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Merge pull request #1030 from UC-Davis-molecular-computing/dev
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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "pub"
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directory: "/" # Directory of pubspec.yaml
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target-branch: "dev"
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schedule:
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interval: "weekly" # daily, weekly, monthly

‎.github/workflows/dart.yml‎

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run_unit_tests:
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if: github.event.pull_request.draft == false
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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steps:
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- name: Setup Dart SDK Step 1
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run: sudo apt-get update
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- name: Setup Dart SDK Step 2
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run: sudo apt-get install apt-transport-https
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- name: Setup Dart SDK Step 3
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run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
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- name: Setup Dart SDK Step 4
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run: sudo sh -c 'wget -qO- https://storage.googleapis.com/download.dartlang.org/linux/debian/dart_stable.list > /etc/apt/sources.list.d/dart_stable.list'
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- name: Setup Dart SDK Step 5
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run: wget -O /tmp/dart_3.5.4-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/3.5.4/linux_packages/dart_3.5.4-1_amd64.deb
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- name: Setup Dart SDK Step 6
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run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
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- uses: actions/checkout@v4
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- name: Checkout branch
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uses: actions/checkout@v4
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- name: Setup Dart SDK # Using Dart 3.8 to match pubspec.yaml constraint
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uses: dart-lang/setup-dart@v1 # https://github.com/dart-lang/setup-dart
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with:
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sdk: 3.8
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- name: Install dependencies
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
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- name: Run tests
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run: PATH="$PATH:/usr/lib/dart/bin" dart run build_runner test
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run: dart pub get
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- name: Run Tests
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run: dart run build_runner test
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fail_if_pull_request_is_draft:
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if: github.event.pull_request.draft == true
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runs-on: ubuntu-18.04
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runs-on: ubuntu-latest
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steps:
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- name: Fails in order to indicate that pull request needs to be marked as ready to review and unit tests workflow needs to pass.
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run: exit 1

‎.github/workflows/dart_formatting.yml‎

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check_formatting:
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if: github.event.pull_request.draft == false
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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steps:
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- name: Setup Dart SDK Step 1
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run: sudo apt-get update
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- name: Setup Dart SDK Step 2
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run: sudo apt-get install apt-transport-https
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- name: Setup Dart SDK Step 3
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run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
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- name: Setup Dart SDK Step 4
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run: sudo sh -c 'wget -qO- https://storage.googleapis.com/download.dartlang.org/linux/debian/dart_stable.list > /etc/apt/sources.list.d/dart_stable.list'
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- name: Setup Dart SDK Step 5
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run: wget -O /tmp/dart_3.5.4-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/3.5.4/linux_packages/dart_3.5.4-1_amd64.deb
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- name: Setup Dart SDK Step 6
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run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
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- uses: actions/checkout@v4
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- name: Checkout branch
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uses: actions/checkout@v4
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- name: Setup Dart SDK # Using Dart 3.8 to match pubspec.yaml constraint
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uses: dart-lang/setup-dart@v1 # https://github.com/dart-lang/setup-dart
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with:
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sdk: 3.8
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- name: Install dependencies
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
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run: dart pub get
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- name: Verify formatting
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run: PATH="$PATH:/usr/lib/dart/bin" dart format -l 110 --output=none --set-exit-if-changed .
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run: dart format -l 110 --output=none --set-exit-if-changed .
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fail_if_pull_request_is_draft:
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if: github.event.pull_request.draft == true
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runs-on: ubuntu-18.04
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runs-on: ubuntu-latest
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steps:
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- name: Fails in order to indicate that pull request needs to be marked as ready to review and formatting workflow needs to pass.
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run: exit 1

‎.github/workflows/gh-pages-dev.yml‎

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jobs:
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deploy:
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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steps:
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- name: Checkout dev branch
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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ref: dev
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- name: Checkout gh-pages branch
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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ref: gh-pages
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path: gh-pages-repo
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- name: Setup Dart SDK Step 1
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run: sudo apt-get update
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- name: Setup Dart SDK Step 2
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run: sudo apt-get install apt-transport-https
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- name: Setup Dart SDK Step 3
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run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
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- name: Setup Dart SDK Step 4
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run: sudo sh -c 'wget -qO- https://storage.googleapis.com/download.dartlang.org/linux/debian/dart_stable.list > /etc/apt/sources.list.d/dart_stable.list'
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- name: Setup Dart SDK Step 5
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run: wget -O /tmp/dart_3.5.4-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/3.5.4/linux_packages/dart_3.5.4-1_amd64.deb
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- name: Setup Dart SDK Step 6
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run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
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- name: Setup Dart SDK # Using Dart 3.8 to match pubspec.yaml constraint
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uses: dart-lang/setup-dart@v1 # https://github.com/dart-lang/setup-dart
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with:
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sdk: 3.8
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- name: Install dependencies
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
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run: dart pub get
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- name: Install webdev
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub global activate webdev
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run: dart pub global activate webdev
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- name: Build into gh-pages repo
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub global run webdev build -o web:gh-pages-repo/dev
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run: dart pub global run webdev build -o web:gh-pages-repo/dev
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3

‎.github/workflows/gh-pages.yml‎

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jobs:
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deploy:
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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steps:
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- name: Checkout main branch
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Checkout gh-pages branch
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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ref: gh-pages
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path: gh-pages-repo
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- name: Setup Dart SDK # Using Dart 3.8 to match pubspec.yaml constraint
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uses: dart-lang/setup-dart@v1 # https://github.com/dart-lang/setup-dart
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with:
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sdk: 3.8
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- name: Setup Dart SDK Step 1
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run: sudo apt-get update
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- name: Setup Dart SDK Step 2
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run: sudo apt-get install apt-transport-https
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- name: Setup Dart SDK Step 3
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run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
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- name: Setup Dart SDK Step 4
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run: sudo sh -c 'wget -qO- https://storage.googleapis.com/download.dartlang.org/linux/debian/dart_stable.list > /etc/apt/sources.list.d/dart_stable.list'
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- name: Setup Dart SDK Step 5
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run: wget -O /tmp/dart_3.5.4-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/3.5.4/linux_packages/dart_3.5.4-1_amd64.deb
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- name: Setup Dart SDK Step 6
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run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
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- name: Install dependencies
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
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- name: Install webdev
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub global activate webdev
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run: dart pub get
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- name: Activate webdev
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run: dart pub global activate webdev
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- name: Build into gh-pages repo
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run: PATH="$PATH:/usr/lib/dart/bin" dart pub global run webdev build -o web:/tmp/scadnano ; cp -r /tmp/scadnano/* gh-pages-repo
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run: dart pub global run webdev build -o web:/tmp/scadnano ; cp -r /tmp/scadnano/* gh-pages-repo
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- name: Retrieve version
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run: echo "VERSION=$(cat lib/src/constants.dart | grep 'const String CURRENT_VERSION = .*' | grep -oP '\d+\.\d+\.\d+')" >> $GITHUB_ENV
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run: echo "VERSION=$(cat lib/src/constants.dart | grep 'const String CURRENT_VERSION = .*' | grep -oP '\d+\.\d+\.\d+')" >> $GITHUB_ENV
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- name: Build into gh-pages-repo/VERSION
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run: |
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if [ "$VERSION" != "" ]; then
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PATH="$PATH:/usr/lib/dart/bin" dart pub global run webdev build -o web:gh-pages-repo/v$VERSION
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dart pub global run webdev build -o web:gh-pages-repo/v$VERSION
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else
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echo "::warning deploying VERSION skipped because VERSION number could not be found"
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fi

‎.github/workflows/release.yml‎

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jobs:
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release:
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name: "Release"
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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steps:
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# ...

‎CONTRIBUTING.md‎

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### Installing Dart
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This project requires using Dart version **3.5.4**, not the latest version. Click on a dropdown below for installation instructions for your operating system.
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This project requires using the latest Dart version. Click on a dropdown below for installation instructions for your operating system.
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<!--TODO: Find a way to use code blocks with syntax highlighting inside <details>-->
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<details><summary><strong>Windows</strong></summary>
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First, install <a href="https://chocolatey.org/install">Chocolatey</a> if you haven't already. If <code>choco help</code> shows a help menu for using Chocolatey, then you've set it up correctly.
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Then, open a shell (cmd/Powershell) with Administrative privileges (go to Start type `cmd`, right-click on "Command Prompt", or type Powershell and right-click on "Powershell"; in both cases pick "Run as administrator") and install Dart 3.5.4:
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Then, open a shell (cmd/Powershell) with Administrative privileges (go to Start type `cmd`, right-click on "Command Prompt", or type Powershell and right-click on "Powershell"; in both cases pick "Run as administrator") and install Dart:
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<pre>
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choco install dart-sdk --version 3.5.4
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</pre>
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To stop Chocolatey from automatically updating Dart to the latest version, pin it:
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<pre>
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choco pin --name="'dart-sdk'" --version="'3.5.4'"
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choco install dart-sdk
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</pre>
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</details>
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It may help to run `brew tap dart-lang/dart` first.
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Then, install Dart 3.5.4:
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<pre>
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brew install dart@3.5.4
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</pre>
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To stop Homebrew from automatically updating Dart to the latest version, pin it:
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Then, install Dart:
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<pre>
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brew pin dart@3.5.4
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brew install dart
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</pre>
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If running `dart` in a terminal now does not work, you may need to follow <a href="https://docs.brew.sh/FAQ#my-mac-apps-dont-find-homebrew-utilities">these instructions</a>.
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echo 'deb [signed-by=/usr/share/keyrings/dart.gpg arch=amd64] https://storage.googleapis.com/download.dartlang.org/linux/debian stable main' | sudo tee /etc/apt/sources.list.d/dart_stable.list
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</pre>
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Then, install Dart 3.5.4:
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Then, install Dart:
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<pre>
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sudo apt-get update
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sudo apt-get install dart=3.5.4
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</pre>
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To stop apt from automatically updating Dart to the latest version, hold it:
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<pre>
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sudo apt-mark hold dart=3.5.4
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sudo apt-get install dart
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</pre>
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</details>

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