Merge pull request #749 from UC-Davis-molecular-computing/dev

Dev
UC-Davis-molecular-computing · Feb 18, 2022 · c5dbfc0 · c5dbfc0
2 parents 8e1a0fc + d2784ba
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,20 @@
+<!--- Provide a general summary of your changes in the Title above -->
+
+## Description
+<!--- Describe your changes in detail -->
+
+## Related Issue
+<!--- If suggesting a new feature or change, please discuss it in an issue first -->
+<!--- If fixing a bug, there should be an issue describing it with steps to reproduce -->
+<!--- Please link to the issue here: -->
+
+## Motivation and Context
+<!--- Why is this change required? What problem does it solve? -->
+<!--- If it fixes an open issue, please link to the issue here. -->
+
+## How Has This Been Tested?
+<!--- Please describe in detail how you tested your changes. -->
+<!--- Include details of your testing environment, and the tests you ran to -->
+<!--- see how your change affects other areas of the code, etc. -->
+
+## Screenshots (if appropriate):
diff --git a/.github/workflows/dart.yml b/.github/workflows/dart.yml
@@ -1,9 +1,12 @@
 name: Dart CI
 
-on: [pull_request]
+on:  
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
 
 jobs:
-  build:
+  run_unit_tests:
+    if: github.event.pull_request.draft == false
 
     runs-on: ubuntu-18.04
 
@@ -17,11 +20,18 @@ 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_2.9.3-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.9.3/linux_packages/dart_2.9.3-1_amd64.deb
+      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_2.9.3-1_amd64.deb
+      run: sudo apt install /tmp/dart_2.13.4-1_amd64.deb
     - uses: actions/checkout@v1
     - 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
+
+  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
diff --git a/.github/workflows/gh-pages-dev.yml b/.github/workflows/gh-pages-dev.yml
@@ -9,11 +9,13 @@ jobs:
   deploy:
     runs-on: ubuntu-18.04
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout dev branch
+        uses: actions/checkout@v2
         with:
           ref: dev
 
-      - uses: actions/checkout@v2
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
         with:
           ref: gh-pages
           path: gh-pages-repo
@@ -29,9 +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_2.9.3-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.9.3/linux_packages/dart_2.9.3-1_amd64.deb
+        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_2.9.3-1_amd64.deb
+        run: sudo apt install /tmp/dart_2.13.4-1_amd64.deb
 
       - name: Install dependencies
         run: PATH="$PATH:/usr/lib/dart/bin" pub get

diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
@@ -9,9 +9,11 @@ jobs:
   deploy:
     runs-on: ubuntu-18.04
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout main branch
+        uses: actions/checkout@v2
 
-      - uses: actions/checkout@v2
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
         with:
           ref: gh-pages
           path: gh-pages-repo
@@ -27,9 +29,9 @@ 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_2.9.3-1_amd64.deb https://storage.googleapis.com/dart-archive/channels/stable/release/2.9.3/linux_packages/dart_2.9.3-1_amd64.deb
+        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_2.9.3-1_amd64.deb
+        run: sudo apt install /tmp/dart_2.13.4-1_amd64.deb
       - name: Install dependencies
         run: PATH="$PATH:/usr/lib/dart/bin" pub get
 

diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,7 @@
 .dart_tool/
 .packages
 # Remove the following pattern if you wish to check in your lock file
-pubspec.lock
+# pubspec.lock
 
 # Conventional directory for build outputs
 build/

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -475,7 +475,7 @@ For any more significant change that is made (e.g., closing an issue, adding a n
 
 7. Commit the changes. In the commit message, reference the issue using the phrase "fixes #123" (for bug fixes) or "closes #123" (for new features) (see [here](https://docs.github.com/en/enterprise/2.16/user/github/managing-your-work-on-github/closing-issues-using-keywords)). Also, in the commit message, describe the issue that was fixed (one easy way is to copy the title of the issue); this message will show up in automatically generated release notes, so this is part of the official documentation of what changed.
 
-8. Create a pull request (PR). **WARNING:** by default, it will want to merge into the `master` branch. Change the destination branch to `dev`.
+8. Create a pull request (PR). **WARNING:** by default, it will want to merge into the `master` branch. Change the destination branch to `dev`. Fill in the automatically provided template.
 
 9. Wait for all checks to complete (see next section), and then merge the changes from the new branch into `dev`. This will typically require someone else to review the code first and possibly request changes.
 
@@ -546,4 +546,4 @@ and WebStorm offers a [plugin](https://plugins.jetbrains.com/plugin/6351-dart).
 The line length should be configured to 110, as the style guide limit of 80
 is a bit too restrictive.
 
-We also follow the [OverReact style guide](https://github.com/Workiva/over_react#component-formatting), in particular, using trailing commas so that dartfmt (Dart's formatting tool) lines up the components nicely.
+We also follow the [OverReact style guide](https://github.com/Workiva/over_react#component-formatting), in particular, using trailing commas so that dartfmt (Dart's formatting tool) lines up the components nicely.
diff --git a/lib/src/actions/actions.dart b/lib/src/actions/actions.dart
@@ -8,6 +8,8 @@ import 'package:built_value/serializer.dart';
 import 'package:color/color.dart';
 import 'package:js/js.dart';
 import 'package:built_collection/built_collection.dart';
+import 'package:scadnano/src/dna_file_type.dart';
+import 'package:scadnano/src/state/dna_assign_options.dart';
 import 'package:scadnano/src/state/domains_move.dart';
 import 'package:scadnano/src/state/export_dna_format_strand_order.dart';
 import 'package:scadnano/src/state/geometry.dart';
@@ -236,6 +238,21 @@ abstract class LocalStorageDesignChoiceSet
   static Serializer<LocalStorageDesignChoiceSet> get serializer => _$localStorageDesignChoiceSetSerializer;
 }
 
+/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// erase localStorage stored design and storable UI settings
+
+abstract class ResetLocalStorage
+    with BuiltJsonSerializable
+    implements Action, Built<ResetLocalStorage, ResetLocalStorageBuilder> {
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ResetLocalStorage() = _$ResetLocalStorage._;
+
+  ResetLocalStorage._();
+
+  static Serializer<ResetLocalStorage> get serializer => _$resetLocalStorageSerializer;
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // Clear helix selection when loading new design
 
@@ -705,17 +722,17 @@ abstract class SetOnlyDisplaySelectedHelices
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // invert y-axis
 
-abstract class InvertXYSet
+abstract class InvertYSet
     with BuiltJsonSerializable
-    implements Action, SvgPngCacheInvalidatingAction, Built<InvertXYSet, InvertXYSetBuilder> {
-  bool get invert_xy;
+    implements Action, SvgPngCacheInvalidatingAction, Built<InvertYSet, InvertYSetBuilder> {
+  bool get invert_y;
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory InvertXYSet({bool invert_xy}) = _$InvertXYSet._;
+  factory InvertYSet({bool invert_y}) = _$InvertYSet._;
 
-  InvertXYSet._();
+  InvertYSet._();
 
-  static Serializer<InvertXYSet> get serializer => _$invertXYSetSerializer;
+  static Serializer<InvertYSet> get serializer => _$invertYSetSerializer;
 }
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -765,7 +782,11 @@ abstract class LoadDNAFile
 
   /************************ begin BuiltValue boilerplate ************************/
   factory LoadDNAFile(
-      {String content, String filename, bool write_local_storage = true, bool unit_testing = false, DNAFileType dna_file_type = DNAFileType.scadnano_file}) {
+      {String content,
+      String filename,
+      bool write_local_storage = true,
+      bool unit_testing = false,
+      DNAFileType dna_file_type = DNAFileType.scadnano_file}) {
     return LoadDNAFile.from((b) => b
       ..content = content
       ..filename = filename
@@ -1591,6 +1612,7 @@ abstract class HelixMinOffsetSetByDomainsAll
       _$helixMinOffsetSetByDomainsAllSerializer;
 }
 
+// when we want each helix to have its own max based on its domains
 abstract class HelixMaxOffsetSetByDomainsAll
     with BuiltJsonSerializable, UndoableAction
     implements Action, Built<HelixMaxOffsetSetByDomainsAll, HelixMaxOffsetSetByDomainsAllBuilder> {
@@ -1603,6 +1625,21 @@ abstract class HelixMaxOffsetSetByDomainsAll
       _$helixMaxOffsetSetByDomainsAllSerializer;
 }
 
+// when we want the same max to be applied to all helices
+abstract class HelixMaxOffsetSetByDomainsAllSameMax
+    with BuiltJsonSerializable, UndoableAction
+    implements
+        Action,
+        Built<HelixMaxOffsetSetByDomainsAllSameMax, HelixMaxOffsetSetByDomainsAllSameMaxBuilder> {
+  /************************ begin BuiltValue boilerplate ************************/
+  factory HelixMaxOffsetSetByDomainsAllSameMax() = _$HelixMaxOffsetSetByDomainsAllSameMax;
+
+  HelixMaxOffsetSetByDomainsAllSameMax._();
+
+  static Serializer<HelixMaxOffsetSetByDomainsAllSameMax> get serializer =>
+      _$helixMaxOffsetSetByDomainsAllSameMaxSerializer;
+}
+
 abstract class HelixOffsetChangeAll
     with BuiltJsonSerializable, UndoableAction
     implements Built<HelixOffsetChangeAll, HelixOffsetChangeAllBuilder> {
@@ -1770,13 +1807,17 @@ abstract class ConvertCrossoverToLoopout
 
   int get length;
 
+  @nullable
+  String get dna_sequence;
+
   StrandPart get strand_part => crossover;
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory ConvertCrossoverToLoopout(Crossover crossover, int length) =>
+  factory ConvertCrossoverToLoopout(Crossover crossover, int length, [String dna_sequence = null]) =>
       ConvertCrossoverToLoopout.from((b) => b
         ..crossover.replace(crossover)
-        ..length = length);
+        ..length = length
+        ..dna_sequence = dna_sequence);
 
   factory ConvertCrossoverToLoopout.from([void Function(ConvertCrossoverToLoopoutBuilder) updates]) =
       _$ConvertCrossoverToLoopout;
@@ -1850,6 +1891,29 @@ abstract class JoinStrandsByCrossover
   static Serializer<JoinStrandsByCrossover> get serializer => _$joinStrandsByCrossoverSerializer;
 }
 
+// used to move a linker (crossover or loopout, stored as potential_crossover.linker)
+// so that one end stays fixed (stored in potential_crossover.dna_end_first_clicked)
+// while the other end moves to dna_end_second_click, editing two strands
+abstract class MoveLinker
+    with BuiltJsonSerializable, UndoableAction
+    implements Action, Built<MoveLinker, MoveLinkerBuilder> {
+  PotentialCrossover get potential_crossover;
+
+  DNAEnd get dna_end_second_click;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  @memoized
+  int get hashCode;
+
+  factory MoveLinker({PotentialCrossover potential_crossover, DNAEnd dna_end_second_click}) = _$MoveLinker._;
+
+  factory MoveLinker.from([void Function(MoveLinkerBuilder) updates]) = _$MoveLinker;
+
+  MoveLinker._();
+
+  static Serializer<MoveLinker> get serializer => _$moveLinkerSerializer;
+}
+
 // JoinStrandsByCrossover cannot be in a BatchAction since the reducer for it looks up strands
 // from the Design, which are invalidated as the Design is modified.
 // Also, to keep the complex logic in the reducer and out of the view code,
@@ -2166,8 +2230,12 @@ abstract class DomainsMoveStartSelectedDomains
     implements Action, Built<DomainsMoveStartSelectedDomains, DomainsMoveStartSelectedDomainsBuilder> {
   Address get address;
 
+  BuiltMap<int, int> get original_helices_view_order_inverse;
+
   /************************ begin BuiltValue boilerplate ************************/
-  factory DomainsMoveStartSelectedDomains({Address address}) = _$DomainsMoveStartSelectedDomains._;
+  factory DomainsMoveStartSelectedDomains(
+      {Address address,
+      BuiltMap<int, int> original_helices_view_order_inverse}) = _$DomainsMoveStartSelectedDomains._;
 
   DomainsMoveStartSelectedDomains._();
 
@@ -2379,15 +2447,22 @@ abstract class AssignDNA
     implements Built<AssignDNA, AssignDNABuilder> {
   Strand get strand;
 
-  String get dna_sequence;
+  DNAAssignOptions get dna_assign_options;
 
-  bool get assign_complements;
+  // convenience getters since we already have a lot of code referencing some of these from the old
+  // design of this Action
+  String get dna_sequence => dna_assign_options.dna_sequence;
 
-  bool get warn_on_change;
+  bool get use_predefined_dna_sequence => dna_assign_options.use_predefined_dna_sequence;
+
+  bool get assign_complements => dna_assign_options.assign_complements;
+
+  bool get disable_change_sequence_bound_strand => dna_assign_options.disable_change_sequence_bound_strand;
+
+  int get m13_rotation => dna_assign_options.m13_rotation;
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory AssignDNA({Strand strand, String dna_sequence, bool assign_complements, bool warn_on_change}) =
-      _$AssignDNA._;
+  factory AssignDNA({Strand strand, DNAAssignOptions dna_assign_options}) = _$AssignDNA._;
 
   AssignDNA._();
 
@@ -2783,6 +2858,31 @@ abstract class ModificationRemove
   static Serializer<ModificationRemove> get serializer => _$modificationRemoveSerializer;
 }
 
+abstract class ModificationConnectorLengthSet
+    with BuiltJsonSerializable
+    implements Action, Built<ModificationConnectorLengthSet, ModificationConnectorLengthSetBuilder> {
+  Strand get strand;
+
+  Modification get modification;
+
+  int get connector_length;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  @memoized
+  int get hashCode;
+
+  factory ModificationConnectorLengthSet({Strand strand, Modification modification, int connector_length}) =
+      _$ModificationConnectorLengthSet._;
+
+  factory ModificationConnectorLengthSet.from(
+      [void Function(ModificationConnectorLengthSetBuilder) updates]) = _$ModificationConnectorLengthSet;
+
+  ModificationConnectorLengthSet._();
+
+  static Serializer<ModificationConnectorLengthSet> get serializer =>
+      _$modificationConnectorLengthSetSerializer;
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // modification edit
 
@@ -3223,7 +3323,7 @@ abstract class AutofitSet with BuiltJsonSerializable implements Action, Built<Au
 }
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// show or hide helix circles/text in main view
+// show or hide helix circles/text, or entire helix (including offset lines) in main view
 
 abstract class ShowHelixCirclesMainViewSet
     with BuiltJsonSerializable
@@ -3238,6 +3338,26 @@ abstract class ShowHelixCirclesMainViewSet
   static Serializer<ShowHelixCirclesMainViewSet> get serializer => _$showHelixCirclesMainViewSetSerializer;
 }
 
+abstract class ShowHelixComponentsMainViewSet
+    with BuiltJsonSerializable
+    implements Action, Built<ShowHelixComponentsMainViewSet, ShowHelixComponentsMainViewSetBuilder> {
+  bool get show_helix_components;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  @memoized
+  int get hashCode;
+
+  factory ShowHelixComponentsMainViewSet({bool show_helix_components}) = _$ShowHelixComponentsMainViewSet._;
+
+  factory ShowHelixComponentsMainViewSet.from(
+      [void Function(ShowHelixComponentsMainViewSetBuilder) updates]) = _$ShowHelixComponentsMainViewSet;
+
+  ShowHelixComponentsMainViewSet._();
+
+  static Serializer<ShowHelixComponentsMainViewSet> get serializer =>
+      _$showHelixComponentsMainViewSetSerializer;
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // show or hide the edit menu