more chatterboxes (#242)

PyLabRobot · Sep 11, 2024 · 5826c73 · 5826c73
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,6 +34,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `PlateCarrierSite` can now take `ResourceStack` as a child, as long as the children are `Plate`s (https://github.com/PyLabRobot/pylabrobot/pull/226)
 - `Resource.get_size_{x,y,z}` now return the size of the resource in local space, not absolute space (https://github.com/PyLabRobot/pylabrobot/pull/235)
 - `Resource.center` now returns the center of the resource in local space, not absolute space (https://github.com/PyLabRobot/pylabrobot/pull/235)
+- Rename `ChatterBoxBackend` to `LiquidHandlerChatterboxBackend` (https://github.com/PyLabRobot/pylabrobot/pull/242)
+- Move `LiquidHandlerChatterboxBackend` from `liquid_handling.backends.chatterbox_backend` to `liquid_handling.backends.chatterbox` (https://github.com/PyLabRobot/pylabrobot/pull/242)
 
 ### Added
 
@@ -61,6 +63,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `HTF_L_ULTRAWIDE`, `ultrawide_high_volume_tip_with_filter` (https://github.com/PyLabRobot/pylabrobot/pull/229/)
 - `get_absolute_size_x`, `get_absolute_size_y`, `get_absolute_size_z` for `Resource` (https://github.com/PyLabRobot/pylabrobot/pull/235)
 - `Cytation5Backend` for plate reading on BioTek Cytation 5 (https://github.com/PyLabRobot/pylabrobot/pull/238)
+- More chatterboxes (https://github.com/PyLabRobot/pylabrobot/pull/242)
+  - `FanChatterboxBackend`
+  - `PlateReaderChatterboxBackend`
+  - `PowderDispenserChatterboxBackend`
+  - `PumpChatterboxBackend`
+  - `PumpArrayChatterboxBackend`
+  - `ScaleChatterboxBackend`
+  - `ShakerChatterboxBackend`
+  - `TemperatureControllerChatterboxBackend`
 
 ### Deprecated
 

diff --git a/docs/pylabrobot.heating_shaking.rst b/docs/pylabrobot.heating_shaking.rst
@@ -21,4 +21,5 @@ Backends
   :nosignatures:
   :recursive:
 
+    chatterbox.HeaterShakerChatterboxBackend
     inheco.InhecoThermoShake
diff --git a/docs/pylabrobot.liquid_handling.backends.rst b/docs/pylabrobot.liquid_handling.backends.rst
@@ -52,4 +52,4 @@ Testing
   :nosignatures:
   :recursive:
 
-    backends.chatterbox_backend.ChatterBoxBackend
+    backends.chatterbox.LiquidHandlerChatterboxBackend
diff --git a/docs/pylabrobot.only_fans.rst b/docs/pylabrobot.only_fans.rst
@@ -22,4 +22,5 @@ Backends
   :recursive:
 
     backend.FanBackend
+    chatterbox.FanChatterboxBackend
     hamilton_hepa_fan.HamiltonHepaFan
diff --git a/docs/pylabrobot.plate_reading.rst b/docs/pylabrobot.plate_reading.rst
@@ -21,4 +21,5 @@ Backends
   :nosignatures:
   :recursive:
 
+    chatterbox.PlateReaderChatterboxBackend
     clario_star.CLARIOStar
diff --git a/docs/pylabrobot.pumps.rst b/docs/pylabrobot.pumps.rst
@@ -21,4 +21,5 @@ Backends
   :nosignatures:
   :recursive:
 
+    chatterbox.PumpChatterboxBackend
     cole_parmer.masterflex.Masterflex
diff --git a/docs/pylabrobot.scales.rst b/docs/pylabrobot.scales.rst
@@ -21,4 +21,5 @@ Backends
   :nosignatures:
   :recursive:
 
+    chatterbox.ScaleChatterboxBackend
     mettler_toledo.MettlerToledoWXS205SDU
diff --git a/docs/pylabrobot.shaking.rst b/docs/pylabrobot.shaking.rst
@@ -22,3 +22,4 @@ Backends
   :recursive:
 
     backend.ShakerBackend
+    chatterbox.ShakerChatterboxBackend
diff --git a/docs/pylabrobot.temperature_controlling.rst b/docs/pylabrobot.temperature_controlling.rst
@@ -22,4 +22,5 @@ Backends
   :nosignatures:
   :recursive:
 
+    chatterbox.TemperatureControllerChatterboxBackend
     opentrons_backend.OpentronsTemperatureModuleBackend
diff --git a/docs/pylabrobot.tilting.rst b/docs/pylabrobot.tilting.rst
@@ -21,5 +21,6 @@ Backends
   :nosignatures:
   :recursive:
 
+    chatterbox.TilterChatterboxBackend
     tilter_backend.TilterBackend
     hamilton_backend.HamiltonTiltModuleBackend
diff --git a/docs/using-the-visualizer.ipynb b/docs/using-the-visualizer.ipynb
@@ -9,7 +9,7 @@
     "\n",
     "The Visualizer is a tool that allows you to visualize the a Resource (like LiquidHandler) including its state to easily see what is going on, for example when executing a protocol on a robot or when developing a new protocol.\n",
     "\n",
-    "When using a backend that does not require access to a physical robot, such as the {class}`~pylabrobot.liquid_handling.backends.chatterbox_backend.ChatterBoxBackend`, the Visualizer can be used to simulate a robot's behavior. Of course, you may also use the Visualizer when working with a real robot to see what is happening in the PLR resource and state trackers."
+    "When using a backend that does not require access to a physical robot, such as the {class}`~pylabrobot.liquid_handling.backends.chatterbox_backend.ChatterboxBackend`, the Visualizer can be used to simulate a robot's behavior. Of course, you may also use the Visualizer when working with a real robot to see what is happening in the PLR resource and state trackers."
    ]
   },
   {
@@ -20,7 +20,7 @@
    "source": [
     "## Setting up a connection with the robot\n",
     "\n",
-    "As described in the [basic liquid handling tutorial](basic), we will use the {class}`~pylabrobot.liquid_handling.liquid_handler.LiquidHandler` class to control the robot. This time, however, instead of using the Hamilton {class}`~pylabrobot.liquid_handling.backends.hamilton.STAR.STAR` backend, we are using the software-only {class}`~pylabrobot.liquid_handling.backends.chatterbox_backend.ChatterBoxBackend` backend. This means that liquid handling will work exactly the same, but commands are simply printed out to the console instead of being sent to a physical robot. We are still using the same deck."
+    "As described in the [basic liquid handling tutorial](basic), we will use the {class}`~pylabrobot.liquid_handling.liquid_handler.LiquidHandler` class to control the robot. This time, however, instead of using the Hamilton {class}`~pylabrobot.liquid_handling.backends.hamilton.STAR.STAR` backend, we are using the software-only {class}`~pylabrobot.liquid_handling.backends.chatterbox_backend.ChatterboxBackend` backend. This means that liquid handling will work exactly the same, but commands are simply printed out to the console instead of being sent to a physical robot. We are still using the same deck."
    ]
   },
   {
@@ -31,7 +31,7 @@
    "outputs": [],
    "source": [
     "from pylabrobot.liquid_handling import LiquidHandler\n",
-    "from pylabrobot.liquid_handling.backends import ChatterBoxBackend\n",
+    "from pylabrobot.liquid_handling.backends import ChatterboxBackend\n",
     "from pylabrobot.visualizer.visualizer import Visualizer"
    ]
   },
@@ -52,7 +52,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lh = LiquidHandler(backend=ChatterBoxBackend(), deck=STARLetDeck())"
+    "lh = LiquidHandler(backend=ChatterboxBackend(), deck=STARLetDeck())"
    ]
   },
   {
@@ -384,7 +384,7 @@
    "source": [
     "### Picking up tips\n",
     "\n",
-    "Note that since we are using the {class}`~pylabrobot.liquid_handling.backends.chatterbox_backend.ChatterBoxBackend`, we just print out \"Picking up tips\" instead of actually performing an operation. The visualizer will show the tips being picked up."
+    "Note that since we are using the {class}`~pylabrobot.liquid_handling.backends.chatterbox_backend.ChatterboxBackend`, we just print out \"Picking up tips\" instead of actually performing an operation. The visualizer will show the tips being picked up."
    ]
   },
   {

diff --git a/docs/using-trackers.ipynb b/docs/using-trackers.ipynb
@@ -28,7 +28,7 @@
       ],
       "source": [
         "from pylabrobot.liquid_handling import LiquidHandler\n",
-        "from pylabrobot.liquid_handling.backends.chatterbox_backend import ChatterBoxBackend\n",
+        "from pylabrobot.liquid_handling.backends.chatterbox_backend import ChatterboxBackend\n",
         "from pylabrobot.resources import (\n",
         "  TIP_CAR_480_A00,\n",
         "  HTF_L,\n",
@@ -39,7 +39,7 @@
         ")\n",
         "from pylabrobot.resources.hamilton import STARLetDeck\n",
         "\n",
-        "lh = LiquidHandler(backend=ChatterBoxBackend(num_channels=8), deck=STARLetDeck())\n",
+        "lh = LiquidHandler(backend=ChatterboxBackend(num_channels=8), deck=STARLetDeck())\n",
         "await lh.setup()"
       ]
     },

diff --git a/pylabrobot/heating_shaking/chatterbox.py b/pylabrobot/heating_shaking/chatterbox.py
@@ -0,0 +1,7 @@
+from pylabrobot.shaking.chatterbox import ShakerChatterboxBackend
+from pylabrobot.temperature_controlling.chatterbox import TemperatureControllerChatterboxBackend
+
+
+class HeaterShakerChatterboxBackend(
+  ShakerChatterboxBackend, TemperatureControllerChatterboxBackend):
+  pass
diff --git a/pylabrobot/liquid_handling/backends/__init__.py b/pylabrobot/liquid_handling/backends/__init__.py
@@ -1,4 +1,5 @@
 from .backend import LiquidHandlerBackend
+from .chatterbox import LiquidHandlerChatterboxBackend
 from .chatterbox_backend import ChatterBoxBackend
 from .serializing_backend import SerializingBackend, SerializingSavingBackend # many rely on this
 from .websocket import WebSocketBackend

diff --git a/pylabrobot/liquid_handling/backends/chatterbox.py b/pylabrobot/liquid_handling/backends/chatterbox.py
@@ -0,0 +1,218 @@
+# pylint: disable=unused-argument, inconsistent-quotes
+
+from typing import List, Union
+
+from pylabrobot.liquid_handling.backends.backend import LiquidHandlerBackend
+from pylabrobot.resources import Resource
+from pylabrobot.liquid_handling.standard import (
+  Pickup,
+  PickupTipRack,
+  Drop,
+  DropTipRack,
+  Aspiration,
+  AspirationPlate,
+  AspirationContainer,
+  Dispense,
+  DispensePlate,
+  DispenseContainer,
+  Move
+)
+
+
+class LiquidHandlerChatterboxBackend(LiquidHandlerBackend):
+  """ Chatter box backend for device-free testing. Prints out all operations. """
+
+  _pip_length = 5
+  _vol_length = 8
+  _resource_length = 20
+  _offset_length = 16
+  _flow_rate_length = 10
+  _blowout_length = 10
+  _lld_z_length = 10
+  _kwargs_length = 15
+  _tip_type_length = 12
+  _max_volume_length = 16
+  _fitting_depth_length = 20
+  _tip_length_length = 16
+  # _pickup_method_length = 20
+  _filter_length = 10
+
+  def __init__(self, num_channels: int = 8):
+    """ Initialize a chatter box backend. """
+    super().__init__()
+    self._num_channels = num_channels
+
+  async def setup(self):
+    await super().setup()
+    print("Setting up the liquid handler.")
+
+  async def stop(self):
+    print("Stopping the liquid handler.")
+
+  def serialize(self) -> dict:
+    return {**super().serialize(), "num_channels": self.num_channels}
+
+  @property
+  def num_channels(self) -> int:
+    return self._num_channels
+
+  async def assigned_resource_callback(self, resource: Resource):
+    print(f"Resource {resource.name} was assigned to the liquid handler.")
+
+  async def unassigned_resource_callback(self, name: str):
+    print(f"Resource {name} was unassigned from the liquid handler.")
+
+  async def pick_up_tips(self, ops: List[Pickup], use_channels: List[int], **backend_kwargs):
+    print("Picking up tips:")
+    header = (
+      f"{'pip#':<{LiquidHandlerChatterboxBackend._pip_length}} "
+      f"{'resource':<{LiquidHandlerChatterboxBackend._resource_length}} "
+      f"{'offset':<{LiquidHandlerChatterboxBackend._offset_length}} "
+      f"{'tip type':<{LiquidHandlerChatterboxBackend._tip_type_length}} "
+      f"{'max volume (µL)':<{LiquidHandlerChatterboxBackend._max_volume_length}} "
+      f"{'fitting depth (mm)':<{LiquidHandlerChatterboxBackend._fitting_depth_length}} "
+      f"{'tip length (mm)':<{LiquidHandlerChatterboxBackend._tip_length_length}} "
+      # f"{'pickup method':<{ChatterboxBackend._pickup_method_length}} "
+      f"{'filter':<{LiquidHandlerChatterboxBackend._filter_length}}"
+    )
+    print(header)
+
+    for op, channel in zip(ops, use_channels):
+      offset = f"{round(op.offset.x, 1)},{round(op.offset.y, 1)},{round(op.offset.z, 1)}"
+      row = (
+        f"  p{channel}: "
+        f"{op.resource.name[-30:]:<{LiquidHandlerChatterboxBackend._resource_length}} "
+        f"{offset:<{LiquidHandlerChatterboxBackend._offset_length}} "
+        f"{op.tip.__class__.__name__:<{LiquidHandlerChatterboxBackend._tip_type_length}} "
+        f"{op.tip.maximal_volume:<{LiquidHandlerChatterboxBackend._max_volume_length}} "
+        f"{op.tip.fitting_depth:<{LiquidHandlerChatterboxBackend._fitting_depth_length}} "
+        f"{op.tip.total_tip_length:<{LiquidHandlerChatterboxBackend._tip_length_length}} "
+        # f"{str(op.tip.pickup_method)[-20:]:<{ChatterboxBackend._pickup_method_length}} "
+        f"{'Yes' if op.tip.has_filter else 'No':<{LiquidHandlerChatterboxBackend._filter_length}}"
+      )
+      print(row)
+
+  async def drop_tips(self, ops: List[Drop], use_channels: List[int], **backend_kwargs):
+    print("Dropping tips:")
+    header = (
+      f"{'pip#':<{LiquidHandlerChatterboxBackend._pip_length}} "
+      f"{'resource':<{LiquidHandlerChatterboxBackend._resource_length}} "
+      f"{'offset':<{LiquidHandlerChatterboxBackend._offset_length}} "
+      f"{'tip type':<{LiquidHandlerChatterboxBackend._tip_type_length}} "
+      f"{'max volume (µL)':<{LiquidHandlerChatterboxBackend._max_volume_length}} "
+      f"{'fitting depth (mm)':<{LiquidHandlerChatterboxBackend._fitting_depth_length}} "
+      f"{'tip length (mm)':<{LiquidHandlerChatterboxBackend._tip_length_length}} "
+      # f"{'pickup method':<{ChatterboxBackend._pickup_method_length}} "
+      f"{'filter':<{LiquidHandlerChatterboxBackend._filter_length}}"
+    )
+    print(header)
+
+    for op, channel in zip(ops, use_channels):
+      offset = f"{round(op.offset.x, 1)},{round(op.offset.y, 1)},{round(op.offset.z, 1)}"
+      row = (
+        f"  p{channel}: "
+        f"{op.resource.name[-30:]:<{LiquidHandlerChatterboxBackend._resource_length}} "
+        f"{offset:<{LiquidHandlerChatterboxBackend._offset_length}} "
+        f"{op.tip.__class__.__name__:<{LiquidHandlerChatterboxBackend._tip_type_length}} "
+        f"{op.tip.maximal_volume:<{LiquidHandlerChatterboxBackend._max_volume_length}} "
+        f"{op.tip.fitting_depth:<{LiquidHandlerChatterboxBackend._fitting_depth_length}} "
+        f"{op.tip.total_tip_length:<{LiquidHandlerChatterboxBackend._tip_length_length}} "
+        # f"{str(op.tip.pickup_method)[-20:]:<{ChatterboxBackend._pickup_method_length}} "
+        f"{'Yes' if op.tip.has_filter else 'No':<{LiquidHandlerChatterboxBackend._filter_length}}"
+      )
+      print(row)
+
+  async def aspirate(self, ops: List[Aspiration], use_channels: List[int], **backend_kwargs):
+    print("Aspirating:")
+    header = (
+      f"{'pip#':<{LiquidHandlerChatterboxBackend._pip_length}} "
+      f"{'vol(ul)':<{LiquidHandlerChatterboxBackend._vol_length}} "
+      f"{'resource':<{LiquidHandlerChatterboxBackend._resource_length}} "
+      f"{'offset':<{LiquidHandlerChatterboxBackend._offset_length}} "
+      f"{'flow rate':<{LiquidHandlerChatterboxBackend._flow_rate_length}} "
+      f"{'blowout':<{LiquidHandlerChatterboxBackend._blowout_length}} "
+      f"{'lld_z':<{LiquidHandlerChatterboxBackend._lld_z_length}}  "
+      # f"{'liquids':<20}" # TODO: add liquids
+    )
+    for key in backend_kwargs:
+      header += f"{key:<{LiquidHandlerChatterboxBackend._kwargs_length}} "[-16:]
+    print(header)
+
+    for o, p in zip(ops, use_channels):
+      offset = f"{round(o.offset.x, 1)},{round(o.offset.y, 1)},{round(o.offset.z, 1)}"
+      row = (
+        f"  p{p}: "
+        f"{o.volume:<{LiquidHandlerChatterboxBackend._vol_length}} "
+        f"{o.resource.name[-20:]:<{LiquidHandlerChatterboxBackend._resource_length}} "
+        f"{offset:<{LiquidHandlerChatterboxBackend._offset_length}} "
+        f"{str(o.flow_rate):<{LiquidHandlerChatterboxBackend._flow_rate_length}} "
+        f"{str(o.blow_out_air_volume):<{LiquidHandlerChatterboxBackend._blowout_length}} "
+        f"{str(o.liquid_height):<{LiquidHandlerChatterboxBackend._lld_z_length}} "
+        # f"{o.liquids if o.liquids is not None else 'none'}"
+      )
+      for key, value in backend_kwargs.items():
+        if isinstance(value, list) and all(isinstance(v, bool) for v in value):
+          value = "".join("T" if v else "F" for v in value)
+        if isinstance(value, list):
+          value = "".join(map(str, value))
+        row += f" {value:<15}"
+      print(row)
+
+  async def dispense(self, ops: List[Dispense], use_channels: List[int], **backend_kwargs):
+    print("Dispensing:")
+    header = (
+      f"{'pip#':<{LiquidHandlerChatterboxBackend._pip_length}} "
+      f"{'vol(ul)':<{LiquidHandlerChatterboxBackend._vol_length}} "
+      f"{'resource':<{LiquidHandlerChatterboxBackend._resource_length}} "
+      f"{'offset':<{LiquidHandlerChatterboxBackend._offset_length}} "
+      f"{'flow rate':<{LiquidHandlerChatterboxBackend._flow_rate_length}} "
+      f"{'blowout':<{LiquidHandlerChatterboxBackend._blowout_length}} "
+      f"{'lld_z':<{LiquidHandlerChatterboxBackend._lld_z_length}}  "
+      # f"{'liquids':<20}" # TODO: add liquids
+    )
+    for key in backend_kwargs:
+      header += f"{key:<{LiquidHandlerChatterboxBackend._kwargs_length}} "[-16:]
+    print(header)
+
+    for o, p in zip(ops, use_channels):
+      offset = f"{round(o.offset.x, 1)},{round(o.offset.y, 1)},{round(o.offset.z, 1)}"
+      row = (
+        f"  p{p}: "
+        f"{o.volume:<{LiquidHandlerChatterboxBackend._vol_length}} "
+        f"{o.resource.name[-20:]:<{LiquidHandlerChatterboxBackend._resource_length}} "
+        f"{offset:<{LiquidHandlerChatterboxBackend._offset_length}} "
+        f"{str(o.flow_rate):<{LiquidHandlerChatterboxBackend._flow_rate_length}} "
+        f"{str(o.blow_out_air_volume):<{LiquidHandlerChatterboxBackend._blowout_length}} "
+        f"{str(o.liquid_height):<{LiquidHandlerChatterboxBackend._lld_z_length}} "
+        # f"{o.liquids if o.liquids is not None else 'none'}"
+      )
+      for key, value in backend_kwargs.items():
+        if isinstance(value, list) and all(isinstance(v, bool) for v in value):
+          value = ''.join('T' if v else 'F' for v in value)
+        if isinstance(value, list):
+          value = "".join(map(str, value))
+        row += f" {value:<{LiquidHandlerChatterboxBackend._kwargs_length}}"
+      print(row)
+
+  async def pick_up_tips96(self, pickup: PickupTipRack, **backend_kwargs):
+    print(f"Picking up tips from {pickup.resource.name}.")
+
+  async def drop_tips96(self, drop: DropTipRack, **backend_kwargs):
+    print(f"Dropping tips to {drop.resource.name}.")
+
+  async def aspirate96(self, aspiration: Union[AspirationPlate, AspirationContainer]):
+    if isinstance(aspiration, AspirationPlate):
+      resource = aspiration.wells[0].parent
+    else:
+      resource = aspiration.container
+    print(f"Aspirating {aspiration.volume} from {resource}.")
+
+  async def dispense96(self, dispense: Union[DispensePlate, DispenseContainer]):
+    if isinstance(dispense, DispensePlate):
+      resource = dispense.wells[0].parent
+    else:
+      resource = dispense.container
+    print(f"Dispensing {dispense.volume} to {resource}.")
+
+  async def move_resource(self, move: Move, **backend_kwargs):
+    print(f"Moving {move}.")