Upgrade to Rails 6.1.7.10 and Ruby 3.0.7

.gitignore

@@ -1,34 +1,40 @@
-*.rbc
-capybara-*.html
-.rspec
-.env
-/log
-/tmp
-/coverage
+# See https://help.github.com/articles/ignoring-files for more about ignoring files.
+#
+# If you find yourself ignoring temporary files generated by your text editor
+# or operating system, you probably want to add a global ignore instead:
+#   git config --global core.excludesfile '~/.gitignore_global'
+
+# Ignore bundler config.
+/.bundle
+
+# Ignore the default SQLite database.
 /db/*.sqlite3
-/db/schema.rb
-/public/system
-/coverage/
-/spec/tmp
-**.orig
-rerun.txt
-pickle-email-*.html
+/db/*.sqlite3-journal
+/db/*.sqlite3-*
 
-# TODO Comment out these rules if you are OK with secrets being uploaded to the repo
-config/initializers/secret_token.rb
+# Ignore all logfiles and tempfiles.
+/log/*
+/tmp/*
+!/log/.keep
+!/tmp/.keep
 
+# Ignore pidfiles, but keep the directory.
+/tmp/pids/*
+!/tmp/pids/
+!/tmp/pids/.keep
 
-## Environment normalisation:
-/.bundle
-/vendor/bundle
+# Ignore uploaded files in development.
+/storage/*
+!/storage/.keep
 
-# these should all be checked in to normalise the environment:
-# Gemfile.lock, .ruby-version, .ruby-gemset
+/public/assets
+.byebug_history
 
-# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
-.rvmrc
+# Ignore master key for decrypting credentials and more.
+/config/master.key
 
-# if using bower-rails ignore default bower_components path bower.json files
-/vendor/assets/bower_components
-*.bowerrc
-bower.json
+# Other files not .gitignored in Rails by default
+.env
+.rspec
+/coverage/*
+!/coverage/.keep

.ruby-version

@@ -1 +1 @@
-2.3.1
+3.0.7

Gemfile

@@ -1,64 +1,120 @@
 source 'https://rubygems.org'
 
-gem 'rails', '4.2.5.2'
-gem 'apipie-rails' # Documentation
-gem 'devise', '>= 3.5.10'
-gem 'annotate'
-gem 'sass-rails'#,   '~> 3.2.3'
-gem 'uglifier'#, '>= 1.0.3'
-gem 'susy', '~> 1.0.9'
-gem 'compass'#, '>= 0.12.2'
-gem 'compass-rails'#, '>= 1.0.3'
-gem 'will_paginate' #, '~> 3.0.6'
-gem 'api_pagination_headers'
-gem 'traco'
-gem 'httparty'
-gem 'select2-rails'
-gem 'groupdate'
-gem "chartkick"
+gem 'rails', '6.1.7.10'
+
+gem 'psych', '~> 4'
+
+# Use Puma as the app server
+gem 'puma', '~> 4.1'
+
+gem 'apipie-rails', '~> 0.6'
+
+# devise provides authentication
+gem 'devise', '~> 4.9.4'
+
+# annotate maintains comments at the top of model files describing the schema,
+# using the database as the source of truth
+gem 'annotate', '3.1.0'
+
+# Frontend CSS and minification
+gem 'sass-rails', '~> 5.0.8'
+gem 'uglifier', '~> 2.7.2'
+
+# Frontend components
+gem 'select2-rails', '~> 4.0.13'
+gem 'chartkick', '~> 1.3.2'
+
+# Provides group_by_day et al. on ActiveRecord models and queries
+gem 'groupdate', '~> 6.2.1'
+
+# pagination
+gem 'will_paginate', '~> 4.0.0'
+gem 'api_pagination_headers', '~> 2.1.1'
+
+# i18n
+gem 'traco', '~> 5.3.3' # TODO: switch to mobility
+
+# HTTP user agent
+gem 'httparty', '~> 0.22'
 
 group :test do
-  gem 'shoulda'
-  gem 'capybara'
-  gem 'factory_girl_rails'
-  gem 'simplecov', require: false
-  gem 'codeclimate-test-reporter', require: nil
-  gem 'link_header'
-  gem 'launchy'
-  gem 'mocha'
+  # Test assertion library.
+  # UPGRADE TODO: Shoulda is tested and supported against Ruby 3.0+, Rails 6.1+,
+  # RSpec 3.x, Minitest 4.x, and Test::Unit 3.x. For Ruby < 3 and Rails < 6.1
+  # compatibility, please use v4.0.0.
+  gem 'shoulda', '~> 5.0.0.rc1'
+
+  # Integration testing
+  gem 'capybara', '~> 2.8'
+
+  # Helps build test fixtures
+  gem 'factory_bot_rails', '~> 4.11.1'
+
+  # coverage reports
+  gem 'simplecov', '~> 0.17.1', require: false
+  # gem 'codeclimate-test-reporter', require: nil # UPGRADE: removed
+
+  # Used in test/controllers/api/v1/taxon_concepts_test.rb to parse HTTP
+  # link headers and verify they're correct
+  gem 'link_header', '~> 0.0.8'
+
+  # For laun
+  # gem 'launchy', '~> 2.4.3'
+
+  # Mocks and stubs. Not equivalent to https://mochajs.org/
+  gem 'mocha', '~> 1.1.0'
 end
 
 group :staging, :production do
   gem 'dotenv-rails'
 end
 
 # Use postgresql as the database for Active Record
-gem 'pg'
-gem 'schema_plus'
+gem 'pg', '~> 1.2'
+
+# gem 'schema_plus', '~> 2.1.0' # was 1.8.7
+gem 'schema_associations', '~> 1.4.0';
+gem 'schema_auto_foreign_keys', '~> 1.1.0';
+gem 'schema_validations', '~> 2.4.1';
+
 # Use CoffeeScript for .js.coffee assets and views
-gem 'coffee-rails', '~> 4.0.0'
+gem 'coffee-rails', '~> 5.0.0'
+
 # See https://github.com/sstephenson/execjs#readme for more supported runtimes
 # gem 'therubyracer',  platforms: :ruby
 
 # Use jquery as the JavaScript library
-gem 'jquery-rails'
+gem 'jquery-rails', '~> 4.6.0'
+
 # Turbolinks makes following links in your web application faster. Read more: https://github.com/rails/turbolinks
-gem 'turbolinks'
+gem 'turbolinks', '~> 2.5.3'
+
 # Build JSON / XML API
-gem 'rabl'
+gem 'rabl', '~> 0.16.1'
+
 # Also add either `oj` or `yajl-ruby` as the JSON parser
-gem 'oj'
+gem 'oj', '~> 3'
+
 # bundle exec rake doc:rails generates the API under doc/api.
-gem 'sdoc', '~> 0.4.0',          group: :doc
+gem 'sdoc', '~> 1.1.0', group: :doc
 
-# Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
-gem 'spring',        group: :development
+# Reduces boot times through caching; required in config/boot.rb
+gem 'bootsnap', '~> 1.18.4', require: false
 
 group :development do
+  # Access an interactive console on exception pages or by calling 'console' anywhere in the code.
+  gem 'web-console', '~> 3.7.0'
+  gem 'listen', '~> 3.2'
+
+  # Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
+  gem 'spring', '~> 1.6.4'
+  gem 'spring-watcher-listen', '~> 2.0.0'
+
+  # Capistrano for rails deployment
   gem 'capistrano', '~> 3.4.0'
-  gem 'capistrano-rails'
-  gem 'capistrano-bundler'
-  gem 'capistrano-rvm'
+  gem 'capistrano-rails', '~> 1.6.3'
+  gem 'capistrano-bundler', '~> 2.1.1'
+  gem 'capistrano-rvm', '~> 0.1.2'
   gem 'capistrano-maintenance', '~> 1.0', require: false
   gem 'capistrano-passenger', '~> 0.1.1', require: false
   gem 'rack-cors', :require => 'rack/cors'
@@ -71,7 +127,9 @@ group :development do
 end
 
 group :development, :test do
-  gem 'byebug'
+  # A better debugger
+  gem 'byebug', '~> 10.0.2'
 end
 
-gem 'appsignal'
+# Error monitoring
+gem 'appsignal', '~> 3.3.11'