chore: Kenneth clean up

.github/dependabot.yml

@@ -0,0 +1,23 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    groups:
+      pip:
+        patterns:
+          - '*'
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: ".github/workflows" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    groups:
+      github:
+        patterns:
+          - '*'

.github/workflows/autoformat-and-lint.yml

@@ -0,0 +1,45 @@
+name: Autoformat and Lint
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  merge_group:
+
+jobs:
+  autoformat-and-lint:
+    name: Autoformat and Lint
+    if: github.actor != 'dependabot[bot]'
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: 🛎 Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+          token: ${{ secrets.WORKFLOW_COMMIT_TOKEN }}
+
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+
+      - name: 📦 Install Hatch
+        run: pip install hatch
+
+      - name: 📝 Format Code
+        run: hatch fmt -f
+
+      - name: ✅ Commit code format changes
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "Autoformat code"
+          skip_fetch: true
+          skip_checkout: true
+
+      - name: 🔍 Lint
+        run: hatch fmt --check

.github/workflows/build.yml

@@ -0,0 +1,36 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+
+      - name: 📦 Install dependencies
+        run: pip install .
+
+      - name: 🛠️ Build
+        run: ./vbl_aquarium_build
+
+      - name: 📤 PR changes
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.PR_TOKEN }}
+          commit-message: "Build Models"
+          title: "chore: Build Models"
+          branch: "build-models"
+          delete-branch: true

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,51 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  schedule:
+    - cron: '32 21 * * 1'
+
+concurrency:
+  group: "codeql"
+  cancel-in-progress: true
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3

.github/workflows/dependency-review.yml

@@ -0,0 +1,14 @@
+name: 'Dependency Review'
+on: [pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  dependency-review:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout Repository'
+        uses: actions/checkout@v4
+      - name: 'Dependency Review'
+        uses: actions/dependency-review-action@v4

models/csharp/dock/BucketModel.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct BucketModel
 {
     public string Token;

models/csharp/dock/LoadModel.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct LoadModel
 {
     public string Bucket;

models/csharp/dock/SaveManagerModel.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct SaveManagerModel
 {
     public string Bucket;

models/csharp/dock/SaveModel.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct SaveModel
 {
     public string Bucket;

models/csharp/ephys_link/AngularResponse.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct AngularResponse
 {
     public Vector3 Angles;

models/csharp/ephys_link/BooleanStateResponse.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct BooleanStateResponse
 {
     public bool State;

models/csharp/ephys_link/CanWriteRequest.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct CanWriteRequest
 {
     public string ManipulatorId;

models/csharp/ephys_link/DriveToDepthRequest.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct DriveToDepthRequest
 {
     public string ManipulatorId;

models/csharp/ephys_link/DriveToDepthResponse.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct DriveToDepthResponse
 {
     public float Depth;

models/csharp/ephys_link/GetManipulatorsResponse.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct GetManipulatorsResponse
 {
     public string[] Manipulators;

models/csharp/ephys_link/GotoPositionRequest.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct GotoPositionRequest
 {
     public string ManipulatorId;

models/csharp/ephys_link/InsideBrainRequest.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct InsideBrainRequest
 {
     public string ManipulatorId;

models/csharp/ephys_link/PositionalResponse.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct PositionalResponse
 {
     public Vector4 Position;

models/csharp/ephys_link/ShankCountResponse.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct ShankCountResponse
 {
     public int ShankCount;

models/csharp/generic/BoolData.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct BoolData
 {
     public string ID;

models/csharp/generic/BoolList.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct BoolList
 {
     public string ID;

models/csharp/generic/ColorData.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct ColorData
 {
     public string ID;

models/csharp/generic/ColorList.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct ColorList
 {
     public string ID;

models/csharp/generic/FloatData.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct FloatData
 {
     public string ID;

models/csharp/generic/FloatList.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct FloatList
 {
     public string ID;

models/csharp/generic/IDData.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct IDData
 {
     public string ID;

models/csharp/generic/IDList.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct IDList
 {
     public string[] IDs;

models/csharp/generic/IDListBoolData.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct IDListBoolData
 {
     public string[] IDs;

models/csharp/generic/IDListBoolList.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct IDListBoolList
 {
     public string[] IDs;

models/csharp/generic/IDListColorData.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct IDListColorData
 {
     public string[] IDs;

models/csharp/generic/IDListColorList.cs

@@ -1,6 +1,6 @@
 
 using UnityEngine;
-    
+
 public struct IDListColorList
 {
     public string[] IDs;

models/csharp/generic/IDListFloatData.cs

@@ -1,6 +1,6 @@
 
 
-    
+
 public struct IDListFloatData
 {
     public string[] IDs;