[release] Merge Develop into Master for 14.90.1

.github/workflows/cucumber_tests.yml

@@ -17,6 +17,9 @@ env:
 
 on:
   push:
+    branches:
+      - develop
+      - master
   pull_request:
     types:
       # defaults
@@ -72,7 +75,7 @@ jobs:
         env:
           DBPORT: ${{ job.services.mysql.ports[3306] }}
         run: |
-          bin/setup
+          bin/setup --skip-server
           bundle exec rake assets:precompile
 
       # Actually run our tests

.github/workflows/lint.yml

@@ -2,6 +2,9 @@ name: Lint
 
 on:
   push:
+    branches:
+      - develop
+      - master
   pull_request:
     types:
       # defaults

.github/workflows/rake_tests.yml

@@ -14,6 +14,9 @@ env:
 
 on:
   push:
+    branches:
+      - develop
+      - master
   pull_request:
     types:
       # defaults

.github/workflows/rspec_feature_tests.yml

@@ -17,6 +17,9 @@ env:
 
 on:
   push:
+    branches:
+      - develop
+      - master
   pull_request:
     types:
       # defaults

.github/workflows/rspec_unit_tests.yml

@@ -17,6 +17,9 @@ env:
 
 on:
   push:
+    branches:
+      - develop
+      - master
   pull_request:
     types:
       # defaults

.gitignore

@@ -44,6 +44,9 @@ app/sample_manifest_excel/doc/
 docs/accessioning/**/*.png
 docs/accessioning/**/*.svg
 
+# Generated files from notification templates
+config/accession/*.j2
+
 # Test files
 capybara*.html
 spec/examples.txt

.nvmrc

@@ -1 +1 @@
-24.14.0
+24.14.1

.prettierignore

@@ -13,6 +13,7 @@
 *.log
 *.log.[0-9]
 *.min.js
+*.mjml
 *.orig
 *.sublime-workspace
 *.swp

.release-version

@@ -1 +1 @@
-14.90.0
+14.90.1

.rubocop.yml

@@ -26,11 +26,12 @@ plugins:
 AllCops:
   NewCops: enable
   Exclude:
+  - bin/*
+  - config/initializers/content_security_policy.rb
   - db/schema.rb
   - db/views_schema.rb
   - features/support/env.rb
   - lib/tasks/cucumber.rake
-  - bin/*
   - node_modules/**/*
   - tmp/**/*
 
@@ -255,6 +256,20 @@ Style/EmptyClassDefinition:
 Style/EmptyMethod:
   EnforcedStyle: expanded
 
+# This is now default in Ruby 3.4
+# Excluding generated files
+Style/FrozenStringLiteralComment:
+  Exclude:
+  - bin/*
+  - config/application.rb
+  - config/boot.rb
+  - config/environment.rb
+  - config/environments/*.rb
+  - config/initializers/content_security_policy.rb
+  - config/initializers/filter_parameter_logging.rb
+  - config/initializers/inflections.rb
+  - config/puma.rb
+
 # Only use shorthand hash syntax when all keys match the variables for better readability
 Style/HashSyntax:
   EnforcedShorthandSyntax: consistent
@@ -269,7 +284,17 @@ Style/QuotedSymbols:
   Exclude:
   - bin/*
 
-# these are generally generated files and don't need excessive linting
+# Files generated by Rails
 Style/StringLiterals:
   Exclude:
   - bin/*
+  - config/application.rb
+  - config/boot.rb
+  - config/environment.rb
+  - config/environments/*.rb
+  - config/puma.rb
+
+# Files generated by Rails and frequently updated
+Style/SymbolArray:
+  Exclude:
+  - config/initializers/filter_parameter_logging.rb

.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config --no-exclude-limit`
-# on 2026-03-13 13:25:22 UTC using RuboCop version 1.85.1.
+# on 2026-04-20 08:03:49 UTC using RuboCop version 1.86.1.
 # The point is for the user to remove these configuration records
 # one by one as the offenses are removed from the code base.
 # Note that changes in the inspected code, or installation of new
@@ -133,7 +133,7 @@ Lint/DuplicateMethods:
     - 'app/models/stock_stamper.rb'
     - 'lib/accession/tag.rb'
 
-# Offense count: 62
+# Offense count: 61
 # Configuration parameters: AllowComments, AllowEmptyLambdas.
 Lint/EmptyBlock:
   Exclude:
@@ -186,7 +186,6 @@ Lint/EmptyBlock:
     - 'test/factories/location_report_factories.rb'
     - 'test/unit/data_release_test.rb'
     - 'test/unit/fragment_test.rb'
-    - 'test/unit/tasks/plate_transfer_task_test.rb'
 
 # Offense count: 1
 # Configuration parameters: AllowComments.
@@ -499,15 +498,14 @@ Naming/PredicatePrefix:
     - 'lib/has_behaviour.rb'
     - 'lib/manifest_util.rb'
 
-# Offense count: 246
+# Offense count: 245
 # Configuration parameters: EnforcedStyle, CheckMethodNames, CheckSymbols, AllowedIdentifiers, AllowedPatterns.
 # SupportedStyles: snake_case, normalcase, non_integer
 # AllowedIdentifiers: TLS1_1, TLS1_2, capture3, iso8601, rfc1123_date, rfc822, rfc2822, rfc3339, x86_64
 Naming/VariableNumber:
   Exclude:
     - 'app/controllers/quad_stamp_controller.rb'
     - 'app/models/transfer_request.rb'
-    - 'config/application.rb'
     - 'db/seeds/0015_transfer_templates.rb'
     - 'spec/api/asset_audit_spec.rb'
     - 'spec/controllers/api/v2/heron/tube_racks_controller_spec.rb'
@@ -972,7 +970,7 @@ RSpec/MultipleDescribes:
     - 'spec/lib/label_printer/asset_labels_spec.rb'
     - 'spec/models/qc_result/qc_result_spec.rb'
 
-# Offense count: 925
+# Offense count: 926
 # Configuration parameters: Max.
 RSpec/MultipleExpectations:
   Exclude:
@@ -1563,14 +1561,6 @@ Rails/InverseOf:
     - 'app/models/well.rb'
     - 'app/models/work_order.rb'
 
-# Offense count: 4
-Rails/LexicallyScopedActionFilter:
-  Exclude:
-    - 'app/controllers/admin/programs_controller.rb'
-    - 'app/controllers/pipelines_controller.rb'
-    - 'app/controllers/projects_controller.rb'
-    - 'app/controllers/sdb/sample_manifests_controller.rb'
-
 # Offense count: 1
 # This cop supports unsafe autocorrection (--autocorrect-all).
 Rails/NegateInclude:
@@ -1602,6 +1592,30 @@ Rails/RootPathnameMethods:
   Exclude:
     - 'spec/rails_helper.rb'
 
+# Offense count: 19
+# This cop supports unsafe autocorrection (--autocorrect-all).
+Rails/StrongParametersExpect:
+  Exclude:
+    - 'app/controllers/admin/bait_libraries/bait_library_suppliers_controller.rb'
+    - 'app/controllers/admin/primer_panels_controller.rb'
+    - 'app/controllers/admin/programs_controller.rb'
+    - 'app/controllers/batches_controller.rb'
+    - 'app/controllers/bulk_submission_excel/downloads_controller.rb'
+    - 'app/controllers/labware_controller.rb'
+    - 'app/controllers/location_reports_controller.rb'
+    - 'app/controllers/npg_actions/assets_controller.rb'
+    - 'app/controllers/phi_x/spiked_buffers_controller.rb'
+    - 'app/controllers/phi_x/stocks_controller.rb'
+    - 'app/controllers/poolings_controller.rb'
+    - 'app/controllers/qc_files_controller.rb'
+    - 'app/controllers/receptacles_controller.rb'
+    - 'app/controllers/report_fails_controller.rb'
+    - 'app/controllers/stock_stampers_controller.rb'
+    - 'app/controllers/tag_groups_controller.rb'
+    - 'app/controllers/tag_layout_templates_controller.rb'
+    - 'app/controllers/tag_sets_controller.rb'
+    - 'app/controllers/tag_substitutions_controller.rb'
+
 # Offense count: 2
 Rails/ThreeStateBooleanColumn:
   Exclude:
@@ -2025,7 +2039,7 @@ Style/NumericPredicate:
     - 'lib/deployed.rb'
     - 'lib/submission_serializer.rb'
 
-# Offense count: 32
+# Offense count: 20
 # Configuration parameters: AllowedClasses.
 Style/OneClassPerFile:
   Exclude:
@@ -2038,14 +2052,6 @@ Style/OneClassPerFile:
     - 'lib/api_tools.rb'
     - 'lib/authenticated_test_helper.rb'
     - 'lib/informatics/test/helpers/authentication_helper.rb'
-    - 'spec/models/broadcast_event/broadcast_event_spec.rb'
-    - 'spec/support/api_v2_resource_matchers.rb'
-    - 'spec/uat_actions/uat_actions_spec.rb'
-    - 'test/controllers/authentication_controller_test.rb'
-    - 'test/lib/label_printer/labels_multiplication_test.rb'
-    - 'test/test_helper.rb'
-    - 'test/unit/eventful_entry_test.rb'
-    - 'test/unit/tasks/plate_transfer_task_test.rb'
 
 # Offense count: 18
 # Configuration parameters: AllowedMethods.

Gemfile

@@ -7,7 +7,7 @@ group :default do
   gem 'concurrent-ruby', '1.3.5'
   gem 'configatron'
   gem 'formtastic'
-  gem 'rails', '~> 7.2.0'
+  gem 'rails', '~> 8.0.0'
 
   # Previously part of ruby or rails, now separate gems
   gem 'drb'