lint, typo, type (not tests yet)

Author: rickwierenga

pylabrobot/liquid_handling/liquid_classes/hamilton/star.py

@@ -4215,7 +4215,7 @@ def get_star_liquid_class(
 # - a break time after dispense with about 10s time counter, makes sure the drop which  residue
 #   after dispense drops back into the probetube
 # - some droplets on tip after dispense are also with more air transport volume not avoidable
-# - sometimes it helpes using Filtertips
+# - sometimes it helps to use Filtertips
 # - Correction Curve is taken from MeOH Liqiudclass
 #
 #
@@ -5581,7 +5581,7 @@ def get_star_liquid_class(
 # - To protect, the distance from Asp. to Disp. should be as short as possible,
 #   because MeOH could be drop out in a long way!
 # - some droplets on tip after dispense are also with more air transport volume not avoidable
-# - sometimes it helpes using Filtertips
+# - sometimes it helps to use Filtertips
 #
 #
 #
@@ -5633,7 +5633,7 @@ def get_star_liquid_class(
 # - To protect, the distance from Asp. to Disp. should be as short as possible,
 #   because MeOH could be drop out in a long way!
 # - some droplets on tip after dispense are also with more air transport volume not avoidable
-# - sometimes it helpes using Filtertips
+# - sometimes it helps to use Filtertips
 #
 #
 #
@@ -12002,7 +12002,7 @@ def get_star_liquid_class(
 # - To protect, the distance from Asp. to Disp. should be as short as possible( about 12slot),
 #   because MeOH could  drop out in a long way!
 # - some droplets on tip after dispense are also with more air transport volume not avoidable
-# - sometimes it helpes using Filtertips
+# - sometimes it helps to use Filtertips
 #
 #
 #
@@ -12054,7 +12054,7 @@ def get_star_liquid_class(
 # - To protect, the distance from Asp. to Disp. should be as short as possible( about 12slot),
 #   because MeOH could  drop out in a long way!
 # - some droplets on tip after dispense are also with more air transport volume not avoidable
-# - sometimes it helpes using Filtertips
+# - sometimes it helps to use Filtertips
 #
 #
 #

pylabrobot/liquid_handling/liquid_classes/hamilton/vantage.py

@@ -10988,7 +10988,7 @@ def get_vantage_liquid_class(
 # - To protect, the distance from Asp. to Disp. should be as short as possible( about 12slot),
 #   because MeOH could  drop out in a long way!
 # - some droplets on tip after dispense are also with more air transport volume not avoidable
-# - sometimes it helpes using Filtertips
+# - sometimes it helps to use Filtertips
 #
 #
 #
@@ -11040,7 +11040,7 @@ def get_vantage_liquid_class(
 # - To protect, the distance from Asp. to Disp. should be as short as possible( about 12slot),
 #   because MeOH could  drop out in a long way!
 # - some droplets on tip after dispense are also with more air transport volume not avoidable
-# - sometimes it helpes using Filtertips
+# - sometimes it helps to use Filtertips
 #
 #
 #

pylabrobot/plate_reading/__init__.py

@@ -1,6 +1,11 @@
 from .biotek_backend import Cytation5Backend, Cytation5ImagingConfig
-from .byonoy_backend import ByonoyAbsorbance96AutomateBackend, ByonoyFluorescence96AutomateBackend
-from .clario_star_backend import CLARIOstarBackend
+from .byonoy import (
+  ByonoyAbsorbance96AutomateBackend,
+  ByonoyLuminescence96AutomateBackend,
+  byonoy_absorbance96_base_and_reader,
+  byonoy_absorbance_adapter,
+)
+from .clario_star_backend import CLARIOStarBackend
 from .image_reader import ImageReader
 from .imager import Imager
 from .plate_reader import PlateReader

pylabrobot/plate_reading/byonoy/__init__.py

@@ -1,2 +1,2 @@
-from .byonoy import byonoy_luminescence96_base_and_reader, byonoy_luminescence_adapter
+from .byonoy import byonoy_absorbance96_base_and_reader, byonoy_absorbance_adapter
 from .byonoy_backend import ByonoyAbsorbance96AutomateBackend, ByonoyLuminescence96AutomateBackend

pylabrobot/plate_reading/byonoy/byonoy.py

@@ -5,7 +5,7 @@
 from pylabrobot.resources import Coordinate, PlateHolder, Resource, ResourceHolder
 
 
-def byonoy_luminescence_adapter(name: str) -> ResourceHolder:
+def byonoy_absorbance_adapter(name: str) -> ResourceHolder:
   return ResourceHolder(
     name=name,
     size_x=127.76,  # measured
@@ -90,7 +90,9 @@ def __init__(self, name, rotation=None, category=None, model=None, barcode=None)
     )
     self.assign_child_resource(self.reader_holder, location=Coordinate.zero())
 
-  def assign_child_resource(self, resource: Resource, location: Coordinate, reassign=True):
+  def assign_child_resource(
+    self, resource: Resource, location: Optional[Coordinate], reassign=True
+  ):
     if isinstance(resource, _ByonoyAbsorbanceReaderPlateHolder):
       if self.plate_holder._byonoy_base is not None:
         raise ValueError("ByonoyBase can only have one plate holder assigned.")
@@ -104,7 +106,7 @@ def check_can_drop_resource_here(self, resource: Resource) -> None:
     )
 
 
-def byonoy_luminescence96_base_and_reader(name: str, assign=True) -> Tuple[ByonoyBase, PlateReader]:
+def byonoy_absorbance96_base_and_reader(name: str, assign=True) -> Tuple[ByonoyBase, PlateReader]:
   """Creates a ByonoyBase and a PlateReader instance."""
   byonoy_base = ByonoyBase(name=name + "_base")
   reader = PlateReader(

pylabrobot/plate_reading/byonoy/byonoy_backend.py

@@ -8,7 +8,6 @@
 
 from pylabrobot.io.hid import HID
 from pylabrobot.plate_reading.backend import PlateReaderBackend
-from pylabrobot.plate_reading.byonoy.parser import encode_hid_report, parse_hid_report
 from pylabrobot.resources.plate import Plate
 from pylabrobot.utils.list import reshape_2d
 
@@ -102,11 +101,9 @@ async def _ping_loop(self) -> None:
     """Main ping loop that runs in the background thread."""
     while not self._stop_background.is_set():
       if self._sending_pings:
-        cmd = b"\x00" + encode_hid_report(
-          {"report_id": 64, "payload_name": "HEARTBEAT_IN", "payload": {"enabled": 1}}
-        )
-        await self.io.write(cmd)
         # don't read in background thread, data might get lost here
+        # not needed?
+        pass
 
       self._stop_background.wait(self._ping_interval)
 

pylabrobot/plate_reading/byonoy/byonoy_tests.py

@@ -1,28 +1,24 @@
 import unittest
 import unittest.mock
 
-from pylabrobot.liquid_handling import (
-  LiquidHandler,
-  LiquidHandlerBackend,
-  LiquidHandlerChatterboxBackend,
-)
+from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend
 from pylabrobot.plate_reading.byonoy import (
-  byonoy_luminescence96_base_and_reader,
-  byonoy_luminescence_adapter,
+  byonoy_absorbance96_base_and_reader,
+  byonoy_absorbance_adapter,
 )
 from pylabrobot.resources import PLT_CAR_L5_DWP, CellVis_96_wellplate_350uL_Fb, Coordinate, STARDeck
 
 
 class ByonoyResourceTests(unittest.IsolatedAsyncioTestCase):
   async def asyncSetUp(self):
-    self.base, self.reader = byonoy_luminescence96_base_and_reader(name="byonoy_test", assign=True)
-    self.adapter = byonoy_luminescence_adapter(name="byonoy_test_adapter")
+    self.base, self.reader = byonoy_absorbance96_base_and_reader(name="byonoy_test", assign=True)
+    self.adapter = byonoy_absorbance_adapter(name="byonoy_test_adapter")
 
-    self.lh = LiquidHandler(deck=STARDeck(), backend=unittest.mock.Mock(spec=LiquidHandlerBackend))
-    # self.lh = LiquidHandler(deck=STARDeck(), backend=LiquidHandlerChatterboxBackend())
+    self.deck = STARDeck()
+    self.lh = LiquidHandler(deck=self.deck, backend=unittest.mock.Mock(spec=LiquidHandlerBackend))
     self.plate_carrier = PLT_CAR_L5_DWP(name="plate_carrier")
     self.plate_carrier[1] = self.adapter
-    self.lh.deck.assign_child_resource(self.plate_carrier, rails=28)
+    self.deck.assign_child_resource(self.plate_carrier, rails=28)
     self.adapter.assign_child_resource(self.base)
     self.plate_carrier[2] = self.plate = CellVis_96_wellplate_350uL_Fb(name="plate")