Merge pull request #1271 from lucaferranti/lf-juliacon-update

juliacon update

.github/workflows/tests.yml

@@ -0,0 +1,41 @@
+name: Tests
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: postgres:13
+        ports: ['5432:5432']
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: secret
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 3.2.2
+          bundler-cache: true
+      - name: Install Elasticsearch
+        uses: ankane/setup-elasticsearch@v1
+        with:
+          elasticsearch-version: 7.12.0
+      - name: Verify Elasticsearch connection and create index
+        env:
+          ELASTICSEARCH_URL: http://localhost:9200
+        run: |
+          echo $ELASTICSEARCH_URL
+          curl -fsSL "$ELASTICSEARCH_URL/_cat/health?h=status"
+          curl -X PUT $ELASTICSEARCH_URL/joss-production
+      - name: Run tests
+        env:
+          ELASTICSEARCH_URL: http://localhost:9200
+          PGUSER: postgres
+          PGPASSWORD: secret
+          RAILS_ENV: test
+          GH_SECRET: 12345
+        run: |
+          bundle exec rails db:create
+          bundle exec rails db:schema:load
+          bundle exec rails spec

.gitignore

@@ -17,6 +17,7 @@
 /tmp
 /.env
 .DS_Store
+.byebug_history
 
 # Ignore readthedocs build
 

.ruby-version

@@ -1 +1 @@
-2.7.2
+3.2.2

CODE_OF_CONDUCT.md

@@ -33,11 +33,11 @@ advances
 
 ## Our Responsibilities
 
-Project maintainers are responsible for clarifying the standards of acceptable
+The JOSS Editors are responsible for clarifying the standards of acceptable
 behavior and are expected to take appropriate and fair corrective action in
 response to any instances of unacceptable behavior.
 
-Project maintainers have the right and responsibility to remove, edit, or
+JOSS Editors have the right and responsibility to remove, edit, or
 reject comments, commits, code, wiki edits, issues, and other contributions
 that are not aligned to this Code of Conduct, or to ban temporarily or
 permanently any contributor for other behaviors that they deem inappropriate,

COI.md

@@ -1,6 +1,6 @@
 # JOSS Conflict of Interest Policy
 
-The definition of a conflict of Interest in peer review is a circumstance that makes you "unable to make an impartial scientific judgment or evaluation." ([PNAS Conflict of Interest Policy](http://www.pnas.org/site/authors/coi.xhtml)). JOSS is concerned with avoiding any actual conflicts of interest, and being sufficiently transparent that we avoid the appearance of conflicts of interest as well.
+The definition of a conflict of Interest in peer review is a circumstance that makes you "unable to make an impartial scientific judgment or evaluation." ([PNAS Editorial Policies - Competing Interest](https://www.pnas.org/author-center/editorial-and-journal-policies#competing-interest)). JOSS is concerned with avoiding any actual conflicts of interest, and being sufficiently transparent that we avoid the appearance of conflicts of interest as well.
 
 As a reviewer, COIs are your present or previous association with any authors of a submission: recent (past four years) collaborators in funded research or work that is published; and lifetime for the family members, business partners, and thesis student/advisor or mentor. In addition, your recent (past year) association with the same organization of a submitter is a COI, for example, being employed at the same institution.
 

Gemfile

@@ -1,64 +1,69 @@
 source 'https://rubygems.org'
-ruby "2.7.2"
+ruby '3.2.2'
 
-gem 'aasm', '~> 5.0.5'
+gem 'aasm', '~> 5.5.0'
 gem 'chartkick'
 gem 'bootsnap'
-gem 'dotenv', '~> 2.7.5'
-gem 'github-markdown', '~> 0.6.9'
+gem 'dotenv', '~> 2.8.1'
 gem 'google_drive'
 gem 'groupdate'
-gem 'honeybadger', '~> 4.5.1'
-gem 'html-pipeline', '~> 2.12.0'
-gem 'commonmarker', '~> 0.20.1'
-gem 'octicons_helper', '~> 9.1'
+gem 'honeybadger', '~> 5.2.0'
+gem 'html-pipeline', '~> 2.14.3'
+gem 'commonmarker', '~> 0.23.10'
+gem 'net-sftp', '~> 4.0'
+gem 'octicons_helper'
 gem 'omniauth-orcid', '~> 2.1.1'
-gem 'octokit', '~> 4.14'
-gem 'pdf-reader', '~> 2.2'
-gem 'pg', '~> 1.1.4'
-gem 'will_paginate', '~> 3.1.8'
-gem 'rails', '6.0.3.2'
+gem 'omniauth-rails_csrf_protection'
+gem 'octokit', '~> 6.0'
+gem 'pdf-reader', '~> 2.11.0'
+gem 'pg', '~> 1.4.6'
+gem 'pagy'
+gem 'rails', '7.0.7.2'
+gem "importmap-rails"
+gem "turbo-rails"
+gem "stimulus-rails"
 gem 'responders'
 gem 'newrelic_rpm'
-gem 'sanitize', '~> 5.2.1'
-gem 'sass-rails', '~> 6.0.0'
+gem 'sanitize', '~> 6.0.1'
 gem 'searchkick'
-gem 'uglifier', '4.1.20'
-gem 'coffee-rails', '~> 5.0.0'
+gem 'elasticsearch', '<7.14'
+gem 'uglifier', '4.2.0'
+gem 'jbuilder', '~> 2.11'
+gem 'issue'
 
 gem 'active_link_to'
 
- # Use Bootstrap for the front-end
-gem 'bootstrap', '~> 4.3.1'
+gem 'mini_racer'
+gem 'sprockets-rails'
 
+# Use Sass to process CSS
+gem "sassc-rails"
 
-# Use jquery as the JavaScript library
-gem 'jquery-rails', '~> 4.3.5'
+# Use Puma as the app server
+gem 'puma'
 
-gem 'custom_error_message', '~> 1.1.1'
-# Use Unicorn as the app server
-gem 'unicorn', '~> 5.5.1'
+# Use Redis for Action Cable
+gem "redis", "~> 5.0"
 
 group :development, :test do
   # Call 'byebug' anywhere in the code to stop execution and get a debugger console
   gem 'pry-byebug'
-  gem 'capybara', '~> 3.28.0'
-  gem 'factory_bot_rails', '~> 5.0.2'
-  gem 'rspec-rails', '~> 4.0.0.beta2'
-  gem 'rails-controller-testing', '~> 1.0.4'
+  gem 'capybara', '~> 3.38'
+  gem 'factory_bot_rails', '~> 6.2.0'
+  gem 'rspec-rails', '~> 6.0.1'
+  gem 'rails-controller-testing', '~> 1.0.5'
+  gem 'selenium-webdriver'
+  gem 'webmock'
 end
 
 group :test do
-  gem 'webmock', '~> 3.6.2'
+  gem 'vcr', '~> 6.1', '>= 6.1.0'
 end
 
 group :development do
   # Access an IRB console on exception pages or by using <%= console %> in views
-  gem 'web-console', '~> 4.0.1'
+  gem 'web-console', '~> 4.2.0'
   # Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
   gem 'spring'
   gem 'spring-commands-rspec', group: :development
-  gem 'guard', '~> 2.15'
-  gem 'guard-livereload', require: false
-  gem 'rack-livereload'
 end