rename deprecated {STAR,Vantage}->Backend

Author: rickwierenga

README.md

@@ -31,11 +31,11 @@ Here's a quick example showing how to move 100uL of liquid from well A1 to A2 us
 
 ```python
 from pylabrobot.liquid_handling import LiquidHandler
-from pylabrobot.liquid_handling.backends import STAR
+from pylabrobot.liquid_handling.backends import STARBackend
 from pylabrobot.resources import Deck
 
 deck = Deck.load_from_json_file("hamilton-layout.json")
-lh = LiquidHandler(backend=STAR(), deck=deck)
+lh = LiquidHandler(backend=STARBackend(), deck=deck)
 await lh.setup()
 
 await lh.pick_up_tips(lh.deck.get_resource("tip_rack")["A1"])
@@ -69,9 +69,9 @@ We also provide a browser-based Visualizer which can visualize the state of the
 Moving a plate to a ClarioStar using a liquid handler, and reading luminescence:
 
 ```python
-from pylabrobot.plate_reading import PlateReader, ClarioStar
+from pylabrobot.plate_reading import PlateReader, CLARIOstarBackend
 
-pr = PlateReader(name="plate reader", backend=ClarioStar(), size_x=1, size_y=1, size_z=1)
+pr = PlateReader(name="plate reader", backend=CLARIOstarBackend(), size_x=1, size_y=1, size_z=1)
 await pr.setup()
 
 # Use in combination with a liquid handler

docs/user_guide/00_liquid-handling/hamilton-star/96head.ipynb

@@ -25,11 +25,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pylabrobot.liquid_handling import LiquidHandler, STAR\n",
+    "from pylabrobot.liquid_handling import LiquidHandler, STARBackend\n",
     "from pylabrobot.resources import STARLetDeck\n",
     "from pylabrobot.resources import (\n",
     "  TIP_CAR_480_A00,\n",
@@ -38,7 +38,7 @@
     "  Cor_96_wellplate_360ul_Fb\n",
     ")\n",
     "\n",
-    "lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())\n",
+    "lh = LiquidHandler(backend=STARBackend(), deck=STARLetDeck())\n",
     "await lh.setup()\n",
     "\n",
     "# assign a tip rack\n",

docs/user_guide/00_liquid-handling/hamilton-star/foil.ipynb

@@ -25,11 +25,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pylabrobot.liquid_handling import LiquidHandler, STAR\n",
+    "from pylabrobot.liquid_handling import LiquidHandler, STARBackend\n",
     "from pylabrobot.resources import STARLetDeck\n",
     "from pylabrobot.resources import (\n",
     "  TIP_CAR_480_A00,\n",
@@ -38,7 +38,7 @@
     "  AGenBio_4_wellplate_Vb\n",
     ")\n",
     "\n",
-    "star = STAR()\n",
+    "star = STARBackend()\n",
     "lh = LiquidHandler(backend=star, deck=STARLetDeck())\n",
     "await lh.setup()\n",
     "\n",

docs/user_guide/00_liquid-handling/hamilton-star/z-probing.ipynb

@@ -23,11 +23,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pylabrobot.liquid_handling import LiquidHandler, STAR\n",
+    "from pylabrobot.liquid_handling import LiquidHandler, STARBackend\n",
     "from pylabrobot.resources import STARLetDeck\n",
     "from pylabrobot.resources import (\n",
     "  TIP_CAR_480_A00,\n",
@@ -36,7 +36,7 @@
     "  Cor_96_wellplate_360ul_Fb\n",
     ")\n",
     "\n",
-    "star = STAR()\n",
+    "star = STARBackend()\n",
     "lh = LiquidHandler(backend=star, deck=STARLetDeck())\n",
     "await lh.setup()\n",
     "\n",

docs/user_guide/00_liquid-handling/moving-channels-around.ipynb

@@ -37,10 +37,10 @@
       "metadata": {},
       "outputs": [],
       "source": [
-        "from pylabrobot.liquid_handling import LiquidHandler, STAR\n",
+        "from pylabrobot.liquid_handling import LiquidHandler, STARBackend\n",
         "from pylabrobot.resources import STARDeck, TIP_CAR_480_A00, hamilton_96_tiprack_1000ul_filter\n",
         "\n",
-        "lh = LiquidHandler(backend=STAR(), deck=STARDeck())\n",
+        "lh = LiquidHandler(backend=STARBackend(), deck=STARDeck())\n",
         "await lh.setup()\n",
         "\n",
         "# assign a tip rack\n",

docs/user_guide/machine-agnostic-features/validation.ipynb

@@ -26,16 +26,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import pylabrobot\n",
     "from pylabrobot.liquid_handling import LiquidHandler\n",
-    "from pylabrobot.liquid_handling.backends import STAR\n",
+    "from pylabrobot.liquid_handling.backends import STARBackend\n",
     "from pylabrobot.resources.hamilton import STARDeck\n",
     "\n",
-    "backend = STAR()\n",
+    "backend = STARBackend()\n",
     "lh = LiquidHandler(backend=backend, deck=STARDeck())"
    ]
   },

docs/user_guide/machine-agnostic-features/writing-robot-agnostic-protocols.md

@@ -9,7 +9,7 @@ This document describes best practices for writing methods that are agnostic to
 It is recommended to keep the layout of the deck separate from the protocol. This allows you to easily change the layout of the deck without having to change the protocol.
 
 ```py
-from pylabrobot.liquid_handling import LiquidHandler, STAR
+from pylabrobot.liquid_handling import LiquidHandler, STARBackend
 from pylabrobot.resources import Deck, TipRack, Plate
 
 # Write a method that creates a deck and defines its layout.
@@ -23,7 +23,7 @@ def make_deck() -> Deck:
 
 # Instantiate the liquid handler using a deck and backend.
 deck = make_deck()
-backend = STAR()
+backend = STARBackend()
 lh = LiquidHandler(backend=backend, deck=deck)
 
 # Get references to the resources you need. Use type hinting for autocompletion.

pylabrobot/liquid_handling/backends/hamilton/STAR_tests.py

@@ -29,10 +29,10 @@
 from pylabrobot.resources.hamilton import STARLetDeck, hamilton_96_tiprack_300uL_filter
 
 from .STAR_backend import (
-  STAR,
   CommandSyntaxError,
   HamiltonNoTipError,
   HardwareError,
+  STARBackend,
   STARFirmwareError,
   UnknownHamiltonError,
   parse_star_fw_string,
@@ -44,7 +44,7 @@ class TestSTARResponseParsing(unittest.TestCase):
 
   def setUp(self):
     super().setUp()
-    self.star = STAR()
+    self.star = STARBackend()
 
   def test_parse_response_params(self):
     parsed = parse_star_fw_string("C0QMid1111", "")
@@ -144,7 +144,7 @@ class TestSTARUSBComms(unittest.IsolatedAsyncioTestCase):
   """Test that USB data is parsed correctly."""
 
   async def asyncSetUp(self):
-    self.star = STAR(read_timeout=2, packet_read_timeout=1)
+    self.star = STARBackend(read_timeout=2, packet_read_timeout=1)
     self.star.set_deck(STARLetDeck())
     self.star.io = unittest.mock.AsyncMock()
     await super().asyncSetUp()
@@ -165,7 +165,7 @@ async def test_send_command_plaintext_response(self):
       await self.star.send_command("C0", command="QM", fmt="id####")
 
 
-class STARCommandCatcher(STAR):
+class STARCommandCatcher(STARBackend):
   """Mock backend for star that catches commands and saves them instead of sending them to the
   machine."""
 
@@ -203,7 +203,7 @@ class TestSTARLiquidHandlerCommands(unittest.IsolatedAsyncioTestCase):
   """Test STAR backend for liquid handling."""
 
   async def asyncSetUp(self):
-    self.STAR = STAR(read_timeout=1)
+    self.STAR = STARBackend(read_timeout=1)
     self.STAR._write_and_read_command = unittest.mock.AsyncMock()
     self.STAR.io = unittest.mock.MagicMock()
     self.STAR.io.setup = unittest.mock.AsyncMock()
@@ -902,10 +902,10 @@ async def test_portrait_tip_rack_handling(self):
     )
 
   def test_serialize(self):
-    serialized = LiquidHandler(backend=STAR(), deck=STARLetDeck()).serialize()
+    serialized = LiquidHandler(backend=STARBackend(), deck=STARLetDeck()).serialize()
     deserialized = LiquidHandler.deserialize(serialized)
     self.assertEqual(deserialized.__class__.__name__, "LiquidHandler")
-    self.assertEqual(deserialized.backend.__class__.__name__, "STAR")
+    self.assertEqual(deserialized.backend.__class__.__name__, "STARBackend")
 
   async def test_move_core(self):
     self.plt_car[1].resource.unassign()
@@ -939,7 +939,7 @@ async def test_move_core(self):
 
 class STARIswapMovementTests(unittest.IsolatedAsyncioTestCase):
   async def asyncSetUp(self):
-    self.STAR = STAR()
+    self.STAR = STARBackend()
     self.STAR._write_and_read_command = unittest.mock.AsyncMock()
     self.deck = STARLetDeck()
     self.lh = LiquidHandler(self.STAR, deck=self.deck)
@@ -1066,7 +1066,7 @@ async def test_move_lid_across_rotated_resources(self):
 
 class STARFoilTests(unittest.IsolatedAsyncioTestCase):
   async def asyncSetUp(self):
-    self.star = STAR()
+    self.star = STARBackend()
     self.star._write_and_read_command = unittest.mock.AsyncMock()
     self.deck = STARLetDeck()
     self.lh = LiquidHandler(backend=self.star, deck=self.deck)

pylabrobot/liquid_handling/backends/hamilton/vantage_tests.py

@@ -15,7 +15,7 @@
 from pylabrobot.resources.hamilton import VantageDeck
 
 from .vantage_backend import (
-  Vantage,
+  VantageBackend,
   VantageFirmwareError,
   parse_vantage_fw_string,
   vantage_response_string_to_error,
@@ -203,7 +203,7 @@ def test_parse_error_response(self):
     )
 
 
-class VantageCommandCatcher(Vantage):
+class VantageCommandCatcher(VantageBackend):
   """Mock backend for Vantage that catches commands and saves them instead of sending them to the
   machine."""