Resolve "Update Jekyll version to 4.0"

.gitignore

 _site
 .sass-cache
-.jekyll-metadata
+.jekyll-metadata
\ No newline at end of file
+.jekyll-cache
+/Thumbs.db
+/.DS_Store
+/.idea

.gitlab-ci.yml

-image: ruby:2.6
+# In case something goes horribly wrong, you can fall back to `image: ruby:latest`
+image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb:1.0
 
 build the website:
   stage: build
   before_script:
+  - gem install bundler -v2.0.2
   - bundle install && bundle update
   script:
   - 'echo "baseurl: /$CI_PROJECT_NAME" >> _config_ci.yml'
@@ -14,7 +16,7 @@ build the website:
     paths:
     - test
   variables:
-    JEKYLL_ENV: production  
+    JEKYLL_ENV: production
 
 pages:
   stage: deploy

Gemfile

@@ -9,13 +9,13 @@ source "https://rubygems.org"
 #
 # This will help ensure the proper Jekyll version is running.
 # Happy Jekylling!
-gem "jekyll", "~> 3.8.5"
-gem "bundler", "> 1.16.1"
+gem "jekyll", "~> 4.0"
+gem "bundler", "> 2.0"
 
 # This is the default theme for new Jekyll sites. You may change this to anything you like.
 gem "minima", "~> 2.5"
-gem 'jekyll-theme-primer', '~> 0.5.3'
-gem 'jekyll-theme-lcsb-default', '~> 0.2.18', :git => "https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default.git", :branch => "master"
+# gem 'jekyll-theme-primer', '~> 0.5.4'
+gem 'jekyll-theme-lcsb-default', '~> 0.3'
 
 # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
 # uncomment the line below. To upgrade, run `bundle update github-pages`.
@@ -23,7 +23,8 @@ gem 'jekyll-theme-lcsb-default', '~> 0.2.18', :git => "https://git-r3lab.uni.lu/
 
 # If you have any plugins, put them here!
 group :jekyll_plugins do
- gem "jekyll-paginate-v2", "~> 1.7"
+ gem "jekyll-paginate-v2", "~> 2",
+     :git => "https://github.com/sverrirs/jekyll-paginate-v2.git"
  gem "jekyll-feed", "~> 0.6"
 end
 
@@ -32,4 +33,3 @@ gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
 
 # Performance-booster for watching directories on Windows
 gem "wdm", "~> 0.1.1" if Gem.win_platform?
-

Gemfile.lock

 GIT
-  remote: https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default.git
-  revision: f1eaba1cc613481c624b3b1a08129f3a91d79819
-  branch: master
+  remote: https://github.com/sverrirs/jekyll-paginate-v2.git
+  revision: f8664cf68b59de823b88d4e6b1b985457f2c13af
   specs:
-    jekyll-theme-lcsb-default (0.2.18)
-      jekyll (~> 3.7)
-      jekyll-seo-tag (~> 2.1)
+    jekyll-paginate-v2 (2.1.0)
+      jekyll (>= 3.0, < 5.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.5.2)
-      public_suffix (>= 2.0.2, < 4.0)
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
     colorator (1.1.0)
-    concurrent-ruby (1.1.4)
+    concurrent-ruby (1.1.5)
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
     eventmachine (1.2.7-x64-mingw32)
-    faraday (0.15.4)
-      multipart-post (>= 1.2, < 3)
-    ffi (1.10.0-x64-mingw32)
+    ffi (1.11.2-x64-mingw32)
     forwardable-extended (2.6.0)
     http_parser.rb (0.6.0)
-    i18n (0.9.5)
+    i18n (1.7.0)
       concurrent-ruby (~> 1.0)
-    jekyll (3.8.5)
+    jekyll (4.0.0)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
-      i18n (~> 0.7)
-      jekyll-sass-converter (~> 1.0)
+      i18n (>= 0.9.5, < 2)
+      jekyll-sass-converter (~> 2.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 1.14)
+      kramdown (~> 2.1)
+      kramdown-parser-gfm (~> 1.0)
       liquid (~> 4.0)
       mercenary (~> 0.3.3)
       pathutil (~> 0.9)
-      rouge (>= 1.7, < 4)
+      rouge (~> 3.0)
       safe_yaml (~> 1.0)
-    jekyll-feed (0.11.0)
-      jekyll (~> 3.3)
-    jekyll-github-metadata (2.12.1)
-      jekyll (~> 3.4)
-      octokit (~> 4.0, != 4.4.0)
-    jekyll-paginate-v2 (1.9.4)
-      jekyll (~> 3.0)
-    jekyll-sass-converter (1.5.2)
-      sass (~> 3.4)
-    jekyll-seo-tag (2.5.0)
-      jekyll (~> 3.3)
-    jekyll-theme-primer (0.5.3)
-      jekyll (~> 3.5)
-      jekyll-github-metadata (~> 2.9)
-      jekyll-seo-tag (~> 2.0)
-    jekyll-watch (2.1.2)
+      terminal-table (~> 1.8)
+    jekyll-feed (0.13.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-sass-converter (2.0.1)
+      sassc (> 2.0.1, < 3.0)
+    jekyll-seo-tag (2.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-theme-lcsb-default (0.3.0)
+      jekyll (~> 4.0)
+      jekyll-seo-tag (~> 2.5)
+    jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (1.17.0)
-    liquid (4.0.1)
-    listen (3.1.5)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-      ruby_dep (~> 1.2)
+    kramdown (2.1.0)
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.3)
+    listen (3.2.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
-    minima (2.5.0)
-      jekyll (~> 3.5)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    multipart-post (2.0.0)
-    octokit (4.13.0)
-      sawyer (~> 0.8.0, >= 0.5.3)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (3.0.3)
+    public_suffix (4.0.1)
     rb-fsevent (0.10.3)
     rb-inotify (0.10.0)
       ffi (~> 1.0)
-    rouge (3.3.0)
-    ruby_dep (1.5.0)
-    safe_yaml (1.0.4)
-    sass (3.7.3)
-      sass-listen (~> 4.0.0)
-    sass-listen (4.0.0)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-    sawyer (0.8.1)
-      addressable (>= 2.3.5, < 2.6)
-      faraday (~> 0.8, < 1.0)
-    thread_safe (0.3.6)
-    tzinfo (1.2.5)
-      thread_safe (~> 0.1)
-    tzinfo-data (1.2018.5)
+    rouge (3.13.0)
+    safe_yaml (1.0.5)
+    sassc (2.2.1-x64-mingw32)
+      ffi (~> 1.9)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    tzinfo (2.0.0)
+      concurrent-ruby (~> 1.0)
+    tzinfo-data (1.2019.3)
       tzinfo (>= 1.0.0)
+    unicode-display_width (1.6.0)
     wdm (0.1.1)
 
 PLATFORMS
   x64-mingw32
 
 DEPENDENCIES
-  bundler (> 1.16.1)
-  jekyll (~> 3.8.5)
+  bundler (> 2.0)
+  jekyll (~> 4.0)
   jekyll-feed (~> 0.6)
-  jekyll-paginate-v2 (~> 1.7)
-  jekyll-theme-lcsb-default (~> 0.2.18)!
-  jekyll-theme-primer (~> 0.5.3)
+  jekyll-paginate-v2 (~> 2)!
+  jekyll-theme-lcsb-default (~> 0.3)
   minima (~> 2.5)
   tzinfo-data
-  wdm (~> 0.1.0)
+  wdm (~> 0.1.1)
 
 BUNDLED WITH
-   1.16.4
+   2.0.2

index.md

@@ -63,5 +63,8 @@ You probably didn't configure `baseurl` parameter in the settings or configured
 ### *The links in the menu are not working (they point to "404: Not found").*
 You probably didn't add `permalink` attribute. Or the post has `published: false` or `draft: true` set. Please take a look on the post file.
 
+### *Something goes wrong with Gitlab-CI*
+It never happened before, please notify us immediately.
+
 ### Other problems?
 Please send us an email! (`lcsb-sysadmins (at) uni.lu`)
\ No newline at end of file