Merge pull request #1071 from UC-Davis-molecular-computing/dev

Dev

Author: dave-doty

.claude/settings.local.json

@@ -0,0 +1,30 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(grep:*)",
+      "Bash(dart pub:*)",
+      "Bash(dart analyze:*)",
+      "Bash(dart format:*)",
+      "Bash(dart:*)",
+      "Bash(scoop update:*)",
+      "Bash(scoop info:*)",
+      "Bash(taskkill:*)",
+      "Bash(TASKKILL:*)",
+      "Bash(Stop-Process -Name \"dart\" -Force)",
+      "Bash(Stop-Process -Name \"dartaotruntime\" -Force)",
+      "WebFetch(domain:github.com)",
+      "Bash(dart run build_runner build:*)",
+      "Bash(python:*)",
+      "WebFetch(domain:raw.githubusercontent.com)",
+      "WebFetch(domain:pub.dev)",
+      "WebSearch",
+      "Bash(scoop install:*)",
+      "Bash(scoop uninstall:*)",
+      "Bash(powershell:*)",
+      "Bash(conda init:*)"
+    ],
+    "deny": [],
+    "ask": [],
+    "defaultMode": "acceptEdits"
+  }
+}

.github/dependabot.yml

@@ -5,3 +5,9 @@ updates:
     target-branch: "dev"
     schedule:
       interval: "weekly" # daily, weekly, monthly
+
+  - package-ecosystem: "npm"
+    directory: "/standalone" # Directory of package.json
+    target-branch: "dev"
+    schedule:
+      interval: "weekly"

.github/workflows/dart.yml

@@ -16,7 +16,7 @@ jobs:
       - 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: 3.8
+          sdk: 3.9
 
       - name: Install dependencies
         run: dart pub get

.github/workflows/dart_formatting.yml

@@ -16,7 +16,7 @@ jobs:
       - 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: 3.8
+          sdk: 3.9
 
       - name: Install dependencies
         run: dart pub get

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

@@ -23,7 +23,7 @@ jobs:
       - 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: 3.8
+          sdk: 3.9
 
       - name: Install dependencies
         run: dart pub get

.github/workflows/gh-pages.yml

@@ -22,7 +22,7 @@ jobs:
       - 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: 3.8
+          sdk: 3.9
 
       - name: Install dependencies
         run: dart pub get

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

@@ -0,0 +1,107 @@
+name: "release"
+
+on:
+  push:
+    branches:
+      - "main"
+
+jobs:
+  create-release:
+    name: "Release"
+    runs-on: ubuntu-latest
+
+    steps:
+      # ...
+      - name: "Build & test"
+        run: |
+          echo "done!"
+      - uses: "marvinpinto/action-automatic-releases@v1.2.1"
+        env:
+          ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
+        with:
+          repo_token: "${{ secrets.GITHUB_TOKEN }}"
+          automatic_release_tag: "latest"
+          prerelease: false
+          title: "Development Build [TODO: Replace label and title with version number]"
+          files: |
+            LICENSE.txt
+
+  upload-artifacts:
+    name: Build on ${{ matrix.os }}
+    needs: [ create-release ]
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        include:
+          - os: ubuntu-latest
+            npm_command: npm run build:lin
+          - os: windows-latest
+            npm_command: npm run build:win
+          - os: macos-latest
+            npm_command: npm run build:mac
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      # Setup Builder
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+      - uses: dart-lang/setup-dart@v1
+        with:
+          sdk: 3.8
+
+      - name: Install ImageMagick
+        shell: bash
+        run: |
+          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
+            sudo apt-get update && sudo apt-get install -y imagemagick libfuse2
+          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
+            brew install imagemagick
+          elif [[ "${{ matrix.os }}" == "windows-latest" ]]; then
+            choco install imagemagick -y
+          fi
+
+      - name: Install NodeJS Dependencies
+        working-directory: ./standalone
+        run: npm install
+
+      - name: Generate Icons
+        working-directory: ./standalone
+        shell: bash
+        run: |
+          chmod +x ./generate-icons.sh
+          ./generate-icons.sh ../web/images/origami-icon-thin-seam.png
+
+      - name: Run build
+        working-directory: ./standalone
+        run: ${{ matrix.npm_command }}
+
+      # Upload the generated artifacts (pattern: scadnano*.<ext>)
+      - name: Upload Build Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: build-${{ matrix.os }}
+          path: |
+            standalone/dist/scadnano*.*
+            !standalone/dist/*.blockmap
+
+  attach-to-release:
+    name: Attach artifacts to release
+    runs-on: ubuntu-latest
+    needs: [upload-artifacts, create-release]
+
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: ./release-files
+
+      - name: Upload to GitHub Release
+        uses: softprops/action-gh-release@v1
+        with:
+          tag_name: latest
+          files: |
+            ./release-files/**/scadnano*.*
+            !./release-files/**/*.blockmap
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -13,7 +13,6 @@ build/
 .vscode/
 
 node_modules/
-package-lock.json
 
 # Directory created by dartdoc
 doc/api/

.gitignore

@@ -0,0 +1,8 @@
+Please read CONTRIBUTING.md for details about this project.
+
+## Important notes
+
+- **`.g.dart` files are auto-generated** by the `built_value` code generator and should generally NOT be read
+  or modified by hand. They are regenerated by running `dart run build_runner build` (or automatically when
+  using `webdev serve`). If you need to understand a built_value class, read only the corresponding `.dart`
+  source file (e.g., read `app_ui_state_storables.dart`, not `app_ui_state_storables.g.dart`).