Merge branch 'main' into byonoy-luminescence

Author: rickwierenga

.github/workflows/test.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        version: [3.9, "3.10", 3.11, 3.12]
+        version: [3.9, "3.10", 3.11, 3.12, 3.13, 3.14]
 
     name: Tests
     runs-on: ${{ matrix.os }}

README.md

@@ -47,9 +47,9 @@ await lh.return_tips()
 To run the same protocol on an **Opentrons**, use the following:
 
 ```python
-from pylabrobot.liquid_handling.backends import OpentronsBackend
+from pylabrobot.liquid_handling.backends import OpentronsOT2Backend
 deck = Deck.load_from_json_file("opentrons-layout.json")
-lh = LiquidHandler(backend=OpentronsBackend(host="x.x.x.x"), deck=deck)
+lh = LiquidHandler(backend=OpentronsOT2Backend(host="x.x.x.x"), deck=deck)
 ```
 
 Or **Tecan** (also works on any operating system!):

docs/api/pylabrobot.liquid_handling.backends.rst

@@ -27,7 +27,7 @@ Hardware
     backends.hamilton.base.HamiltonLiquidHandler
     backends.hamilton.STAR_backend.STAR
     backends.hamilton.vantage_backend.Vantage
-    backends.opentrons_backend.OpentronsBackend
+    backends.opentrons_backend.OpentronsOT2Backend
     backends.tecan.EVO_backend.EVOBackend
 
 Net

docs/api/pylabrobot.resources.rst

@@ -142,9 +142,7 @@ Opentrons
     opentrons
     opentrons.deck
     opentrons.load
-    opentrons.plates
     opentrons.tip_racks
-    opentrons.tube_racks
 
 
 Porvair

docs/img/supported_by/logo_nugget.png

@@ -52,6 +52,12 @@ PyHamilton is a Windows only interface to Hamilton's VENUS.
 :target: https://byonoy.com
 ```
 
+```{image} /img/supported_by/logo_nugget.png
+:alt: Nugget
+:class: company
+:target: https://www.nuggetscientific.com
+```
+
 ## Used by
 
 ```{image} /img/used_by/logo_mit.jpg

docs/index.md

@@ -2,3 +2,5 @@ Deck
 ====
 
 The :class:`~pylabrobot.resources.deck.Deck` class is used to model the decks of liquid handling robots. This is the part that is different for each robot.
+
+You can clear the resources on the deck by calling :meth:`~pylabrobot.resources.deck.Deck.clear`.

docs/resources/deck/deck.rst

@@ -114,7 +114,7 @@ PLR's `Resource` subclasses in the inheritance tree are:
     However, in our discussions, it became evident that the term "labware" has different meanings to different stakeholders
     (e.g., "A plate is clearly labware, but is a liquid handler or a plate reader labware?").
     As a result, PLR avoids the ambiguous term "labware".</p>
-    <p><u>Every physical item (describable via its <code>item_x</code>, <code>item_y</code>, <code>item_z</code>) is a "resource"</u>.</p>
+    <p><u>Every physical item (describable by its physical dimensions <code>size_x</code>, <code>size_y</code>, <code>size_z</code>) is a `Resource`</u>.</p>
 </details>
 
 <hr>
@@ -167,6 +167,7 @@ If you cannot find something, please contribute what you are looking for!
 :caption: Resource Library
 
 library/agenbio
+library/agilent
 library/alpaqua
 library/azenta
 library/bioer

docs/resources/index.md

@@ -6,7 +6,7 @@ In PyLabRobot, a {class}`pylabrobot.resources.resource.Resource` is a piece of l
 
 While you can instantiate a `Resource` directly, several subclasses of methods exist to provide additional functionality and model specific resource attributes. For example, a {class}`pylabrobot.resources.plate.Plate` has methods for easily accessing {class}`pylabrobot.resources.well.Well`s.
 
-The relation between resources is modelled by a tree, specifically an [_arborescence_](<https://en.wikipedia.org/wiki/Arborescence_(graph_theory)>) (a directed, rooted tree). The location of a resource in the tree is a Cartesian coordinate and always relative to the bottom front left corner of its immediate parent. The absolute location can be computed using {meth}`~pylabrobot.resources.resource.Resource.get_absolute_location`. The x-axis is left (smaller) and right (larger); the y-axis is front (small) and back (larger); the z-axis is down (smaller) and up (higher). Each resource has `children` and `parent` attributes that allow you to navigate the tree.
+The relation between resources is modelled by a tree, specifically an [_arborescence_](<https://en.wikipedia.org/wiki/Arborescence_(graph_theory)>) (a directed, rooted tree). The location of a resource in the tree is a Cartesian coordinate and always relative to the bottom front left corner of its immediate parent. The absolute location, the location of the resource wrt the root of the tree it is in, can be computed using {meth}`~pylabrobot.resources.resource.Resource.get_absolute_location`. The location wrt any resource between a given one and the root can be computed using {meth}`~pylabrobot.resources.resource.Resource.get_location_wrt`. The x-axis is left (smaller) and right (larger); the y-axis is front (small) and back (larger); the z-axis is down (smaller) and up (higher). Each resource has `children` and `parent` attributes that allow you to navigate the tree.
 
 {class}`pylabrobot.machines.machine.Machine` is a special type of resource that represents a physical machine, such as a liquid handling robot ({class}`pylabrobot.liquid_handling.liquid_handler.LiquidHandler`) or a plate reader ({class}`pylabrobot.plate_reading.plate_reader.PlateReader`). Machines have a `backend` attribute linking to the backend that is responsible for converting PyLabRobot commands into commands that a specific machine can understand. Other than that, Machines, including {class}`pylabrobot.liquid_handling.liquid_handler.LiquidHandler`, are just like any other Resource.
 

docs/resources/introduction.md

@@ -0,0 +1,9 @@
+# Agilent
+
+[Company Page](https://www.agilent.com)
+
+## Plates
+
+| Description | Image | PLR definition |
+|-|-|-|
+| 'agilent_96_wellplate_150uL_Ub'<br>Part no.: 5042-8502<br>[manufacturer website](https://www.agilent.com/store/en_US/Prod-5042-8502/5042-8502) | ![](img/agilent/agilent_96_wellplate_150uL_Ub.jpg) | `agilent_96_wellplate_150uL_Ub` |