Merge pull request #989 from UC-Davis-molecular-computing/419-migrate…

…-to-dart-null-safety-mode

419 migrate to dart null safety mode

.github/workflows/dart.yml

@@ -1,8 +1,8 @@
 name: Dart CI
 
-on:  
+on:
   pull_request:
-    types: [opened, synchronize, reopened, ready_for_review]
+    types: [ opened, synchronize, reopened, ready_for_review ]
 
 jobs:
   run_unit_tests:
@@ -11,27 +11,27 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-    - name: Setup Dart SDK Step 1
-      run: sudo apt-get update
-    - name: Setup Dart SDK Step 2
-      run: sudo apt-get install apt-transport-https
-    - name: Setup Dart SDK Step 3
-      run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
-    - 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_2.13.4-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.13.4/linux_packages/dart_2.13.4-1_amd64.deb
-    - name: Setup Dart SDK Step 6
-      run: sudo apt install /tmp/dart_2.13.4-1_amd64.deb
-    - uses: actions/checkout@v3
-    - name: Install dependencies
-      run: PATH="$PATH:/usr/lib/dart/bin" pub get
-    - name: Run tests
-      run: PATH="$PATH:/usr/lib/dart/bin" pub run build_runner test
+      - name: Setup Dart SDK Step 1
+        run: sudo apt-get update
+      - name: Setup Dart SDK Step 2
+        run: sudo apt-get install apt-transport-https
+      - name: Setup Dart SDK Step 3
+        run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
+      - 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
+      - name: Setup Dart SDK Step 6
+        run: sudo apt install /tmp/dart_2.19.6-1_amd64.deb
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
+      - name: Run tests
+        run: PATH="$PATH:/usr/lib/dart/bin" dart run build_runner test
 
   fail_if_pull_request_is_draft:
     if: github.event.pull_request.draft == true
     runs-on: ubuntu-18.04
     steps:
-    - name: Fails in order to indicate that pull request needs to be marked as ready to review and unit tests workflow needs to pass.
-      run: exit 1
+      - name: Fails in order to indicate that pull request needs to be marked as ready to review and unit tests workflow needs to pass.
+        run: exit 1

.github/workflows/dart_formatting.yml

@@ -1,8 +1,8 @@
 name: Dart Formatting
 
-on:  
+on:
   pull_request:
-    types: [opened, synchronize, reopened, ready_for_review]
+    types: [ opened, synchronize, reopened, ready_for_review ]
 
 jobs:
   check_formatting:
@@ -11,27 +11,27 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-    - name: Setup Dart SDK Step 1
-      run: sudo apt-get update
-    - name: Setup Dart SDK Step 2
-      run: sudo apt-get install apt-transport-https
-    - name: Setup Dart SDK Step 3
-      run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
-    - 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_2.13.4-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.13.4/linux_packages/dart_2.13.4-1_amd64.deb
-    - name: Setup Dart SDK Step 6
-      run: sudo apt install /tmp/dart_2.13.4-1_amd64.deb
-    - uses: actions/checkout@v3
-    - name: Install dependencies
-      run: PATH="$PATH:/usr/lib/dart/bin" pub get
-    - name: Verify formatting
-      run: dart format -l 110 --output=none --set-exit-if-changed .
-      
+      - name: Setup Dart SDK Step 1
+        run: sudo apt-get update
+      - name: Setup Dart SDK Step 2
+        run: sudo apt-get install apt-transport-https
+      - name: Setup Dart SDK Step 3
+        run: sudo sh -c 'wget -qO- https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -'
+      - name: Setup Dart SDK Step 4
+        run: sudo sh -c 'wget -qO- https://storage.googleapis.com/download.dartlang.org/linux/debian/dart_stable.list > /etc/apt/sources.list.d/dart_stable.list'
+      - name: Setup Dart SDK Step 5
+        run: wget -O /tmp/dart_2.19.6-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.19.6/linux_packages/dart_2.19.6-1_amd64.deb
+      - name: Setup Dart SDK Step 6
+        run: sudo apt install /tmp/dart_2.19.6-1_amd64.deb
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: PATH="$PATH:/usr/lib/dart/bin" dart pub get
+      - name: Verify formatting
+        run: dart format -l 110 --output=none --set-exit-if-changed .
+
   fail_if_pull_request_is_draft:
     if: github.event.pull_request.draft == true
     runs-on: ubuntu-18.04
     steps:
-    - name: Fails in order to indicate that pull request needs to be marked as ready to review and formatting workflow needs to pass.
-      run: exit 1
+      - name: Fails in order to indicate that pull request needs to be marked as ready to review and formatting workflow needs to pass.
+        run: exit 1

.gitignore

@@ -4,6 +4,9 @@
 # Remove the following pattern if you wish to check in your lock file
 # pubspec.lock
 
+# I used this to add `// @dart=2.9` to the top of all dart files
+add-line.py
+
 # Conventional directory for build outputs
 build/
 

CONTRIBUTING.md

@@ -350,7 +350,7 @@ server](https://dart.dev/tools/webdev#serve).
 
 Sometimes it may be necessary to clean out the generated files and cache if this has an error. See the file `clean.sh`, which has this line: `dart run build_runner clean`. Also see `remove_g.sh`, which removes all `.g.dart` files from the project, which can also help to fix compilation errors.
 
-If that does not work, try `dart run build_runner clean --delete-conflicting-outputs`.
+If that does not work, try `dart run build_runner build --delete-conflicting-outputs`, and then run `webdev serve`.
 
 Running `webdev serve --release` will compile the project in production mode (instead of development mode), which is claimed to be faster in principle if you are not doing development and just want to run scadnano offline.
 However, in scadnano, it doesn't appear to make a big difference whether development or production mode is used.

analysis_options.yaml

@@ -7,9 +7,23 @@ analyzer:
     uri_has_not_been_generated: ignore
     hash_and_equals: ignore
     unused_import: ignore
+  plugins:
+    - over_react
 #   exclude:
 #     - path/to/excluded/files/**
 
+# rules: https://workiva.github.io/over_react/analyzer_plugin/lints/
+over_react:
+  errors:
+    over_react_required_props: error
+    # I'd like the next but it mistakenly says I can do this when I can't, e.g., when using
+    # the spread operator, a for loop, or a conditional expression
+    over_react_variadic_children: ignore
+#    over_react_boilerplate_error: error
+#    over_react_incorrect_doc_comment_location: warning
+#    over_react_unnecessary_key: info
+#    over_react_pseudo_static_lifecycle: ignore
+
 # Lint rules and documentation, see http://dart-lang.github.io/linter/lints
 linter:
   rules:
@@ -20,4 +34,3 @@ linter:
     - test_types_in_equals
     - unrelated_type_equality_checks
     - valid_regexps
-

clean.bat

@@ -0,0 +1,4 @@
+dart run build_runner clean
+dart run build_runner build --delete-conflicting-outputs
+
+