Merge pull request #443 from sanger/develop

Develop into Master

.github/workflows/add_prs_to_tech_debt_project.yml

@@ -0,0 +1,19 @@
+# Calls a reusable workflow in the .github repo,
+# which adds the PR that triggered this to the Technical Debt project board, if it is a depfu one.
+# Passes the 'PSD-AddToProject' GitHub App key and App Id as secrets to the reusable workflow.
+
+name: Add dependencies to technical debt project
+
+on:
+  # Triggered on creation of pull requests with any label,
+  # or when a label is added to an existing pull request.
+  pull_request:
+    types:
+      - labeled
+
+jobs:
+  call-workflow-add_to_technical_debt_project:
+    uses: sanger/.github/.github/workflows/add_to_tech_debt_project_reusable.yml@master
+    secrets:
+      app_id: ${{ secrets.ADD_TO_PROJECT_APP_ID_PSD }}
+      app_key: ${{ secrets.ADD_TO_PROJECT_APP_KEY_PSD }}

.github/workflows/assign_issue_number.yml

@@ -0,0 +1,12 @@
+name: Assign Issue Number
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  call-add-to-project:
+    uses: sanger/.github/.github/workflows/generate_issue_number.yml@master
+    secrets:
+      app_id: ${{ secrets.ISSUE_GEN_APP_ID }}
+      app_key: ${{ secrets.ISSUE_GEN_APP_KEY }}

.github/workflows/check_release_version.yml

@@ -14,7 +14,7 @@ jobs:
 
       - name: Get specific changed files
         id: changed-files-specific
-        uses: tj-actions/changed-files@v23
+        uses: tj-actions/changed-files@v41
         with:
           files: |
             .release-version

.release-version

@@ -1 +1 @@
-3.7.0
+3.8.0

.rubocop.yml

@@ -15,5 +15,6 @@ require:
  - rubocop-rspec
 AllCops:
   NewCops: enable
+  SuggestExtensions: false
 Layout/LineLength:
   Max: 120

.rubocop_todo.yml

@@ -15,13 +15,13 @@ Lint/DuplicateMethods:
 # Offense count: 7
 Lint/MissingSuper:
   Exclude:
-    - 'app/presenters/asset/asset.rb'
-    - 'app/presenters/asset/index.rb'
-    - 'app/presenters/asset_type/asset_type.rb'
-    - 'app/presenters/batch/show.rb'
-    - 'app/presenters/report/new.rb'
-    - 'app/presenters/report/show.rb'
-    - 'app/presenters/workflow/show.rb'
+    - 'app/presenters/asset_presenter/asset.rb'
+    - 'app/presenters/asset_presenter/index.rb'
+    - 'app/presenters/asset_type_presenter/asset_type.rb'
+    - 'app/presenters/batch_presenter/show.rb'
+    - 'app/presenters/report_presenter/new.rb'
+    - 'app/presenters/report_presenter/show.rb'
+    - 'app/presenters/workflow_presenter/show.rb'
 
 # Offense count: 6
 Lint/UselessAssignment:
@@ -328,15 +328,15 @@ Style/CaseEquality:
 # SupportedStyles: nested, compact
 Style/ClassAndModuleChildren:
   Exclude:
-    - 'app/presenters/admin/index.rb'
-    - 'app/presenters/asset/asset.rb'
-    - 'app/presenters/asset/index.rb'
-    - 'app/presenters/asset_type/asset_type.rb'
-    - 'app/presenters/batch/new.rb'
-    - 'app/presenters/batch/show.rb'
-    - 'app/presenters/report/new.rb'
-    - 'app/presenters/report/show.rb'
-    - 'app/presenters/workflow/show.rb'
+    - 'app/presenters/admin_presenter/index.rb'
+    - 'app/presenters/asset_presenter/asset.rb'
+    - 'app/presenters/asset_presenter/index.rb'
+    - 'app/presenters/asset_type_presenter/asset_type.rb'
+    - 'app/presenters/batch_presenter/new.rb'
+    - 'app/presenters/batch_presenter/show.rb'
+    - 'app/presenters/report_presenter/new.rb'
+    - 'app/presenters/report_presenter/show.rb'
+    - 'app/presenters/workflow_presenter/show.rb'
 
 # Offense count: 69
 Style/Documentation:
@@ -359,15 +359,6 @@ Style/Documentation:
     - 'app/models/event.rb'
     - 'app/models/report.rb'
     - 'app/models/workflow.rb'
-    - 'app/presenters/asset/asset.rb'
-    - 'app/presenters/asset/index.rb'
-    - 'app/presenters/asset_type/asset_type.rb'
-    - 'app/presenters/batch/new.rb'
-    - 'app/presenters/batch/show.rb'
-    - 'app/presenters/presenter.rb'
-    - 'app/presenters/report/new.rb'
-    - 'app/presenters/report/show.rb'
-    - 'app/presenters/workflow/show.rb'
     - 'config/application.rb'
     - 'config/data/asset_types.rb'
     - 'config/data/pipeline_destinations.rb'
@@ -436,16 +427,7 @@ Style/FrozenStringLiteralComment:
     - 'app/models/report.rb'
     - 'app/models/state.rb'
     - 'app/models/workflow.rb'
-    - 'app/presenters/admin/index.rb'
-    - 'app/presenters/asset/asset.rb'
-    - 'app/presenters/asset/index.rb'
-    - 'app/presenters/asset_type/asset_type.rb'
-    - 'app/presenters/batch/new.rb'
-    - 'app/presenters/batch/show.rb'
-    - 'app/presenters/presenter.rb'
-    - 'app/presenters/report/new.rb'
-    - 'app/presenters/report/show.rb'
-    - 'app/presenters/workflow/show.rb'
+    - 'app/presenters/report_presenter/show.rb'
     - 'config.ru'
     - 'config/application.rb'
     - 'config/boot.rb'
@@ -611,3 +593,11 @@ Style/ZeroLengthPredicate:
   Exclude:
     - 'app/controllers/batches_controller.rb'
     - 'app/presenters/asset/index.rb'
+
+Rails/ThreeStateBooleanColumn:
+  Exclude:
+    - 'db/migrate/20190923133947_add_qc_flow_column_to_workflows.rb'
+
+Layout/LineLength:
+  Exclude:
+    - 'config/initializers/new_framework_defaults_7_0.rb'

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
-gem 'rails', '~> 6.1.6'
+gem 'rails', '~> 7.0.8'
 # Use mysql2 as the database for Active Record
 gem 'mysql2'
 # Use SCSS for stylesheets