Merge remote-tracking branch 'origin/develop' into allow_submission_f…

…rom_stock_plate_test_branch

.github/workflows/automated_release.yml

@@ -27,17 +27,17 @@ jobs:
         with:
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
 
-      # Actually run our build
-      - name: Create Build
-        run: ./compile-build
-
       # Create a release tag based on the branch name and .release-version file
       - name: Set release tag
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         # On the develop branch this might create RELEASE_VERSION=2.4.6-987654321-develop
         # On the master branch this would then only create RELEASE_VERSION=2.4.6
         run: echo "RELEASE_VERSION=$(printf -- '%s%s\n' $(cat .release-version) $([ ${BRANCH_NAME} = "develop" ] && printf -- '-%s-develop' ${GITHUB_RUN_ID} || echo ""))" >> $GITHUB_ENV
 
+      # Actually run our build
+      - name: Create Build
+        run: ./compile-build '' v${{ env.RELEASE_VERSION }} ${BRANCH_NAME}
+
       # Create a GitHub release with the release asset as an artifact
       - name: Create release and upload release.tar.gz
         uses: ncipollo/[email protected]

.github/workflows/check_release_version.yml

@@ -5,10 +5,19 @@ on:
   pull_request:
     branches:
       - master
+    types:
+      # defaults
+      - opened
+      - synchronize
+      - reopened
+      # custom
+      - ready_for_review # required for Github-created PRs
 
 jobs:
   check:
     runs-on: ubuntu-latest
+    # only run when PR is not draft
+    if: ${{ !github.event.pull_request.draft }}
     steps:
       - uses: actions/checkout@v4
 

.github/workflows/create_release_pr.yml

@@ -0,0 +1,61 @@
+# Create or update merge-to-master pull requests for production releases
+# Note that by design, creating or editing a PR will not trigger a downstream `pull_request` event as this could lead to recursion
+name: Release
+on:
+  push:
+    branches:
+      - develop
+jobs:
+  pull_request:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Create or update PR
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          PR_TITLE="[automated] Merge Develop into Master"
+
+          # Extract numbers from PRs that have been merged into develop
+          PR_NUMBERS=$(gh api repos/:owner/:repo/compare/master...develop --jq '
+          .commits[]
+          | select(.commit.message
+          | startswith("Merge pull request"))
+          | .commit.message
+          | capture("#(?<pr_number>\\d+)")
+          | .pr_number'
+          )
+
+          # Fetch titles for each PR number
+          PR_NUMBERS_AND_TITLES=$(for PR_NUMBER in $PR_NUMBERS; do
+            gh pr view $PR_NUMBER --json number,title --jq '{number: .number, title: .title}'
+          done | jq -s 'sort_by(.title)')
+
+          # Sort extracted PR numbers by title
+          SORTED_PR_NUMBERS=$(jq -r '.[].number' <<< "$PR_NUMBERS_AND_TITLES")
+
+          STORIES=$(xargs -I {} gh pr view {} --json body --jq '.body | if . | test("Closes #\\d+") then capture("Closes #(?<issue_number>\\d+)") | "- #{}
+            - Closes #" + .issue_number else "- #{}" end' <<< "$SORTED_PR_NUMBERS") # Note the line-break on this line is for formatting
+
+          PR_BODY="#### Changes proposed in this pull request
+
+          $(echo "$STORIES")
+
+          #### Instructions for Reviewers
+
+          - _Check stories are ready for release._
+          - _Check for any database migrations._
+          - _Check for debug code._
+          - _Check version is appropriate._
+
+          This description will be overwritten on the next push
+          This PR was auto-generated on $(TZ=Europe/London date --iso-8601=seconds)"
+
+          # Check if a PR already exists
+          EXISTING_PR=$(gh pr list --base master --head develop --json number --jq '.[0].number')
+
+          if [ -z "$EXISTING_PR" ]; then
+            gh pr create --base master --head develop --title "$PR_TITLE" --body "$PR_BODY" --draft
+          else
+            gh pr edit "$EXISTING_PR" --body "$PR_BODY"
+          fi

.prettierignore

@@ -10,6 +10,7 @@ public/stylesheets/*.css
 .sass-cache/
 *.orig
 *.sublime-workspace
+/bin
 /public/packs
 /public/packs-test
 /node_modules

.prettierrc.json

@@ -1,5 +1,7 @@
 {
   "printWidth": 120,
   "semi": false,
-  "singleQuote": true
+  "rubySingleQuote": true,
+  "singleQuote": true,
+  "plugins": ["@prettier/plugin-ruby"]
 }

.pryrc

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+if defined?(PryByebug)
+  Pry.commands.alias_command 's', 'step'
+  Pry.commands.alias_command 'n', 'next'
+  Pry.commands.alias_command 'f', 'finish'
+  Pry.commands.alias_command 'c', 'continue'
+end

.release-version

@@ -1 +1 @@
-3.60.0
+3.61.1

.rubocop.yml

@@ -22,6 +22,11 @@ Rails/FindBy:
   Enabled: false
 Style/ClassAndModuleChildren:
   Enabled: false
+
+# Only use shorthand hash syntax when all keys match the variables for better readability
+Style/HashSyntax:
+  EnforcedShorthandSyntax: consistent
+
 # Filter out all the DSLs
 Metrics/BlockLength:
   CountAsOne:

.rubocop_todo.yml

@@ -1,17 +1,52 @@
 # This configuration was generated by
-# `rubocop --auto-gen-config`
-# on 2023-10-17 14:45:52 UTC using RuboCop version 1.39.0.
+# `rubocop --auto-gen-config --no-exclude-limit`
+# on 2024-09-20 10:20:24 UTC using RuboCop version 1.65.1.
 # 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
 # versions of RuboCop, may require this file to be generated again.
 
-# Offense count: 7
-# Configuration parameters: CountComments, CountAsOne, ExcludedMethods, AllowedMethods, AllowedPatterns, IgnoredMethods.
-Metrics/MethodLength:
-  Max: 21
-
+# Offense count: 2
+# Configuration parameters: LengthThreshold.
 Metrics/CollectionLiteralLength:
   Exclude:
-    - 'spec/models/labware_creators/quadrant_split_plate_spec.rb'
     - 'spec/helpers/well_helpers_spec.rb'
+    - 'spec/models/labware_creators/quadrant_split_plate_spec.rb'
+
+# Offense count: 36
+# Configuration parameters: CountComments, Max, CountAsOne, AllowedMethods, AllowedPatterns.
+Metrics/MethodLength:
+  Exclude:
+    - 'app/controllers/labware_controller.rb'
+    - 'app/controllers/pipeline_work_in_progress_controller.rb'
+    - 'app/controllers/plates_controller.rb'
+    - 'app/helpers/plate_helper.rb'
+    - 'app/models/concerns/labware_creators/donor_pooling_calculator.rb'
+    - 'app/models/concerns/presenters/extended_csv.rb'
+    - 'app/models/concerns/presenters/statemachine.rb'
+    - 'app/models/labware_creators/custom_tagged_plate.rb'
+    - 'app/models/labware_creators/final_tube.rb'
+    - 'app/models/labware_creators/multi_stamp_tubes.rb'
+    - 'app/models/labware_creators/multi_stamp_tubes_using_tube_rack_scan.rb'
+    - 'app/models/labware_creators/pcr_cycles_binned_plate/csv_file/well_details_header_base.rb'
+    - 'app/models/labware_creators/pcr_cycles_binned_plate_for_t_nano_seq.rb'
+    - 'app/models/labware_creators/plate_split_to_tube_racks.rb'
+    - 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb'
+    - 'app/models/labware_creators/well_filter_allowing_partials.rb'
+    - 'app/models/pipeline_list.rb'
+    - 'app/models/print_job.rb'
+    - 'app/models/robots/splitting_robot.rb'
+    - 'app/models/sequencescape_submission.rb'
+    - 'app/models/utility/common_dilution_calculations.rb'
+    - 'app/models/utility/concentration_binning_calculator.rb'
+    - 'app/models/utility/normalised_binning_calculator.rb'
+    - 'app/models/validators/stock_state_validator.rb'
+    - 'config/initializers/settings.rb'
+    - 'spec/support/api_url_helper.rb'
+    - 'spec/support/factory_bot_extensions.rb'
+    - 'spec/support/feature_helpers.rb'
+    - 'spec/support/with_pmb_stubbed.rb'
+
+Style/NumericPredicate:
+  Exclude:
+    - 'lib/deployed_version.rb'

.ruby-version

@@ -1 +1 @@
-3.0.6
+3.2.5

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:3.0.6-slim
+FROM ruby:3.2.5-slim
 
 ARG bundlerWithout="development test lint"
 ARG yarnFlags="--production"

Gemfile

@@ -67,4 +67,11 @@ group :lint do
   gem 'rubocop', require: false
   gem 'rubocop-performance', require: false
   gem 'rubocop-rails', require: false
+
+  # Ruby dependencies specifically requested by prettier/plugin-ruby v4
+  # https://github.com/prettier/plugin-ruby
+  gem 'prettier_print', require: false
+  gem 'syntax_tree', require: false
+  gem 'syntax_tree-haml', require: false
+  gem 'syntax_tree-rbs', require: false
 end

Gemfile.lock

@@ -186,6 +186,10 @@ GEM
       guard (~> 2.1)
       guard-compat (~> 1.1)
       rspec (>= 2.99.0, < 4.0)
+    haml (6.3.0)
+      temple (>= 0.8.2)
+      thor
+      tilt
     hashdiff (1.1.0)
     hashie (5.0.0)
     i18n (1.14.5)
@@ -247,6 +251,7 @@ GEM
     parser (3.3.4.0)
       ast (~> 2.4.1)
       racc
+    prettier_print (1.2.1)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
@@ -309,6 +314,8 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
+    rbs (3.5.3)
+      logger
     rdoc (6.7.0)
       psych (>= 4.0.0)
     regexp_parser (2.9.2)
@@ -386,7 +393,19 @@ GEM
     state_machines (0.6.0)
     stringio (3.1.1)
     strscan (3.1.0)
+    syntax_tree (6.2.0)
+      prettier_print (>= 1.2.0)
+    syntax_tree-haml (4.0.3)
+      haml (>= 5.2)
+      prettier_print (>= 1.2.1)
+      syntax_tree (>= 6.0.0)
+    syntax_tree-rbs (1.0.0)
+      prettier_print
+      rbs
+      syntax_tree (>= 2.0.1)
+    temple (0.10.3)
     thor (1.3.1)
+    tilt (2.4.0)
     timeout (0.4.1)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
@@ -407,7 +426,7 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
     websocket (1.2.11)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
@@ -432,6 +451,7 @@ DEPENDENCIES
   launchy
   oj
   pmb-client (= 0.1.0)!
+  prettier_print
   pry
   pry-byebug
   puma
@@ -452,11 +472,14 @@ DEPENDENCIES
   simplecov-lcov
   sprint_client
   state_machines
+  syntax_tree
+  syntax_tree-haml
+  syntax_tree-rbs
   vite_rails
   vite_ruby
   web-console
   webmock
   yard
 
 BUNDLED WITH
-   2.2.33
+   2.5.19

README.md

@@ -28,19 +28,19 @@ You must have Docker Desktop installed on your machine. Then the only command
 you should need to run is:
 
 ```shell
-docker-compose up
+docker compose up
 ```
 
 Variations on this command include:
 
-- `docker-compose up -d` which starts the container as a background task
-  (freeing up the terminal). You can then use `docker-compose down` to turn it
+- `docker compose up -d` which starts the container as a background task
+  (freeing up the terminal). You can then use `docker compose down` to turn it
   off again.
-- `GENERATE_CONFIG=false docker-compose up` which will avoid running the
+- `GENERATE_CONFIG=false docker compose up` which will avoid running the
   `config:generate` rake task as Limber is started.
-- `PRECOMPILE_ASSETS=false docker-compose up` which will avoid precompiling the
+- `PRECOMPILE_ASSETS=false docker compose up` which will avoid precompiling the
   assets as Limber is started.
-- `docker-compose up --build` which forces a rebuild of the Docker image if your
+- `docker compose up --build` which forces a rebuild of the Docker image if your
   changes to the Dockerfile or related scripts don't seem to be taking effect.
 
 Limber should be accessible via [http://localhost:3001](http://localhost:3001).
@@ -158,7 +158,7 @@ Alternatively, run `./compile_build.sh` to compile the build files or run `yarn
 If during development changes do not seem to be taking effect, try:
 
 - Restart the application:
-- Destroy and recreate the Docker container `docker-compose down && GENERATE_CONFIG=false docker-compose up -d`
+- Destroy and recreate the Docker container `docker compose down && GENERATE_CONFIG=false docker compose up -d`
 - Rebuild the Docker image, particularly useful for changing dependencies
 - Clobber local resources `rails assets:clobber`
 
@@ -167,7 +167,7 @@ If during development changes do not seem to be taking effect, try:
 The rest of the sections shown here were written for and apply to the native
 installation, but can also be used in the Docker container if required. In order
 to use Docker, it's probably best to create a shell in the running container.
-Assuming you started the container via `docker-compose` you can access the shell
+Assuming you started the container via `docker compose` you can access the shell
 using:
 
 ```shell

app/controllers/health_controller.rb

@@ -2,5 +2,6 @@
 
 # Controller to display a page stating that Limber is up, as a health check endpoint
 class HealthController < ApplicationController
-  def show; end
+  def show
+  end
 end

app/controllers/labware_controller.rb

@@ -22,8 +22,9 @@ def show # rubocop:todo Metrics/AbcSize
       format.html { render @presenter.page }
       format.csv do
         render @presenter.csv
-        response.headers['Content-Disposition'] =
-          "attachment; filename=#{@presenter.filename(params['offset'])}" if @presenter.filename
+        response.headers[
+          'Content-Disposition'
+        ] = "attachment; filename=#{@presenter.filename(params['offset'])}" if @presenter.filename
       end
       format.json
     end
@@ -35,7 +36,7 @@ def update # rubocop:todo Metrics/AbcSize
     notice = +"Labware: #{params[:labware_barcode]} has been changed to a state of #{params[:state].titleize}."
     notice << ' The customer will still be charged.' if update_params[2]
 
-    respond_to { |format| format.html { redirect_to(search_path, notice: notice) } }
+    respond_to { |format| format.html { redirect_to(search_path, notice:) } }
   rescue StateChangers::StateChangeError => e
     respond_to do |format|
       format.html { redirect_to(search_path, alert: e.message) }
@@ -89,7 +90,7 @@ def state_changer_for(purpose_uuid, labware_uuid)
   end
 
   def presenter_for(labware)
-    presenter = Presenters.lookup_for(labware).new(labware: labware)
+    presenter = Presenters.lookup_for(labware).new(labware:)
 
     # TODO: {Y24-190} - Remove this line when the API v1 is removed from Presenters::ExtendedCsv
     presenter.api = api if presenter.respond_to?(:api=)