Merge branch 'main' into byonoy-luminescence

Author: rickwierenga

.github/workflows/typo.yml

@@ -0,0 +1,24 @@
+name: Typo check
+
+permissions:
+  contents: read
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+env:
+  CLICOLOR: 1
+
+jobs:
+  spelling:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+      - name: Spell Check Repo
+        uses: crate-ci/typos@v1

.pre-commit-config.yaml

@@ -7,3 +7,9 @@ repos:
         language: system
         files: ^pylabrobot/.*$
 
+  - repo: https://github.com/crate-ci/typos
+    rev: v1
+    hooks:
+      - id: typos
+        files: ^pylabrobot/.*$
+        args: ["--force-exclude"]

.vscode/settings.json

@@ -1,31 +1,6 @@
 {
   "editor.tabSize": 2,
   "files.trimTrailingWhitespace": true,
-  "cSpell.words": [
-    "agrow",
-    "agrowpumps",
-    "coro",
-    "cytomat",
-    "decalibrate",
-    "Defaultable",
-    "Deprecated",
-    "frontmost",
-    "hepa",
-    "Inheco",
-    "iswap",
-    "jsonify",
-    "klass",
-    "labware",
-    "modbus",
-    "pylabrobot",
-    "pytest",
-    "subclassing",
-    "subresource",
-    "tadm",
-    "tiprack",
-    "usascientific",
-    "websockets"
-  ],
   "python.linting.mypyEnabled": true,
   "python.linting.enabled": true,
   "python.testing.pytestArgs": ["."],

CHANGELOG.md

@@ -60,6 +60,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `location` parameter of `assign_child_resource` is not optional (https://github.com/PyLabRobot/pylabrobot/pull/336)
 - `Resource.get_absolute_location` raises `NoLocationError` instead of `AssertionError` when absolute location is not defined (https://github.com/PyLabRobot/pylabrobot/pull/338)
 - `no_trash` and `no_teaching_rack` were renamed to `with_trash` and `with_teaching_rack` to avoid double negatives (https://github.com/PyLabRobot/pylabrobot/pull/347)
+- `ItemizedResource.row` accepts a string ("A"-"P") in addition to an integer index.
 
 ### Added
 
@@ -134,7 +135,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
     - `plate_width: Optional[float] = None`
     - `use_unsafe_hotel: bool = False`
     - `iswap_collision_control_level: int = 0`
-    - `iswap_fold_up_sequence_at_the_end_of_process: bool = True`
+    - `iswap_fold_up_sequence_at_the_end_of_process: bool = False`
   - STAR.drop_resource
     - `minimum_traverse_height_at_beginning_of_a_command: Optional[float] = None`
     - `z_position_at_the_command_end: Optional[float] = None`

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
@@ -149,16 +149,40 @@ await fan.setup()
 await fan.turn_on(intensity=100, duration=60)
 ```
 
+### Thermocyclers ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/thermocycling/thermocycling.html))
+
+Running a thermocycler with a simple protocol:
+
+```python
+await tc.run_pcr_profile(
+  denaturation_temp=98.0,
+  denaturation_time=10.0,
+  annealing_temp=55.0,
+  annealing_time=30.0,
+  extension_temp=72.0,
+  extension_time=60.0,
+  num_cycles=2,
+  block_max_volume=25.0,
+  lid_temperature=105.0,
+  pre_denaturation_temp=95.0,
+  pre_denaturation_time=180.0,
+  final_extension_temp=72.0,
+  final_extension_time=300.0,
+  storage_temp=4.0,
+  storage_time=600.0,
+)
+```
+
 ## Resources
 
 ### Documentation
 
 [docs.pylabrobot.org](https://docs.pylabrobot.org)
 
-- [Installation](https://docs.pylabrobot.org/installation.html)
-- [Getting Started](https://docs.pylabrobot.org/basic.html)
-- [Contributing](CONTRIBUTING.md)
-- [API Reference](https://docs.pylabrobot.org/pylabrobot.html)
+- [Installation](https://docs.pylabrobot.org/user_guide/_getting-started/installation.html)
+- [Getting Started](https://docs.pylabrobot.org/user_guide/index.html)
+- [Contributing](https://docs.pylabrobot.org/contributor_guide/index.html)
+- [API Reference](https://docs.pylabrobot.org/api/pylabrobot.html)
 
 ### Support
 

_typos.toml

@@ -0,0 +1,27 @@
+[default]
+extend-ignore-identifiers-re = [
+    "AttributeID.*Supress.*",
+]
+
+[default.extend-identifiers]
+AttributeIDSupressMenu = "AttributeIDSupressMenu"
+
+[default.extend-words]
+# words that should not be corrected
+dot_acn = ".acn"
+dot_fot = ".fot"
+dot_ist = ".ist"
+OT = "OT"
+ot = "ot"
+ser = "ser"
+ba = "ba"
+nd = "nd"
+PN = "PN"
+tro = "tro"
+FO = "FO"
+UE = "UE"
+
+[files]
+extend-exclude = [
+    "*.ipynb"
+]

docs/api/pylabrobot.heating_shaking.rst

@@ -22,4 +22,7 @@ Backends
   :recursive:
 
     chatterbox.HeaterShakerChatterboxBackend
-    inheco_backend.InhecoThermoShakeBackend
+    inheco.thermoshake_backend.InhecoThermoshakeBackend
+    inheco.thermoshake.inheco_thermoshake_ac
+    inheco.thermoshake.inheco_thermoshake
+    inheco.thermoshake.inheco_thermoshake_rm

docs/api/pylabrobot.rst

@@ -21,5 +21,6 @@ Subpackages
     pylabrobot.scales
     pylabrobot.shaking
     pylabrobot.temperature_controlling
+    pylabrobot.thermocycling
     pylabrobot.tilting
     pylabrobot.utils

docs/api/pylabrobot.temperature_controlling.rst

@@ -24,3 +24,6 @@ Backends
 
     chatterbox.TemperatureControllerChatterboxBackend
     opentrons_backend.OpentronsTemperatureModuleBackend
+    inheco.control_box.InhecoTECControlBox
+    inheco.cpac_backend.InhecoCPACBackend
+    inheco.cpac.inheco_cpac_ultraflat

docs/api/pylabrobot.thermocycling.rst

@@ -0,0 +1,28 @@
+.. currentmodule:: pylabrobot.thermocycling
+
+pylabrobot.thermocycling package
+================================
+
+This package contains APIs for working with thermocyclers.
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+  thermocycler.Thermocycler
+  opentrons.OpentronsThermocyclerModuleV1
+  opentrons.OpentronsThermocyclerModuleV2
+
+
+Backends
+--------
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+  backend.ThermocyclerBackend
+  chatterbox.ThermocyclerChatterboxBackend
+  opentrons_backend.OpentronsThermocyclerBackend