deprecate _L and _P in resource definitions (#288)

CHANGELOG.md

@@ -59,14 +59,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `Thermo_TS_96_wellplate_1200ul_Rb` (https://github.com/PyLabRobot/pylabrobot/pull/215)
 - `Thermo_AB_96_wellplate_300ul_Vb_EnduraPlate` (https://github.com/PyLabRobot/pylabrobot/pull/215)
 - `adapter_hole_size_z` and `plate_z_offset` parameters to `PlateAdapter` (https://github.com/PyLabRobot/pylabrobot/pull/215)
-- `wide_high_volume_tip_with_filter` and `HTF_L_WIDE` (https://github.com/PyLabRobot/pylabrobot/pull/222)
+- `wide_high_volume_tip_with_filter` and `HTF_WIDE` (https://github.com/PyLabRobot/pylabrobot/pull/222)
 - Serialize code cells and closures (https://github.com/PyLabRobot/pylabrobot/pull/220)
 - `Container.get_anchor()` now supports `"cavity_bottom"` as an argument for `z` (https://github.com/PyLabRobot/pylabrobot/pull/205/)
 - `pylabrobot.resources.utils.query` for basic querying (https://github.com/PyLabRobot/pylabrobot/commit/4a07f6a32a9a33d0370eb9c29015567c98aea002)
 - `HamiltonLiquidHandler.allow_firmware_planning` to allow STAR/Vantage to plan complex liquid handling operations automatically (may break hardware agnosticity unexpectedly) (https://github.com/PyLabRobot/pylabrobot/pull/224)
 - `size_z` and `nesting_z_height` for `Cor_96_wellplate_360ul_Fb_Lid` (https://github.com/PyLabRobot/pylabrobot/pull/226)
 - `NestedTipRack` (https://github.com/PyLabRobot/pylabrobot/pull/228)
-- `HTF_L_ULTRAWIDE`, `ultrawide_high_volume_tip_with_filter` (https://github.com/PyLabRobot/pylabrobot/pull/229/)
+- `HTF_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)
   - imaging (https://github.com/PyLabRobot/pylabrobot/pull/277)
@@ -93,6 +93,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `ThermoScientific_96_DWP_1200ul_Rd` in favor of `Thermo_TS_96_wellplate_1200ul_Rb` (https://github.com/PyLabRobot/pylabrobot/pull/215)
 - `Azenta4titudeFrameStar_96_wellplate_skirted` in favor of `Azenta4titudeFrameStar_96_wellplate_200ul_Vb` (https://github.com/PyLabRobot/pylabrobot/pull/205/)
 - `Cos_96_DWP_2mL_Vb` in favor of `Cos_96_wellplate_2mL_Vb (https://github.com/PyLabRobot/pylabrobot/pull/205/)`
+- Resource definitions with `_L` and `_P`, it is easy enough to use the stem and `.rotated(z=90)` for `_P` (https://github.com/PyLabRobot/pylabrobot/pull/288)
 
 ### Fixed
 

docs/user_guide/basic.ipynb

@@ -115,7 +115,7 @@
     "- {class}`~pylabrobot.resources.ml_star.tip_carriers.TIP_CAR_480_A00` tip carrier\n",
     "- {class}`~pylabrobot.resources.ml_star.plate_carriers.PLT_CAR_L5AC_A00` plate carrier\n",
     "- {class}`~pylabrobot.resources.corning_costar.plates.Cor_96_wellplate_360ul_Fb` wells\n",
-    "- {class}`~pylabrobot.resources.ml_star.tip_racks.HTF_L` tips"
+    "- {class}`~pylabrobot.resources.ml_star.tip_racks.HTF` tips"
    ]
   },
   {
@@ -128,7 +128,7 @@
     "  TIP_CAR_480_A00,\n",
     "  PLT_CAR_L5AC_A00,\n",
     "  Cor_96_wellplate_360ul_Fb,\n",
-    "  HTF_L,\n",
+    "  HTF,\n",
     ")"
    ]
   },
@@ -146,7 +146,7 @@
    "outputs": [],
    "source": [
     "tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\n",
-    "tip_car[0] = HTF_L(name=\"tips_01\")"
+    "tip_car[0] = HTF(name=\"tips_01\")"
    ]
   },
   {

docs/user_guide/moving-channels-around.ipynb

@@ -38,14 +38,14 @@
    "outputs": [],
    "source": [
     "from pylabrobot.liquid_handling import LiquidHandler, STAR\n",
-    "from pylabrobot.resources import STARDeck, TIP_CAR_480_A00, HTF_L\n",
+    "from pylabrobot.resources import STARDeck, TIP_CAR_480_A00, HTF\n",
     "\n",
     "lh = LiquidHandler(backend=STAR(), deck=STARDeck())\n",
     "await lh.setup()\n",
     "\n",
     "# assign a tip rack\n",
     "tip_carrier = TIP_CAR_480_A00(name=\"tip_carrier\")\n",
-    "tip_carrier[0] = tip_rack = HTF_L(name=\"tip_rack\")\n",
+    "tip_carrier[0] = tip_rack = HTF(name=\"tip_rack\")\n",
     "lh.deck.assign_child_resource(tip_carrier, rails=0)"
    ]
   },

docs/user_guide/using-the-visualizer.ipynb

@@ -143,7 +143,7 @@
     "    TIP_CAR_480_A00,\n",
     "    PLT_CAR_L5AC_A00,\n",
     "    Cor_96_wellplate_360ul_Fb,\n",
-    "    HTF_L\n",
+    "    HTF\n",
     ")"
    ]
   },
@@ -155,11 +155,11 @@
    "outputs": [],
    "source": [
     "tip_car = TIP_CAR_480_A00(name='tip carrier')\n",
-    "tip_car[0] = tip_rack1 = HTF_L(name='tips_01', with_tips=False)\n",
-    "tip_car[1] = tip_rack2 = HTF_L(name='tips_02', with_tips=False)\n",
-    "tip_car[2] = tip_rack3 = HTF_L(name='tips_03', with_tips=False)\n",
-    "tip_car[3] = tip_rack4 = HTF_L(name='tips_04', with_tips=False)\n",
-    "tip_car[4] = tip_rack5 = HTF_L(name='tips_05', with_tips=False)"
+    "tip_car[0] = tip_rack1 = HTF(name='tips_01', with_tips=False)\n",
+    "tip_car[1] = tip_rack2 = HTF(name='tips_02', with_tips=False)\n",
+    "tip_car[2] = tip_rack3 = HTF(name='tips_03', with_tips=False)\n",
+    "tip_car[3] = tip_rack4 = HTF(name='tips_04', with_tips=False)\n",
+    "tip_car[4] = tip_rack5 = HTF(name='tips_05', with_tips=False)"
    ]
   },
   {

docs/user_guide/using-trackers.ipynb

@@ -31,7 +31,7 @@
         "from pylabrobot.liquid_handling.backends.chatterbox_backend import ChatterboxBackend\n",
         "from pylabrobot.resources import (\n",
         "  TIP_CAR_480_A00,\n",
-        "  HTF_L,\n",
+        "  HTF,\n",
         "  PLT_CAR_L5AC_A00,\n",
         "  Cor_96_wellplate_360ul_Fbate_360ul_Fb,\n",
         "  set_tip_tracking,\n",
@@ -105,7 +105,7 @@
       "metadata": {},
       "outputs": [],
       "source": [
-        "tip_carrier[0] = tip_rack = HTF_L(name=\"tip rack\")"
+        "tip_carrier[0] = tip_rack = HTF(name=\"tip rack\")"
       ]
     },
     {
@@ -142,7 +142,7 @@
       "metadata": {},
       "outputs": [],
       "source": [
-        "tip_carrier[1] = empty_tip_rack = HTF_L(name=\"empty tip rack\", with_tips=False)"
+        "tip_carrier[1] = empty_tip_rack = HTF(name=\"empty tip rack\", with_tips=False)"
       ]
     },
     {
@@ -996,4 +996,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 2
-}
+}

pylabrobot/gui/gui.py

@@ -50,58 +50,58 @@ def list_resources():
   return jsonify(
     plates=[
       "Cos_1536_10ul",
-      "Cos_1536_10ul_L",
+      "Cos_1536_10ul",
       "Cos_1536_10ul_P",
       "Cos_384_DW",
-      "Cos_384_DW_L",
+      "Cos_384_DW",
       "Cos_384_DW_P",
       "Cos_384_PCR",
-      "Cos_384_PCR_L",
+      "Cos_384_PCR",
       "Cos_384_PCR_P",
       "Cos_384_Sq",
-      "Cos_384_Sq_L",
+      "Cos_384_Sq",
       "Cos_384_Sq_P",
       "Cos_384_Sq_Rd",
-      "Cos_384_Sq_Rd_L",
+      "Cos_384_Sq_Rd",
       "Cos_384_Sq_Rd_P",
       "Cos_96_DW_1mL",
-      "Cos_96_DW_1mL_L",
+      "Cos_96_DW_1mL",
       "Cos_96_DW_1mL_P",
       "Cos_96_DW_2mL",
-      "Cos_96_DW_2mL_L",
+      "Cos_96_DW_2mL",
       "Cos_96_DW_2mL_P",
       "Cos_96_DW_500ul",
-      "Cos_96_DW_500ul_L",
+      "Cos_96_DW_500ul",
       "Cos_96_DW_500ul_P",
       "Cor_96_wellplate_360ul_Fb",
-      "Cor_96_wellplate_360ul_Fb_L",
+      "Cor_96_wellplate_360ul_Fb",
       "Cor_96_wellplate_360ul_Fb_P",
       "Cos_96_FL",
       "Cos_96_Filter",
-      "Cos_96_Filter_L",
+      "Cos_96_Filter",
       "Cos_96_Filter_P",
-      "Cos_96_Fl_L",
+      "Cos_96_Fl",
       "Cos_96_Fl_P",
       "Cos_96_HalfArea",
-      "Cos_96_HalfArea_L",
+      "Cos_96_HalfArea",
       "Cos_96_HalfArea_P",
       "Cos_96_PCR",
-      "Cos_96_PCR_L",
+      "Cos_96_PCR",
       "Cos_96_PCR_P",
       "Cos_96_ProtCryst",
-      "Cos_96_ProtCryst_L",
+      "Cos_96_ProtCryst",
       "Cos_96_ProtCryst_P",
       "Cos_96_Rd",
-      "Cos_96_Rd_L",
+      "Cos_96_Rd",
       "Cos_96_Rd_P",
       "Cos_96_SpecOps",
-      "Cos_96_SpecOps_L",
+      "Cos_96_SpecOps",
       "Cos_96_SpecOps_P",
       "Cos_96_UV",
-      "Cos_96_UV_L",
+      "Cos_96_UV",
       "Cos_96_UV_P",
       "Cos_96_Vb",
-      "Cos_96_Vb_L",
+      "Cos_96_Vb",
       "Cos_96_Vb_P",
     ],
     plate_carriers=[
@@ -197,21 +197,21 @@ def list_resources():
       "TIP_CAR_NTR_A00",
     ],
     tip_racks=[
-      "FourmlTF_L",
+      "FourmlTF",
       "FourmlTF_P",
-      "FivemlT_L",
+      "FivemlT",
       "FivemlT_P",
-      "HTF_L",
+      "HTF",
       "HTF_P",
-      "HT_L",
+      "HT",
       "HT_P",
-      "LTF_L",
+      "LTF",
       "LTF_P",
-      "LT_L",
+      "LT",
       "LT_P",
-      "STF_L",
+      "STF",
       "STF_P",
-      "ST_L",
+      "ST",
       "ST_P",
     ],
   )

pylabrobot/liquid_handling/backends/chatterbox_tests.py

@@ -6,7 +6,7 @@
 )
 from pylabrobot.resources import (
   Cor_96_wellplate_360ul_Fb,
-  HTF_L,
+  HTF,
   Coordinate,
 )
 from pylabrobot.resources.hamilton import STARLetDeck
@@ -19,7 +19,7 @@ def setUp(self) -> None:
     self.deck = STARLetDeck()
     self.backend = LiquidHandlerChatterboxBackend(num_channels=8)
     self.lh = LiquidHandler(self.backend, deck=self.deck)
-    self.tip_rack = HTF_L(name="tip_rack")
+    self.tip_rack = HTF(name="tip_rack")
     self.deck.assign_child_resource(self.tip_rack, rails=3)
     self.plate = Cor_96_wellplate_360ul_Fb(name="plate")
     self.deck.assign_child_resource(self.plate, rails=9)

pylabrobot/liquid_handling/backends/hamilton/STAR_tests.py

@@ -17,13 +17,13 @@
   TIP_CAR_480_A00,
   TIP_CAR_288_C00,
   PLT_CAR_L5AC_A00,
-  HT_P,
-  HTF_L,
+  HT,
+  HTF,
   Cor_96_wellplate_360ul_Fb,
   no_volume_tracking,
 )
 from pylabrobot.resources.hamilton import STARLetDeck
-from pylabrobot.resources.ml_star import STF_L
+from pylabrobot.resources.ml_star import STF
 
 from tests.usb import MockDev, MockEndpoint
 
@@ -221,8 +221,8 @@ async def asyncSetUp(self):
     self.lh = LiquidHandler(self.mockSTAR, deck=self.deck)
 
     self.tip_car = TIP_CAR_480_A00(name="tip carrier")
-    self.tip_car[1] = self.tip_rack = STF_L(name="tip_rack_01")
-    self.tip_car[2] = self.tip_rack2 = HTF_L(name="tip_rack_02")
+    self.tip_car[1] = self.tip_rack = STF(name="tip_rack_01")
+    self.tip_car[2] = self.tip_rack2 = HTF(name="tip_rack_02")
     self.deck.assign_child_resource(self.tip_car, rails=1)
 
     self.plt_car = PLT_CAR_L5AC_A00(name="plate carrier")
@@ -900,12 +900,10 @@ async def test_discard_tips(self):
     )
 
   async def test_portrait_tip_rack_handling(self):
-    # Test with an alternative setup.
-
     deck = STARLetDeck()
     lh = LiquidHandler(self.mockSTAR, deck=deck)
     tip_car = TIP_CAR_288_C00(name="tip carrier")
-    tip_car[0] = tr = HT_P(name="tips_01")
+    tip_car[0] = tr = HT(name="tips_01").rotated(z=90)
     assert tr.rotation.z == 90
     assert tr.location == Coordinate(82.6, 0, 0)
     deck.assign_child_resource(tip_car, rails=2)

pylabrobot/liquid_handling/backends/hamilton/vantage_tests.py

@@ -6,8 +6,8 @@
   Coordinate,
   TIP_CAR_480_A00,
   PLT_CAR_L5AC_A00,
-  HT_L,
-  LT_L,
+  HT,
+  LT,
   Cor_96_wellplate_360ul_Fb,
 )
 from pylabrobot.resources.hamilton import VantageDeck
@@ -244,8 +244,8 @@ async def asyncSetUp(self):
     self.lh = LiquidHandler(self.mockVantage, deck=self.deck)
 
     self.tip_car = TIP_CAR_480_A00(name="tip carrier")
-    self.tip_car[0] = self.tip_rack = HT_L(name="tip_rack_01")
-    self.tip_car[1] = self.small_tip_rack = LT_L(name="tip_rack_02")
+    self.tip_car[0] = self.tip_rack = HT(name="tip_rack_01")
+    self.tip_car[1] = self.small_tip_rack = LT(name="tip_rack_02")
     self.deck.assign_child_resource(self.tip_car, rails=18)
 
     self.plt_car = PLT_CAR_L5AC_A00(name="plate carrier")

pylabrobot/liquid_handling/backends/http_tests.py

@@ -9,7 +9,7 @@
 from pylabrobot.resources import (
   PLT_CAR_L5AC_A00,
   TIP_CAR_480_A00,
-  HTF_L,
+  HTF,
   Cor_96_wellplate_360ul_Fb,
   no_tip_tracking,
   no_volume_tracking,
@@ -74,7 +74,7 @@ async def asyncSetUp(self) -> None:  # type: ignore
 
     self.deck = STARLetDeck()
     self.tip_carrier = TIP_CAR_480_A00(name="tip_carrier")
-    self.tip_carrier[0] = self.tip_rack = HTF_L(name="tiprack")
+    self.tip_carrier[0] = self.tip_rack = HTF(name="tiprack")
     self.plate_carrier = PLT_CAR_L5AC_A00(name="plate_carrier")
     self.plate_carrier[0] = self.plate = Cor_96_wellplate_360ul_Fb(name="plate")
     self.deck.assign_child_resource(self.tip_carrier, rails=3)

pylabrobot/liquid_handling/backends/serializing_backend_tests.py

@@ -9,7 +9,7 @@
   TIP_CAR_480_A00,
   PLT_CAR_L5AC_A00,
   Cor_96_wellplate_360ul_Fb,
-  STF_L,
+  STF,
   Coordinate,
   no_tip_tracking,
   no_volume_tracking,
@@ -27,7 +27,7 @@ async def asyncSetUp(self) -> None:
     await self.lh.setup()
 
     self.tip_car = TIP_CAR_480_A00(name="tip carrier")
-    self.tip_car[0] = self.tip_rack = STF_L(name="tip_rack_01")
+    self.tip_car[0] = self.tip_rack = STF(name="tip_rack_01")
     self.deck.assign_child_resource(self.tip_car, rails=1)
 
     self.plt_car = PLT_CAR_L5AC_A00(name="plate carrier")