Merge pull request #1083 from UC-Davis-molecular-computing/dev

Dev

Author: dave-doty

.claude/settings.local.json

@@ -1,6 +1,7 @@
 {
   "permissions": {
     "allow": [
+      "Bash(*)",
       "Bash(grep:*)",
       "Bash(dart pub:*)",
       "Bash(dart analyze:*)",
@@ -27,4 +28,4 @@
     "ask": [],
     "defaultMode": "acceptEdits"
   }
-}
+}

.github/actions/setup-dart/action.yml

@@ -0,0 +1,11 @@
+name: Setup Dart SDK
+inputs:
+  sdk:
+    default: "3.11"
+    description: The Dart SDK to use. Defaults to 3.11 if none is provided.
+runs:
+  using: composite
+  steps:
+    - uses: dart-lang/setup-dart@v1
+      with:
+        sdk: ${{ inputs.sdk }}

.github/workflows/dart.yml

@@ -13,14 +13,17 @@ jobs:
       - name: Checkout branch
         uses: actions/checkout@v4
 
-      - name: Setup Dart SDK  # Using Dart 3.8 to match pubspec.yaml constraint
-        uses: dart-lang/setup-dart@v1  # https://github.com/dart-lang/setup-dart
-        with:
-          sdk: 3.9
+      - name: Setup Dart SDK
+        uses: ./.github/actions/setup-dart
 
       - name: Install dependencies
         run: dart pub get
 
+      - name: Build generated files for sub-packages
+        run: |
+          cd scadnano_state_actions && dart run build_runner build --delete-conflicting-outputs && cd ..
+          cd scadnano_reducers && dart run build_runner build --delete-conflicting-outputs && cd ..
+
       - name: Run Tests
         run: dart run build_runner test
 

.github/workflows/dart_formatting.yml

@@ -13,16 +13,14 @@ jobs:
       - name: Checkout branch
         uses: actions/checkout@v4
 
-      - name: Setup Dart SDK  # Using Dart 3.8 to match pubspec.yaml constraint
-        uses: dart-lang/setup-dart@v1  # https://github.com/dart-lang/setup-dart
-        with:
-          sdk: 3.9
+      - name: Setup Dart SDK
+        uses: ./.github/actions/setup-dart
 
       - name: Install dependencies
         run: dart pub get
 
       - name: Verify formatting
-        run: dart format -l 110 --output=none --set-exit-if-changed .
+        run: dart format -l 120 --output=none --set-exit-if-changed .
 
   fail_if_pull_request_is_draft:
     if: github.event.pull_request.draft == true

.github/workflows/gh-pages-dev.yml

@@ -20,14 +20,17 @@ jobs:
           ref: gh-pages
           path: gh-pages-repo
 
-      - name: Setup Dart SDK  # Using Dart 3.8 to match pubspec.yaml constraint
-        uses: dart-lang/setup-dart@v1  # https://github.com/dart-lang/setup-dart
-        with:
-          sdk: 3.9
+      - name: Setup Dart SDK
+        uses: ./.github/actions/setup-dart
 
       - name: Install dependencies
         run: dart pub get
 
+      - name: Build generated files for sub-packages
+        run: |
+          cd scadnano_state_actions && dart run build_runner build --delete-conflicting-outputs && cd ..
+          cd scadnano_reducers && dart run build_runner build --delete-conflicting-outputs && cd ..
+
       - name: Install webdev
         run: dart pub global activate webdev
 

.github/workflows/gh-pages.yml

@@ -19,14 +19,17 @@ jobs:
           ref: gh-pages
           path: gh-pages-repo
 
-      - name: Setup Dart SDK  # Using Dart 3.8 to match pubspec.yaml constraint
-        uses: dart-lang/setup-dart@v1  # https://github.com/dart-lang/setup-dart
-        with:
-          sdk: 3.9
+      - name: Setup Dart SDK
+        uses: ./.github/actions/setup-dart
 
       - name: Install dependencies
         run: dart pub get
 
+      - name: Build generated files for sub-packages
+        run: |
+          cd scadnano_state_actions && dart run build_runner build --delete-conflicting-outputs && cd ..
+          cd scadnano_reducers && dart run build_runner build --delete-conflicting-outputs && cd ..
+
       - name: Activate webdev
         run: dart pub global activate webdev
 

.github/workflows/release-and-upload-artifacts.yml

@@ -44,11 +44,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       # Setup Builder
-      - uses: actions/checkout@v4
-      - uses: actions/setup-node@v4
-      - uses: dart-lang/setup-dart@v1
-        with:
-          sdk: 3.8
+      - name: Checkout Repository
+        uses: actions/checkout@v6
+
+      - name: Setup Node
+        uses: actions/setup-node@v6
+
+      - name: Setup Dart SDK
+        uses: ./.github/actions/setup-dart
 
       - name: Install ImageMagick
         shell: bash
@@ -80,6 +83,7 @@ jobs:
       - name: Upload Build Artifact
         uses: actions/upload-artifact@v4
         with:
+          retention-days: 1 # reduce from 90-day default. This is only required for passing artifacts between jobs.
           name: build-${{ matrix.os }}
           path: |
             standalone/dist/scadnano*.*

.gitignore

@@ -26,4 +26,7 @@ codenano.html
 
 todo.txt
 
-todo extensions.txt
+todo extensions.txt
+
+# Auto-generated by built_value
+*.g.dart