
   tip: Tip
@@ -74,10 +64,8 @@ class Dispense:
   liquids: List[Tuple[Optional[Liquid], float]]
 
 
-@dataclass
+@dataclass(frozen=True)
 class AspirationPlate:
-  """ Contains information about an aspiration from a plate (in a single movement). """
-
   wells: List[Well]
   offset: Coordinate
   tips: List[Tip]
@@ -88,10 +76,8 @@ class AspirationPlate:
   liquids: List[List[Tuple[Optional[Liquid], float]]]
 
 
-@dataclass
+@dataclass(frozen=True)
 class DispensePlate:
-  """ Contains information about an aspiration from a plate (in a single movement). """
-
   wells: List[Well]
   offset: Coordinate
   tips: List[Tip]
@@ -101,10 +87,8 @@ class DispensePlate:
   blow_out_air_volume: Optional[float]
   liquids: List[List[Tuple[Optional[Liquid], float]]]
 
-@dataclass
+@dataclass(frozen=True)
 class AspirationContainer:
-  """ Contains information about an aspiration from a plate (in a single movement). """
-
   container: Container
   offset: Coordinate
   tips: List[Tip]
@@ -115,10 +99,8 @@ class AspirationContainer:
   liquids: List[List[Tuple[Optional[Liquid], float]]]
 
 
-@dataclass
+@dataclass(frozen=True)
 class DispenseContainer:
-  """ Contains information about an aspiration from a plate (in a single movement). """
-
   container: Container
   offset: Coordinate
   tips: List[Tip]
@@ -130,17 +112,15 @@ class DispenseContainer:
 
 
 class GripDirection(enum.Enum):
-  """ A direction from which to grab the resource. """
   FRONT = enum.auto()
   BACK = enum.auto()
   LEFT = enum.auto()
   RIGHT = enum.auto()
 
 
-@dataclass
+@dataclass(frozen=True)
 class Move:
-  """ A move operation.
-
+  """
   Attributes:
     resource: The resource to move.
     destination: The destination of the move.