Move to 2019 version

Author: RalfG

.gitignore

@@ -1,4 +1,5 @@
 _site
 .sass-cache
-_site/
-Gemfile.lock
+.jekyll-metadata
+node_modules
+Gemfile.lock

404.html

@@ -0,0 +1,10 @@
+---
+layout: default
+---
+
+<div class="container text-center">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>

Gemfile

@@ -1,2 +1,16 @@
-source 'https://rubygems.org'
-gem 'github-pages', group: :jekyll_plugins
+source "https://rubygems.org"
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+#gem "jekyll", "~> 3.7.3"
+
+
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+gem "github-pages", group: :jekyll_plugins

Gemfile.lock

@@ -1,12 +1,12 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (4.2.10)
+    activesupport (4.2.11.1)
       i18n (~> 0.7)
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.5.2)
+    addressable (2.6.0)
       public_suffix (>= 2.0.2, < 4.0)
     coffee-script (2.4.1)
       coffee-script-source
@@ -27,13 +27,13 @@ GEM
     execjs (2.7.0)
     faraday (0.15.4)
       multipart-post (>= 1.2, < 3)
-    ffi (1.10.0)
+    ffi (1.11.1)
     forwardable-extended (2.6.0)
-    gemoji (3.0.0)
-    github-pages (197)
-      activesupport (= 4.2.10)
+    gemoji (3.0.1)
+    github-pages (198)
+      activesupport (= 4.2.11.1)
       github-pages-health-check (= 1.16.1)
-      jekyll (= 3.7.4)
+      jekyll (= 3.8.5)
       jekyll-avatar (= 0.6.0)
       jekyll-coffeescript (= 1.1.1)
       jekyll-commonmark-ghpages (= 0.1.5)
@@ -81,13 +81,13 @@ GEM
       octokit (~> 4.0)
       public_suffix (~> 3.0)
       typhoeus (~> 1.3)
-    html-pipeline (2.10.0)
+    html-pipeline (2.11.1)
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.6.0)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    jekyll (3.7.4)
+    jekyll (3.8.5)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
@@ -204,39 +204,39 @@ GEM
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
     minitest (5.11.3)
-    multipart-post (2.0.0)
-    nokogiri (1.10.2)
+    multipart-post (2.1.1)
+    nokogiri (1.10.3)
       mini_portile2 (~> 2.4.0)
     octokit (4.14.0)
       sawyer (~> 0.8.0, >= 0.5.3)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (3.0.3)
+    public_suffix (3.1.1)
     rb-fsevent (0.10.3)
     rb-inotify (0.10.0)
       ffi (~> 1.0)
     rouge (2.2.1)
     ruby-enum (0.7.2)
       i18n
     ruby_dep (1.5.0)
-    rubyzip (1.2.2)
+    rubyzip (1.2.3)
     safe_yaml (1.0.5)
     sass (3.7.4)
       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)
+    sawyer (0.8.2)
+      addressable (>= 2.3.5)
+      faraday (> 0.8, < 2.0)
     terminal-table (1.8.0)
       unicode-display_width (~> 1.1, >= 1.1.1)
     thread_safe (0.3.6)
     typhoeus (1.3.1)
       ethon (>= 0.9.0)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)
-    unicode-display_width (1.5.0)
+    unicode-display_width (1.6.0)
 
 PLATFORMS
   ruby
@@ -245,4 +245,4 @@ DEPENDENCIES
   github-pages
 
 BUNDLED WITH
-   1.16.1
+   2.0.2

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Nicolas Vanhoren
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,5 +1,63 @@
-# Compomics Documentation Website
+# compomics.github.io
+Overview and documentation of CompOmics GitHub repositories.
 
-This repository contains the compomics.github.io site, which collates documentation from all Compomics projects on Github. The site is built automatically as the result of a Jenkins build triggered by a Github webhook. This runs a Groovy postbuild script (see [https://gist.github.com/iain8/d6cd41e4e2ef920c50af](here)) which passes the project name and github url to the script `generate-docs.py`, which retrieves the readme and wiki files and adds the necessary front-matter for Jekyll to parse them. Links in wiki pages are automatically amended to still point to the correct place.
+## Run website locally
+- Install Jekyll requirements
+- Install webpage dependencies: `bundle install`
+- Run Jekyll web server: `bundle exec jekyll serve`
+- The website is now hosted at http://localhost:4000
 
-The site can be viewed locally using `bundle exec jekyll serve` (useful for troubleshooting). It is strongly advised to separate all elements in a markdown file with newlines, as the jekyll parser is a lot less forgiving than the one on github wiki pages.
+## Create pages for GitHub repositories
+The entire pages folder can be generated automatically by `generate_docs.py`.
+This script can be configured trough a YAML config file or the command line
+interface (run `python generate_docs.py -h`). See `requirements.txt` for the
+required Python packages.
+
+### Folder structure
+Requires the following folder structure for projects:
+```
+pages/
+|-- sample_project/
+    |-- sample_project.md
+    |-- wiki/
+        |-- sample_wikipage.md
+        |-- sample_wikipage2.md
+```
+where every GitHub repository has one folder with in its root the README file
+and a subfolder containing all wiki pages of that repository.
+
+
+### Jekyll file headers
+The project markdown files need to contain the following items in their header:
+
+#### README file
+```
+---
+name: "simple"
+description: "A simple tool"
+layout: default
+tags: project_home, simple
+permalink: /projects/simple
+project: simple
+github_project: "https://github.com/compomics/simple"
+---
+```
+
+#### Wiki page
+```
+---
+name: docs
+title: docs
+layout: default
+permalink: "/projects/simple/wiki/docs"
+tags: wiki, simple
+project: simple
+github_project: https://github.com/compomics/simple
+---
+```
+
+# Created with
+- Jekyll template [Boostrap 4 Github Pages](https://nicolas-van.github.io/bootstrap-4-github-pages/).
+- Bootstrap 4
+- Font Awesome 4.7.0
+- ...

_config.yml

@@ -1,32 +1,42 @@
+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely edit after that. If you find
+# yourself editing this file very often, consider using Jekyll's data files
+# feature for the data you need to update frequently.
+#
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
+
 # Site settings
-title: Compomics Docs
-email: [email protected]
-description: > # this means to ignore newlines until "baseurl:"
- Welcome to the website for software projects created and maintained by the Computational Omics and 
- Systems Biology Group. Below you can find a list of software we have developed, and on the subsequent 
- pages are documentation and links to downloads and source code (hosted on our Github page).
-baseurl: "" # the subpath of your site, e.g. /blog/
-url: "http://compomics.github.io" # the base hostname & protocol for your site
-twitter_username: compomics
+# These are used to personalize your new site. If you look in the HTML files,
+# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
+# You can create any custom variable you would like, and they will be accessible
+# in the templates via {{ site.myvariable }}.
+title: CompOmics documentation
+email: "compomics"
+description: >- # this means to ignore newlines until "baseurl:"
+  CompOmics projects documentation
+#baseurl: "" # the subpath of your site, e.g. /blog
+#url: "" # the base hostname & protocol for your site, e.g. http://example.com
+twitter_username: CompOmics
 github_username:  compomics
 
-exclude: ["generate-docs.py", "README.md", "Gemfile", "Gemfile.lock"]
+repository: "compomics/compomics.github.io"
 
 # Build settings
-markdown: kramdown
-kramdown:
-  input: GFM
+plugins:
+#  - jekyll-feed
+  - jekyll-sitemap
 
-defaults:
-  -
-    scope:
-      type: projects
-    values:
-      layout: "default"
-      page_type: project
+# A list of the pages to display in the navigation bar
+header_pages:
 
-collections:
-  projects:
-    output: true
-    output_ext: html
-    permalink: /projects/:path.html
+# Exclude from processing.
+# The following items will not be processed, by default. Create a custom list
+# to override the default setting.
+exclude:
+  - Gemfile
+  - Gemfile.lock
+  - node_modules
+  - update_boostrap.sh

_includes/footer.html

@@ -1,12 +1,29 @@
-<footer id="footer">
 
-  <div class="outer">
+<div class="py-2 border-top">
+  <div class="container">
+    <div class="row">
 
-    Made by <a href="http://compomics.com">Compomics</a>. Site last <a href="https://github.com/compomics/compomics.github.io">generated</a> at {{ site.time | date: "%R on %F" }}.
+      <div class="col-sm">
+        <ul class="list-unstyled">
+          <li>
+            Made by <a href="https://www.compomics.com" target="_blank">CompOmics</a>
+          </li>
+          <li>
+            Site last <a href="https://github.com/compomics/compomics.github.io" target="_blank">generated</a> at {{ site.time | date: "%R on %F" }}.
+          </li>
+        </ul>
+      </div>
 
-  </div>
+      <div class="col-sm text-right">
+        <span class="footer-social-icons">
+          <a href="https://www.compomics.com" target="_blank"><i class="fa fa-home px-1"></i></a>
+          <a href="https://github.com/CompOmics" target="_blank"><i class="fa fa-github px-1"></i></a>
+          <a href="https://twitter.com/CompOmics" target="_blank"><i class="fa fa-twitter px-1"></i></a>
+          <a href="https://www.youtube.com/channel/UCX7yNSWDCUeZx7WOTQ6MO1A" target="_blank"><i class="fa fa-youtube px-1"></i></a>
+        </span>
+      </div>
+
+    </div>
 
-</footer>
-<link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/8.6/styles/darkula.min.css">
-<script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/8.6/highlight.min.js"></script>
-<script>hljs.initHighlightingOnLoad();</script>
+  </div>
+</div>

_includes/head.html

@@ -1,14 +1,10 @@
 <head>
-  <meta charset="utf-8">
+ <meta charset="utf-8">
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
-
-  <title>{% if page.name and page.url != "/index.html" %}
-  {{ page.name }} - {% endif %}
-  {{ site.title }}</title>
-  <meta name="description" content="{% if page.excerpt %}{{ page.excerpt | strip_html | strip_newlines | truncate: 160 }}{% else %}{{ site.description }}{% endif %}">
-
-  <link rel="stylesheet" href="{{ "/css/main.css" | prepend: site.baseurl }}">
-  <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css">
-  <link rel="canonical" href="{{ page.url | replace:'index.html','' | prepend: site.baseurl | prepend: site.url }}">
-</head>
+  {%- seo -%}
+  <link rel="stylesheet" href="{{ "/assets/main.css" | relative_url }}">
+  <link href="//maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">
+  <script src="{{ "/assets/javascript/bootstrap/jquery.min.js" | relative_url }}"></script>
+  <script src="{{ "/assets/javascript/bootstrap/bootstrap.bundle.min.js" | relative_url }}"></script>
+</head>