fix lint and typecheck

pylabrobot/liquid_handling/backends/hamilton/STAR.py

@@ -1404,7 +1404,7 @@ async def aspirate(
     minimum_traverse_height_at_beginning_of_a_command: int = 2450,
     min_z_endpos: int = 2450,
 
-    hamilton_liquid_classes: List[HamiltonLiquidClass] = None
+    hamilton_liquid_classes: Optional[List[Optional[HamiltonLiquidClass]]] = None
   ):
     """ Aspirate liquid from the specified channels.
 
@@ -1666,7 +1666,7 @@ async def dispense(
     min_z_endpos: int = 2450,
     side_touch_off_distance: int = 0,
 
-    hamilton_liquid_classes: List[HamiltonLiquidClass] = None
+    hamilton_liquid_classes: Optional[List[Optional[HamiltonLiquidClass]]] = None
   ):
     """ Dispense liquid from the specified channels.
 

pylabrobot/liquid_handling/backends/hamilton/vantage.py

@@ -521,7 +521,7 @@ async def aspirate(
         is_core=False,
         is_tip=True,
         has_filter=op.tip.has_filter,
-        liquid=op.liquid or Liquid.WATER,
+        liquid=op.liquids[-1][0] or Liquid.WATER,
         jet=False, # for aspiration
         empty=False # for aspiration
       ) for op in ops]
@@ -665,7 +665,7 @@ def should_empty(op):
         is_core=False,
         is_tip=True,
         has_filter=op.tip.has_filter,
-        liquid=op.liquid or Liquid.WATER,
+        liquid=op.liquids[-1][0] or Liquid.WATER,
         jet=jet,
         empty=empty
       ) for jet, empty, op in zip(jet, empty, ops)]
@@ -823,7 +823,8 @@ async def aspirate96(
       is_core=True,
       is_tip=True,
       has_filter=tip.has_filter,
-      liquid=aspiration.liquid or Liquid.WATER,
+      # first part of tuple in last liquid of first well
+      liquid=aspiration.liquids[0][-1][0] or Liquid.WATER,
       jet=jet,
       empty=empty
     )
@@ -930,7 +931,8 @@ async def dispense96(
       is_core=True,
       is_tip=True,
       has_filter=tip.has_filter,
-      liquid=dispense.liquid or Liquid.WATER,
+      # first part of tuple in last liquid of first well
+      liquid=dispense.liquids[0][-1][0] or Liquid.WATER,
       jet=jet,
       empty=empty
     )

pylabrobot/liquid_handling/backends/tecan/EVO.py

@@ -301,7 +301,7 @@ async def aspirate(
     tecan_liquid_classes = [
       get_liquid_class(
         target_volume=op.volume,
-        liquid_class=op.liquid or Liquid.WATER,
+        liquid_class=op.liquids[-1][0] or Liquid.WATER,
         tip_type=op.tip.tip_type
       ) if isinstance(op.tip, TecanTip) else None for op in ops]
 
@@ -390,7 +390,7 @@ async def dispense(
     tecan_liquid_classes = [
       get_liquid_class(
         target_volume=op.volume,
-        liquid_class=op.liquid or Liquid.WATER,
+        liquid_class=op.liquids[-1][0] or Liquid.WATER,
         tip_type=op.tip.tip_type
       ) if isinstance(op.tip, TecanTip) else None for op in ops]
 

pylabrobot/liquid_handling/liquid_handler.py

@@ -9,7 +9,7 @@
 import numbers
 import threading
 import time
-from typing import Any, Callable, Dict, Union, Optional, List, Sequence, Set
+from typing import Any, Callable, Dict, Union, Optional, List, Sequence, Set, Tuple
 import warnings
 
 from pylabrobot.machine import MachineFrontend, need_setup_finished
@@ -32,6 +32,7 @@
   does_tip_tracking,
   does_volume_tracking
 )
+from pylabrobot.resources.liquid import Liquid
 from pylabrobot.resources.errors import NoTipError
 from pylabrobot.utils.list import expand
 
@@ -652,7 +653,7 @@ async def aspirate(
     assert len(vols) == len(offsets) == len(flow_rates) == len(liquid_height)
 
     # liquid(s) for each channel. If volume tracking is disabled, use None as the liquid.
-    liquids = []
+    liquids: List[List[Tuple[Optional[Liquid], float]]] = []
     for r, vol in zip(resources, vols):
       if r.tracker.is_disabled or not does_volume_tracking():
         liquids.append([(None, vol)])
@@ -1043,7 +1044,7 @@ async def aspirate_plate(
       raise ValueError("Aspirating from plate with lid")
 
     # liquid(s) for each channel. If volume tracking is disabled, use None as the liquid.
-    liquids = []
+    liquids: List[List[Tuple[Optional[Liquid], float]]] = []
     for w in plate.get_all_items():
       if w.tracker.is_disabled or not does_volume_tracking():
         liquids.append([(None, volume)])
@@ -1107,7 +1108,7 @@ async def dispense_plate(
       raise ValueError("Dispensing to plate with lid")
 
     # liquid(s) for each channel. If volume tracking is disabled, use None as the liquid.
-    liquids = []
+    liquids: List[List[Tuple[Optional[Liquid], float]]] = []
     for w in plate.get_all_items():
       if w.tracker.is_disabled or not does_volume_tracking():
         liquids.append([(None, volume)])

pylabrobot/resources/plate.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import Callable, List, Optional, Sequence, Tuple, Union, cast
+from typing import List, Optional, Sequence, Tuple, Union, cast
 
 
 from .liquid import Liquid

pylabrobot/resources/volume_tracker.py

@@ -102,7 +102,7 @@ def get_free_volume(self) -> float:
 
     return self.max_volume - self.get_used_volume()
 
-  def get_liquids(self, top_volume: float) -> List[Tuple[Liquid, float]]:
+  def get_liquids(self, top_volume: float) -> List[Tuple[Optional[Liquid], float]]:
     """ Get the liquids in the top `top_volume` uL """
 
     if top_volume > self.get_used_volume():

pylabrobot/server/liquid_handling_server.py

@@ -5,16 +5,16 @@
 import json
 import os
 import threading
-from typing import Any, Coroutine, List, Tuple, Type, TypeVar, Optional, cast
+from typing import Any, Coroutine, List, Tuple, Type, Optional, cast
 
 from flask import Blueprint, Flask, request, jsonify, current_app
 import werkzeug
 
 from pylabrobot.liquid_handling import LiquidHandler
 from pylabrobot.liquid_handling.backends.backend import LiquidHandlerBackend
-from pylabrobot.liquid_handling.standard import PipettingOp, Pickup, Aspiration, Dispense, Drop
+from pylabrobot.liquid_handling.standard import Pickup, Aspiration, Dispense, Drop
 from pylabrobot.resources import Coordinate, Deck, Tip, Liquid
-from pylabrobot.serializer import serialize, deserialize
+from pylabrobot.serializer import deserialize
 
 
 lh_api = Blueprint("liquid handling", __name__)
@@ -191,7 +191,7 @@ async def aspirate():
       flow_rate = sc["flow_rate"]
       liquid_height = sc["liquid_height"]
       blow_out_air_volume = sc["blow_out_air_volume"]
-      liquids = cast(List[Liquid], deserialize(sc["liquids"]))
+      liquids = cast(Type[List[Tuple[Liquid | None, float]]], deserialize(sc["liquids"]))
       aspirations.append(Aspiration(resource=resource, tip=tip, offset=offset, volume=volume,
         flow_rate=flow_rate, liquid_height=liquid_height, blow_out_air_volume=blow_out_air_volume,
         liquids=liquids))
@@ -228,7 +228,7 @@ async def dispense():
       flow_rate = sc["flow_rate"]
       liquid_height = sc["liquid_height"]
       blow_out_air_volume = sc["blow_out_air_volume"]
-      liquids = cast(Type[Liquid], deserialize(sc["liquids"]))
+      liquids = cast(Type[List[Tuple[Liquid | None, float]]], deserialize(sc["liquids"]))
       dispenses.append(Dispense(resource=resource, tip=tip, offset=offset, volume=volume,
         flow_rate=flow_rate, liquid_height=liquid_height, blow_out_air_volume=blow_out_air_volume,
         liquids=liquids))