switch to jekyll and github pages

Author: letmaik

.github/workflows/publish.yml

@@ -0,0 +1,17 @@
+name: "Jekyll build and publish"
+
+on:
+  push:
+    branches: [master]
+  workflow_dispatch:
+
+jobs:
+  jekyll:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - uses: helaili/jekyll-action@v2
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        target_branch: gh-pages

.gitignore

@@ -1 +1,6 @@
-compiled/*
+_site
+.sass-cache
+.jekyll-cache
+.jekyll-metadata
+vendor
+Gemfile.lock

Gemfile

@@ -0,0 +1,10 @@
+source "https://rubygems.org"
+
+gem "jekyll", "~> 4.2.2"
+gem 'kramdown-parser-gfm', '~> 1.1'
+
+gem "minima", "~> 2.5"
+
+group :jekyll_plugins do
+  
+end

README.md

@@ -1,35 +1,18 @@
-A default blog scaffold for **ruhoh** compatible static blog parsers.
+# adp-multi.github.io
 
-**This version is for [ruhohSpec v1.0](http://ruhoh.com/universal-blog-api/) and is only compatible with ruhoh gem 1.0.x.x**
+## Build locally on Ubuntu
 
-See <http://ruhoh.com> for more information.
+Install tools:
 
-## Usage and Documentation
+```sh
+sudo apt install build-essential ruby ruby-dev
+sudo gem install bundler
+bundle config set --local path 'vendor/bundle'
+bundle install
+```
 
-See <http://ruhoh.com/usage> for full usage and documentation.
-
-Currently the only parser is available in ruby as a ruby gem:
-
-````bash
-$ gem install ruhoh --version '1.0.0.alpha'
-$ ruhoh help
-````
-
-Once you have the gem you can run your blog locally:
-
-Assume USERNAME is your GitHub username.
-
-````bash
-$ git clone git://github.com/ruhoh/blog.git USERNAME.ruhoh.com
-$ cd USERNAME.ruhoh.com
-$ rackup -p 9292
-````
-
-Using your GitHub username is useful for automatically publishing to ruhoh.com
-
-For all publishing options including self-hosting see: <http://ruhoh.com/usage/publish>
-
-## License
-
-Released under the [MIT License](http://www.opensource.org/licenses/MIT)
+Build the site and start a local server:
 
+```sh
+bundle exec jekyll serve --livereload
+```

_config.yml

@@ -0,0 +1,63 @@
+# 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.
+#
+# If you need help with YAML syntax, here are some quick references for you: 
+# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
+# https://learnxinyminutes.com/docs/yaml/
+#
+# Site settings
+# 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: adp-multi
+author: Maik Riechert
+description: >- # this means to ignore newlines until "baseurl:"
+  adp-multi is an adaptation of the Algebraic Dynamic Programming 
+  method for multiple context-free languages.
+baseurl: "" # the subpath of your site, e.g. /blog
+url: "https://adp-multi.github.io" # the base hostname & protocol for your site, e.g. http://example.com
+#twitter_username: jekyllrb
+github_username:  adp-multi
+
+# Build settings
+theme: minima
+markdown: kramdown
+mathjax: true
+plugins:
+  - jekyll-seo-tag
+
+header_pages:
+  - quick_start.md
+  - MCFL.md
+  - adp_for_mcfl.md
+  - syntax.md
+  - tabulation.md
+
+# Exclude from processing.
+# The following items will not be processed, by default.
+# Any item listed under the `exclude:` key here will be automatically added to
+# the internal "default list".
+#
+# Excluded items can be processed by explicitly listing the directories or
+# their entries' file path in the `include:` list.
+#
+# exclude:
+#   - .sass-cache/
+#   - .jekyll-cache/
+#   - gemfiles/
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules/
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/

_includes/head.html

@@ -0,0 +1,17 @@
+<head>
+    <meta charset="utf-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    {%- seo -%}
+    <link rel="stylesheet" href="{{ "/assets/main.css" | relative_url }}">
+    <script>
+    window.MathJax = {
+        tex: {
+          inlineMath: [['$', '$'], ['\\(', '\\)']]
+        }
+      };
+    </script>
+    <script type="text/javascript" id="MathJax-script" async
+        src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js">
+    </script>
+</head>

partials/tabulation_length_slider _includes/tabulation_length_slider.html

@@ -0,0 +1,7 @@
+<script src="//code.jquery.com/jquery-1.10.1.min.js"></script>
+<script src="//code.jquery.com/ui/1.10.3/jquery-ui.js"></script>
+<link rel="stylesheet" href="//code.jquery.com/ui/1.10.3/themes/smoothness/jquery-ui.css">
+<script type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/three.js/r58/three.min.js"></script>
+<script type="text/javascript" src="/assets/three.js/TrackballControls.js"></script>
+<script type="text/javascript" src="/assets/three.js/Tabulation.js"></script>
+<script src="/assets/three.js/helvetiker_regular.typeface.js"></script>

_includes/tabulation_libs.html

@@ -1,6 +1,7 @@
 ---
+layout: page
+permalink: /adp_for_mcfl/
 title : ADP for MCFL
-description:
 ---
 
 An in-depth description of ADP for MCFL can be found in my [master's thesis](https://github.com/adp-multi/thesis/releases). Below is a very short end-user summary.

partials/tabulation_speed_slider _includes/tabulation_speed_slider.html

@@ -1,3 +1,3 @@
-based on http://www.ekevanbatenburg.nl/PKBASE/PKB00163.HTML
-visualized with jViz.Rna (http://jviz.cs.sfu.ca)
+based on http://www.ekevanbatenburg.nl/PKBASE/PKB00163.HTML
+visualized with jViz.Rna (http://jviz.cs.sfu.ca)
 modified with Inkscape

partials/tabulation_subword_slider _includes/tabulation_subword_slider.html

@@ -3,7 +3,6 @@ var __bind = function(fn, me){ return function(){ return fn.apply(me, arguments)
 function Tabulation (container, len) {
 
 	this.freshScene = __bind(this.freshScene, this);
-	this.render = __bind(this.render, this);
 	this.addCube = __bind(this.addCube, this);
 
 	this.len = len;
@@ -40,8 +39,7 @@ Tabulation.prototype.init = function(container) {
 
 	this.geometry = new THREE.CubeGeometry(1, 1, 1);
 
-	var texture = THREE.ImageUtils.loadTexture( '/assets/media/three.js/tex.gif', new THREE.UVMapping(),
-		this.render.bind(this));
+	var texture = THREE.ImageUtils.loadTexture( '/assets/three.js/tex.gif', new THREE.UVMapping());
 	texture.anisotropy = this.renderer.getMaxAnisotropy();
 
 	this.material = new THREE.MeshLambertMaterial( { map: texture} );

_plugins/mathjax.rb

@@ -1,10 +1,11 @@
 ---
-title: adp-multi
-description: adp-multi is an adaptation of the Algebraic Dynamic Programming 
-             method for multiple context-free languages
-layout: page_index
+layout: home
 ---
 
+<div align="center">
+    <img src="/assets/adpmulti_logo.svg" alt="adp-multi logo" width="260" />
+</div>
+
 ## What is adp-multi?
 
 adp-multi is an implementation of [Algebraic Dynamic Programming](http://bibiserv.techfak.uni-bielefeld.de/adp/) for [multiple context-free languages](mcfl).
@@ -32,16 +33,8 @@ After that, you should go to the [quick start guide](/quick_start) where you lea
 what's different compared to original Haskell-ADP and how to write your own grammars.
 
 There's also a short motivational/introductional talk called 
-"[Predicting Pseudoknots Without Hacking in C]({{urls.media}}/talk_herbstseminar2012.pdf)"
+"[Predicting Pseudoknots Without Hacking in C](/assets/talk_herbstseminar2012.pdf)"
 that I gave at the "10. Herbstseminar der Bioinformatik" (2012) which summarizes why adp-multi is useful and in which direction future work might go.
 Note that the adp-multi syntax in the slides is outdated.
 
-In July 2013 I defended my thesis (giving a presentation and answering questions). The (german) [slides are available]({{urls.media}}/verteidigung_2013.pdf) and contain more up-to-date information than the ones from 2012 above. For in-depth information, have a look at [my thesis](https://github.com/adp-multi/thesis/releases), it's in English.
-
-## Questions? Comments? Bugs?
-
-For code-related bugs or suggestions, please create an issue in the [issue tracker](https://github.com/adp-multi/adp-multi/issues).
-
-For everything else, just 
-<a href="http://www.google.com/recaptcha/mailhide/d?k=01K7XApM3NHiteg6XLnkZqAw==&amp;c=62TLgKB3Xjvp60pkxY897qejXI-cQ7FMlvLMAOB-cpw=" onclick="window.open('http://www.google.com/recaptcha/mailhide/d?k\07501K7XApM3NHiteg6XLnkZqAw\75\75\46c\07562TLgKB3Xjvp60pkxY897qejXI-cQ7FMlvLMAOB-cpw\075', '', 'toolbar=0,scrollbars=0,location=0,statusbar=0,menubar=0,resizable=0,width=500,height=300'); return false;" title="Reveal this e-mail address">
-email</a> me.
+In July 2013 I defended my thesis (giving a presentation and answering questions). The (german) [slides are available](/assets/verteidigung_2013.pdf) and contain more up-to-date information than the ones from 2012 above. For in-depth information, have a look at [my thesis](https://github.com/adp-multi/thesis/releases), it's in English.

pages/adp_for_mcfl.md adp_for_mcfl.md

@@ -1,6 +1,7 @@
 ---
+layout: page
+permalink: /mcfl/
 title : Multiple Context-Free Languages
-description:
 ---
 
 If you already know what multiple context-free languages and grammars are, then you can head over to the [ADP for MCFL](/adp_for_mcfl) page if you're interested in how MCFGs were merged with ADP.