Merge pull request #225 from CDL-Dryad/bundler-2

Upgrade Bundler, Rubocop, and other gems

.rubocop.yml

@@ -1,13 +1,20 @@
 AllCops:
+  NewCops: enable
   Exclude:
     - 'bin/**/*'
     - 'config/**/*'
     - 'db/**/*'
     - 'script/**/*'
     - 'vendor/**/*'
     - 'documentation/**/*'
+    - 'stash/stash_engine/app/models/stash_engine/lock.rb'
+    - 'stash/stash_engine/bin/**/*'
+    - 'stash/stash_engine/config/**/*'
+    - 'stash/stash_engine/db/**/*'
     - 'stash/stash_engine/node_modules/**/*'
-
+    - 'stash/stash_engine/script/**/*'
+    - 'stash/stash_engine/vendor/**/*'
+    - 'stash/stash_engine/ui-library/**/*'
   # Suppress complaints about post-2.0 syntax
   TargetRubyVersion: 2.6
 
@@ -51,7 +58,10 @@ Metrics/MethodLength:
 
 # reasonable complexity
 Metrics/PerceivedComplexity:
-  Max: 10
+  Max: 15
+
+Metrics/CyclomaticComplexity:
+  Max: 15
 
 # We meant to do that
 Naming/MemoizedInstanceVariableName:
@@ -61,6 +71,10 @@ Naming/MemoizedInstanceVariableName:
 Naming/MethodParameterName:
   Enabled: False
 
+# Confusing and weird
+Naming/VariableNumber:
+  Enabled: False
+
 # Do what's readable in the context you're in
 Style/AccessModifierDeclarations:
   Enabled: false
@@ -77,6 +91,10 @@ Style/CommentedKeyword:
 Style/Documentation:
   Enabled: false
 
+# Doesn't necessarily make anything more readable
+Style/ExplicitBlockArgument:
+  Enabled: false
+
 # Adding more line noise to format strings will not improve them
 Style/FormatStringToken:
   Enabled: false
@@ -101,10 +119,6 @@ Style/SafeNavigation:
 Style/SingleLineBlockParams:
   Enabled: false
 
-# Confusing and weird
-Naming/VariableNumber:
-  Enabled: false
-
 # Allow some special handling for engines
 Bundler/OrderedGems:
   TreatCommentsAsGroupSeparators: true

.travis.yml

@@ -1,5 +1,5 @@
 # the STASH tests were spending a long, long time installing gems but then only using the libraries installed in the main app, anyway
-# so I disabled the bundle installs for the separate apps and rely on the main bundle to do the job for now.
+# so I disabled the bundle installs for the separate apps and rely on the main bundle to do the job for now
 
 matrix:
   include:
@@ -30,7 +30,7 @@ before_install:
   - if [ "$TO_TEST" = "MAIN" ]; then sudo apt-get install mutt; fi
   - gem update --system
   - gem uninstall -v '>= 2' -i $(rvm gemdir)@global -ax bundler || true
-  - gem install bundler -v 1.17.3
+  - gem install bundler -v 2.1.4
   - gem install colorize
   - if [ "$TO_TEST" = "MAIN" ]; then ./travis-prep.sh; fi
 

Gemfile

@@ -27,7 +27,7 @@ gem 'capistrano', '~> 3.11'
 gem 'capistrano-passenger'
 gem 'capistrano-rails', '~> 1.4'
 gem 'passenger', '~> 6.0.5'
-gem 'rubocop', '~> 0.85.1'
+gem 'rubocop', '~> 0.90.0'
 
 # ############################################################
 # UI

Gemfile.lock

@@ -91,43 +91,43 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (5.2.4.3)
-      actionpack (= 5.2.4.3)
+    actioncable (5.2.4.4)
+      actionpack (= 5.2.4.4)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailer (5.2.4.3)
-      actionpack (= 5.2.4.3)
-      actionview (= 5.2.4.3)
-      activejob (= 5.2.4.3)
+    actionmailer (5.2.4.4)
+      actionpack (= 5.2.4.4)
+      actionview (= 5.2.4.4)
+      activejob (= 5.2.4.4)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (5.2.4.3)
-      actionview (= 5.2.4.3)
-      activesupport (= 5.2.4.3)
+    actionpack (5.2.4.4)
+      actionview (= 5.2.4.4)
+      activesupport (= 5.2.4.4)
       rack (~> 2.0, >= 2.0.8)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.2)
-    actionview (5.2.4.3)
-      activesupport (= 5.2.4.3)
+    actionview (5.2.4.4)
+      activesupport (= 5.2.4.4)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.3)
-    activejob (5.2.4.3)
-      activesupport (= 5.2.4.3)
+    activejob (5.2.4.4)
+      activesupport (= 5.2.4.4)
       globalid (>= 0.3.6)
-    activemodel (5.2.4.3)
-      activesupport (= 5.2.4.3)
-    activerecord (5.2.4.3)
-      activemodel (= 5.2.4.3)
-      activesupport (= 5.2.4.3)
+    activemodel (5.2.4.4)
+      activesupport (= 5.2.4.4)
+    activerecord (5.2.4.4)
+      activemodel (= 5.2.4.4)
+      activesupport (= 5.2.4.4)
       arel (>= 9.0)
-    activestorage (5.2.4.3)
-      actionpack (= 5.2.4.3)
-      activerecord (= 5.2.4.3)
+    activestorage (5.2.4.4)
+      actionpack (= 5.2.4.4)
+      activerecord (= 5.2.4.4)
       marcel (~> 0.3.1)
-    activesupport (5.2.4.3)
+    activesupport (5.2.4.4)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -146,7 +146,7 @@ GEM
     ast (2.4.1)
     autoprefixer-rails (9.8.6.3)
       execjs
-    bcrypt (3.1.15)
+    bcrypt (3.1.16)
     benchmark_methods (0.7)
     bibtex-ruby (5.1.4)
       latex-decode (~> 0.0)
@@ -300,7 +300,7 @@ GEM
       concurrent-ruby (~> 1.0)
       dry-core (~> 0.2)
       dry-equalizer (~> 0.2)
-    dry-schema (1.5.3)
+    dry-schema (1.5.4)
       concurrent-ruby (~> 1.0)
       dry-configurable (~> 0.8, >= 0.8.3)
       dry-core (~> 0.4)
@@ -315,13 +315,13 @@ GEM
       dry-equalizer (~> 0.3)
       dry-inflector (~> 0.1, >= 0.1.2)
       dry-logic (~> 1.0, >= 1.0.2)
-    dry-validation (1.5.4)
+    dry-validation (1.5.6)
       concurrent-ruby (~> 1.0)
       dry-container (~> 0.7, >= 0.7.1)
       dry-core (~> 0.4)
       dry-equalizer (~> 0.2)
       dry-initializer (~> 3.0)
-      dry-schema (~> 1.5)
+      dry-schema (~> 1.5, >= 1.5.2)
     ebnf (2.1.1)
       htmlentities (~> 4.3)
       rdf (~> 3.1)
@@ -433,7 +433,7 @@ GEM
     i18n (1.8.5)
       concurrent-ruby (~> 1.0)
     iso8601 (0.9.1)
-    jbuilder (2.10.0)
+    jbuilder (2.10.1)
       activesupport (>= 5.0.0)
     jquery-fileupload-rails (1.0.0)
       actionpack (>= 3.1)
@@ -491,7 +491,7 @@ GEM
     loofah (2.7.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
-    lumberjack (1.2.7)
+    lumberjack (1.2.8)
     mail (2.7.1)
       mini_mime (>= 0.1.1)
     marcel (0.3.3)
@@ -517,7 +517,7 @@ GEM
     mimemagic (0.3.5)
     mini_mime (1.0.2)
     mini_portile2 (2.4.0)
-    minitest (5.14.1)
+    minitest (5.14.2)
     mize (0.4.0)
       protocol (~> 2.0)
     mocha (1.11.2)
@@ -534,7 +534,7 @@ GEM
       net-ssh (>= 2.6.5, < 7.0.0)
     net-ssh (6.1.0)
     netrc (0.11.0)
-    nio4r (2.5.2)
+    nio4r (2.5.3)
     noid (0.9.0)
     nokogiri (1.10.10)
       mini_portile2 (~> 2.4.0)
@@ -553,7 +553,7 @@ GEM
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
-    oj (3.10.13)
+    oj (3.10.14)
     oj_mimic_json (1.0.1)
     omniauth (1.9.1)
       hashie (>= 3.4.6)
@@ -593,32 +593,32 @@ GEM
       pry (~> 0.9)
       slop (~> 3.0)
     public_suffix (2.0.5)
-    puma (4.3.5)
+    puma (4.3.6)
       nio4r (~> 2.0)
     rack (2.2.3)
     rack-test (1.1.0)
       rack (>= 1.0, < 3)
-    rails (5.2.4.3)
-      actioncable (= 5.2.4.3)
-      actionmailer (= 5.2.4.3)
-      actionpack (= 5.2.4.3)
-      actionview (= 5.2.4.3)
-      activejob (= 5.2.4.3)
-      activemodel (= 5.2.4.3)
-      activerecord (= 5.2.4.3)
-      activestorage (= 5.2.4.3)
-      activesupport (= 5.2.4.3)
+    rails (5.2.4.4)
+      actioncable (= 5.2.4.4)
+      actionmailer (= 5.2.4.4)
+      actionpack (= 5.2.4.4)
+      actionview (= 5.2.4.4)
+      activejob (= 5.2.4.4)
+      activemodel (= 5.2.4.4)
+      activerecord (= 5.2.4.4)
+      activestorage (= 5.2.4.4)
+      activesupport (= 5.2.4.4)
       bundler (>= 1.3.0)
-      railties (= 5.2.4.3)
+      railties (= 5.2.4.4)
       sprockets-rails (>= 2.0.0)
     rails-dom-testing (2.0.3)
       activesupport (>= 4.2.0)
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.3.0)
       loofah (~> 2.3)
-    railties (5.2.4.3)
-      actionpack (= 5.2.4.3)
-      activesupport (= 5.2.4.3)
+    railties (5.2.4.4)
+      actionpack (= 5.2.4.4)
+      activesupport (= 5.2.4.4)
       method_source
       rake (>= 0.8.7)
       thor (>= 0.19.0, < 2.0)
@@ -628,7 +628,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rb-readline (0.5.5)
-    rdf (3.1.5)
+    rdf (3.1.6)
       hamster (~> 3.0)
       link_header (~> 0.0, >= 0.0.8)
     rdf-aggregate-repo (3.1.0)
@@ -692,20 +692,20 @@ GEM
       rspec-mocks (~> 3.9)
       rspec-support (~> 3.9)
     rspec-support (3.9.3)
-    rubocop (0.85.1)
+    rubocop (0.90.0)
       parallel (~> 1.10)
-      parser (>= 2.7.0.1)
+      parser (>= 2.7.1.1)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.7)
       rexml
-      rubocop-ast (>= 0.0.3)
+      rubocop-ast (>= 0.3.0, < 1.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 2.0)
-    rubocop-ast (0.3.0)
+    rubocop-ast (0.4.0)
       parser (>= 2.7.1.4)
     ruby-progressbar (1.10.1)
     ruby_dig (0.0.2)
-    ruby_parser (3.14.2)
+    ruby_parser (3.15.0)
       sexp_processor (~> 4.9)
     rubyzip (2.3.0)
     safe_yaml (1.0.5)
@@ -718,8 +718,8 @@ GEM
     sass-listen (4.0.0)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
-    sass-rails (5.0.7)
-      railties (>= 4.0.0, < 6)
+    sass-rails (5.1.0)
+      railties (>= 5.2.0)
       sass (~> 3.1)
       sprockets (>= 2.8, < 4.0)
       sprockets-rails (>= 2.0, < 4.0)
@@ -735,15 +735,15 @@ GEM
       faraday_middleware (>= 0.12.2, < 0.15.0)
       multi_json (~> 1.13, >= 1.13.1)
       thor (>= 0.20, < 1.1)
-    sexp_processor (4.15.0)
+    sexp_processor (4.15.1)
     shellany (0.0.1)
     shoulda (4.0.0)
       shoulda-context (~> 2.0)
       shoulda-matchers (~> 4.0)
     shoulda-context (2.0.0)
-    shoulda-matchers (4.3.0)
+    shoulda-matchers (4.4.1)
       activesupport (>= 4.2.0)
-    simplecov (0.18.5)
+    simplecov (0.19.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
     simplecov-console (0.7.2)
@@ -760,7 +760,7 @@ GEM
     sprockets (3.7.2)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
-    sprockets-rails (3.2.1)
+    sprockets-rails (3.2.2)
       actionpack (>= 4.0)
       activesupport (>= 4.0)
       sprockets (>= 3.0.0)
@@ -814,7 +814,7 @@ GEM
       nokogiri (~> 1.6)
       rubyzip (>= 1.3.0)
       selenium-webdriver (>= 3.0, < 4.0)
-    webmock (3.8.3)
+    webmock (3.9.1)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -874,7 +874,7 @@ DEPENDENCIES
   rb-readline (~> 0.5.5)
   rspec-collection_matchers
   rspec-rails
-  rubocop (~> 0.85.1)
+  rubocop (~> 0.90.0)
   sass-rails (~> 5.0)
   selenium-webdriver (~> 3.142.0)
   shoulda

config.ru

@@ -1,4 +1,4 @@
 # This file is used by Rack-based servers to start the application.
 
-require ::File.expand_path('../config/environment', __FILE__)
+require ::File.expand_path('config/environment', __dir__)
 run Rails.application

documentation/dryad_install.md

@@ -134,7 +134,7 @@ rbenv install $(cat .ruby-version) # installs the ruby-version set in the .ruby-
 gem update --system
 
 # install bundler to handle gem dependencies
-gem install bundler:1.17.3
+gem install bundler:2.1.4
 ```
 
 **If you are running on OSX, ensure some gems are compatible with the system:**