Merge pull request #1010 from UC-Davis-molecular-computing/990-upgrad…

…e-to-dart-3

Fixes #990 - Upgrade to Dart 3

.github/workflows/dart.yml

@@ -20,10 +20,10 @@ jobs:
       - name: Setup Dart SDK Step 4
         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'
       - name: Setup Dart SDK Step 5
-        run: wget -O /tmp/dart_2.19.6-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.19.6/linux_packages/dart_2.19.6-1_amd64.deb
+        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
       - name: Setup Dart SDK Step 6
-        run: sudo apt install /tmp/dart_2.19.6-1_amd64.deb
-      - uses: actions/checkout@v3
+        run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
+      - uses: actions/checkout@v4
       - name: Install dependencies
         run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
       - name: Run tests

.github/workflows/dart_formatting.yml

@@ -20,14 +20,14 @@ jobs:
       - name: Setup Dart SDK Step 4
         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'
       - name: Setup Dart SDK Step 5
-        run: wget -O /tmp/dart_2.19.6-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.19.6/linux_packages/dart_2.19.6-1_amd64.deb
+        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
       - name: Setup Dart SDK Step 6
-        run: sudo apt install /tmp/dart_2.19.6-1_amd64.deb
-      - uses: actions/checkout@v3
+        run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
+      - uses: actions/checkout@v4
       - name: Install dependencies
         run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
       - name: Verify formatting
-        run: dart format -l 110 --output=none --set-exit-if-changed .
+        run: PATH="$PATH:/usr/lib/dart/bin" dart format -l 110 --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

@@ -31,9 +31,9 @@ jobs:
       - name: Setup Dart SDK Step 4
         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'
       - name: Setup Dart SDK Step 5
-        run: wget -O /tmp/dart_2.19.6-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.19.6/linux_packages/dart_2.19.6-1_amd64.deb
+        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
       - name: Setup Dart SDK Step 6
-        run: sudo apt install /tmp/dart_2.19.6-1_amd64.deb
+        run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
 
       - name: Install dependencies
         run: PATH="$PATH:/usr/lib/dart/bin" dart pub get

.github/workflows/gh-pages.yml

@@ -29,14 +29,14 @@ jobs:
       - name: Setup Dart SDK Step 4
         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'
       - name: Setup Dart SDK Step 5
-        run: wget -O /tmp/dart_2.19.6-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.19.6/linux_packages/dart_2.19.6-1_amd64.deb
+        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
       - name: Setup Dart SDK Step 6
-        run: sudo apt install /tmp/dart_2.19.6-1_amd64.deb
+        run: sudo apt install /tmp/dart_3.5.4-1_amd64.deb
       - name: Install dependencies
-        run: PATH="$PATH:/usr/lib/dart/bin" pub get
+        run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
 
       - name: Install webdev
-        run: PATH="$PATH:/usr/lib/dart/bin" pub global activate webdev
+        run: PATH="$PATH:/usr/lib/dart/bin" dart pub global activate webdev
 
 
       - name: Build into gh-pages repo

CONTRIBUTING.md

@@ -241,23 +241,23 @@ git checkout dev
 
 ### Installing Dart
 
-This project requires using Dart version **2.19.6**, not the latest version, which is 3.x. Click on a dropdown below for installation instructions for your operating system.
+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.
 
 <!--TODO: Find a way to use code blocks with syntax highlighting inside <details>-->
 
 <details><summary><strong>Windows</strong></summary>
 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.
 
-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 2.19.6:
+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:
 
 <pre>
-choco install dart-sdk --version 2.19.6
+choco install dart-sdk --version 3.5.4
 </pre>
 
 To stop Chocolatey from automatically updating Dart to the latest version, pin it:
 
 <pre>
-choco pin --name="'dart-sdk'" --version="'2.19.6'"
+choco pin --name="'dart-sdk'" --version="'3.5.4'"
 </pre>
 
 </details>
@@ -267,16 +267,16 @@ First, install <a href="https://brew.sh/">Homebrew</a> if you haven't already. I
 
 It may help to run `brew tap dart-lang/dart` first.
 
-Then, install Dart 2.19.6:
+Then, install Dart 3.5.4:
 
 <pre>
-brew install dart@2.19.6
+brew install dart@3.5.4
 </pre>
 
 To stop Homebrew from automatically updating Dart to the latest version, pin it:
 
 <pre>
-brew pin dart@2.19.6
+brew pin dart@3.5.4
 </pre>
 
 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>.
@@ -292,17 +292,17 @@ wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | sudo gpg --dea
 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
 </pre>
 
-Then, install Dart 2.19.6:
+Then, install Dart 3.5.4:
 
 <pre>
 sudo apt-get update
-sudo apt-get install dart=2.19.6
+sudo apt-get install dart=3.5.4
 </pre>
 
 To stop apt from automatically updating Dart to the latest version, hold it:
 
 <pre>
-sudo apt-mark hold dart=2.19.6
+sudo apt-mark hold dart=3.5.4
 </pre>
 
 </details>
@@ -323,6 +323,8 @@ Try running the unit tests like this:
 dart run build_runner test
 ```
 
+If the above command fails, it should be run as sudo or an administrator.
+
 It should report something like this after running the tests:
 
 ```
@@ -347,7 +349,7 @@ Built test:test.
 `webdev` is used to run a local server for running scadnano in your browser for testing. Install it with:
 
 ```
-pub global activate webdev
+dart pub global activate webdev
 ```
 
 Note that often a message like this appears:

analysis_options.yaml

@@ -29,8 +29,6 @@ linter:
   rules:
     - cancel_subscriptions
     - hash_and_equals
-    - iterable_contains_unrelated_type
-    - list_remove_unrelated_type
     - test_types_in_equals
     - unrelated_type_equality_checks
     - valid_regexps

lib/src/middleware/export_cadnano_file.dart

@@ -358,7 +358,7 @@ have different parity of row number: respectively ${helix_from_dct['row']} and $
   } else if (!forward_from && !forward_to) {
     helix_from_dct[strand_type][start_from]
         .setRange(2, helix_from_dct[strand_type][start_from].length, [helix_to, end_to - 1]);
-    helix_to_dct[strand_type][start_to].setRange(0, 2, [helix_from, end_from - 1]);
+    helix_to_dct[strand_type][end_to - 1].setRange(0, 2, [helix_from, start_from]);
     if (helix_from_dct['row'] % 2 != helix_to_dct['row'] % 2) {
       throw new IllegalCadnanoDesignError('''\
 Paranemic crossovers are only allowed between helices that have the same parity of