Fix Typos And Add Typos Pre-Commit Hook (#655)

Co-authored-by: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com>

Author: O957

.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": ["."],

_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/contributor_guide/contributing.md

@@ -17,7 +17,7 @@ It is recommend that you use VSCode, as we provide a workspace config in `/.vsco
 Some VSCode Extensions I'd recommend:
 
 - [Python](https://marketplace.visualstudio.com/items?itemName=ms-python.python)
-- [Code Spell Checker](https://marketplace.visualstudio.com/items?itemName=streetsidesoftware.code-spell-checker)
+- [Typos Checker](https://github.com/tekumara/typos-lsp)
 - [mypy](https://marketplace.visualstudio.com/items?itemName=matangover.mypy)
 
 ## Testing, linting, formatting

docs/resources/index.md

@@ -152,7 +152,7 @@ If you cannot find something, please contribute what you are looking for!
     </ul>
     <p>As a result, many automation software systems believe that it is impossible to reuse resource definitions.
     In contrast, PyLabRobot is convinced that carefully created resource definitions combined with smart automation can be reused most of the time.</p>
-    <p>PLR is actively addressing these resource resuse constraints in numerous ways:</p>
+    <p>PLR is actively addressing these resource reuse constraints in numerous ways:</p>
     <ul>
         <li>Development of self-correcting machine backend methods.</li>
         <li>Using Coordinate Measurement Machine-based generation of resource "ground truths" (e.g., via liquid handler-based resource probing or 3D scanning).</li>

docs/resources/library/eppendorf.md

@@ -12,7 +12,7 @@ Company page: [Eppendorf Wikipedia](https://en.wikipedia.org/wiki/Eppendorf_(com
 
 | Description               | Image              | PLR definition |
 |--------------------|--------------------|--------------------|
-| 'Eppendorf_96_wellplate_250ul_Vb'<br>Part no.: 0030133374<br>[manufacturer website](https://www.eppendorf.com/gb-en/Products/Laboratory-Consumables/Plates/Eppendorf-twintec-PCR-Plates-p-0030133374) <br><br> - Material: polycarbonate (frame), polypropylene (wells)<br> - part of the twin.tec(R) product line<br> - WARNING: not ANSI/SLAS 1-2004 footprint dimenions (123x81 mm^2!) ==> requires `PlateAdapter`<br> - 'Can be divided into 4 segments of 24 wells each to prevent waste and save money'. | ![](img/eppendorf/Eppendorf_96_wellplate_250ul_Vb_COMPLETE.png) ![](img/eppendorf/Eppendorf_96_wellplate_250ul_Vb_DIVIDED.png) | `Eppendorf_96_wellplate_250ul_Vb` |
+| 'Eppendorf_96_wellplate_250ul_Vb'<br>Part no.: 0030133374<br>[manufacturer website](https://www.eppendorf.com/gb-en/Products/Laboratory-Consumables/Plates/Eppendorf-twintec-PCR-Plates-p-0030133374) <br><br> - Material: polycarbonate (frame), polypropylene (wells)<br> - part of the twin.tec(R) product line<br> - WARNING: not ANSI/SLAS 1-2004 footprint dimensions (123x81 mm^2!) ==> requires `PlateAdapter`<br> - 'Can be divided into 4 segments of 24 wells each to prevent waste and save money'. | ![](img/eppendorf/Eppendorf_96_wellplate_250ul_Vb_COMPLETE.png) ![](img/eppendorf/Eppendorf_96_wellplate_250ul_Vb_DIVIDED.png) | `Eppendorf_96_wellplate_250ul_Vb` |
 
 ## Tubes
 

docs/resources/library/porvair.md

@@ -2,7 +2,7 @@
 
 Company history: [Porvair Filtration Group](https://www.porvairfiltration.com/about/our-history/)
 
-> Porvair Filtration Group, a wholly owned subsidiary of Porvair plc, is a specialist filtration and environmental technology group involved in developing, designing and manufacturing filtration and separation solutions to industry sectors such as the aviation, molten metal, energy, water treatment and life sciences markets. Porvair plc is a publically owned company with four principal subsidiaries: Porvair Filtration Group Ltd., Porvair Sciences Ltd., Selee Corporation and Seal Analytical Ltd.
+> Porvair Filtration Group, a wholly owned subsidiary of Porvair plc, is a specialist filtration and environmental technology group involved in developing, designing and manufacturing filtration and separation solutions to industry sectors such as the aviation, molten metal, energy, water treatment and life sciences markets. Porvair plc is a publicly owned company with four principal subsidiaries: Porvair Filtration Group Ltd., Porvair Sciences Ltd., Selee Corporation and Seal Analytical Ltd.
 
 ## Plates
 

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

@@ -20,7 +20,7 @@
    "source": [
     "## Example: Hamilton STARLet\n",
     "\n",
-    "Here, we'll use a Hamilton STARLet as an example. For other robots, simply change the deck layout, makign sure that you have at least a tip rack and a plate to use."
+    "Here, we'll use a Hamilton STARLet as an example. For other robots, simply change the deck layout, making sure that you have at least a tip rack and a plate to use."
    ]
   },
   {

docs/user_guide/00_liquid-handling/hamilton-star/hardware/replacing-iswap.md

@@ -2,7 +2,7 @@
 
 This guide provides instructions for replacing the iSWAP arm on a Hamilton STAR liquid handling system.
 
-Caution/Disclaimer: 
+Caution/Disclaimer:
 1. This procedure is a work in progress and the user assumes all responsibility for any damage that may be done as a result.
 2. This procedure should not be performed on any system that are either under the OEM Warranty period or currently on a service contract with the OEM or any third party service organization. This will certainly void the OEM Warranty/Service contract and likely invalidate any service agreement with third parties.
 3. This procedure DOES NOT encapsulate the entire OEM adjustment procedure which includes specialized tooling and software to perform. Consult [iSWAP Auto Adjustment Guide](adjusting-iswap.md) for auto-calibrating arm after installation proceduce.
@@ -39,9 +39,9 @@ Note: Due to the way the iSWAP is taught, the calibration positions from machine
 
 ## Attaching the New iSWAP Arm and rough leveling
 
-6. Place the replacement arm on the system, insert and tighten the two fixing screws, reattach the comunication and Y-drive ribon cables.
+6. Place the replacement arm on the system, insert and tighten the two fixing screws, reattach the communication and Y-drive ribon cables.
 
-Note: Once physically installed on the system it is recomended that you level the arm in relation to the deck.
+Note: Once physically installed on the system it is recommended that you level the arm in relation to the deck.
 
 7. Loosen the two fixing screws until the iSWAP is fixed in position but can still be rotated about the X Axis (left to right) of the machine.
 8. Manually position the X-Arm in the center of the machine and the iSWAP in the middle of the X-Arm.