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‎.github/workflows/jekyll-github-pages.yml

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name: Build and Deploy a Jekyll Site to GitHub Pages
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on:
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push:
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branches:
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- master
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jobs:
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jekyll:
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runs-on: windows-latest
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steps:
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- name: 📂 setup
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uses: actions/checkout@v2
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# include the lines below if you are using jekyll-last-modified-at
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# or if you would otherwise need to fetch the full commit history
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# however this may be very slow for large repositories!
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# with:
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# fetch-depth: '0'
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- name: 💎 setup ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: 2.7
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- name: 🔨 install dependencies & build site
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uses: limjh16/jekyll-action-ts@v2
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with:
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enable_cache: true
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- name: 🚀 deploy
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./_site
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# if the repo you are deploying to is <username>.github.io, uncomment the line below.
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# if you are including the line below, make sure your source files are NOT in the "main" branch:
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# publish_branch: main

‎.gitignore

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_site/
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.sass-cache/
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.jekyll-cache/
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_site
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.sass-cache
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.jekyll-cache
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.jekyll-metadata
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vendor

‎404.html

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---
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permalink: /404.html
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layout: default
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---
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<style type="text/css" media="screen">
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.container {
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margin: 10px auto;
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max-width: 600px;
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text-align: center;
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}
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h1 {
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margin: 30px 0;
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font-size: 4em;
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line-height: 1;
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letter-spacing: -1px;
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}
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</style>
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<div class="container">
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<h1>404</h1>
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<p><strong>Page not found :(</strong></p>
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<p>The requested page could not be found.</p>
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</div>

‎Gemfile

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source "https://rubygems.org"
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# Hello! This is where you manage which Jekyll version is used to run.
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# When you want to use a different version, change it below, save the
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# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
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#
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# bundle exec jekyll serve
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#
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# This will help ensure the proper Jekyll version is running.
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# Happy Jekylling!
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gem "jekyll", "~> 4.2.0"
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# This is the default theme for new Jekyll sites. You may change this to anything you like.
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gem "minima", "~> 2.5"
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# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
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# uncomment the line below. To upgrade, run `bundle update github-pages`.
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# gem "github-pages", group: :jekyll_plugins
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# If you have any plugins, put them here!
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group :jekyll_plugins do
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gem "jekyll-feed", "~> 0.12"
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end
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# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
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# and associated library.
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platforms :mingw, :x64_mingw, :mswin, :jruby do
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gem "tzinfo", "~> 1.2"
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gem "tzinfo-data"
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end
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# Performance-booster for watching directories on Windows
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gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
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gem "jekyll-theme-simplex"
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gem "webrick", "~> 1.7"

‎Gemfile.lock

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GEM
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remote: https://rubygems.org/
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specs:
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addressable (2.8.0)
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public_suffix (>= 2.0.2, < 5.0)
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colorator (1.1.0)
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concurrent-ruby (1.1.9)
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em-websocket (0.5.2)
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eventmachine (>= 0.12.9)
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http_parser.rb (~> 0.6.0)
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eventmachine (1.2.7-x64-mingw32)
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ffi (1.15.3-x64-mingw32)
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forwardable-extended (2.6.0)
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http_parser.rb (0.6.0)
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i18n (1.8.10)
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concurrent-ruby (~> 1.0)
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jekyll (4.2.0)
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addressable (~> 2.4)
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colorator (~> 1.0)
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em-websocket (~> 0.5)
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i18n (~> 1.0)
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jekyll-sass-converter (~> 2.0)
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jekyll-watch (~> 2.0)
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kramdown (~> 2.3)
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kramdown-parser-gfm (~> 1.0)
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liquid (~> 4.0)
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mercenary (~> 0.4.0)
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pathutil (~> 0.9)
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rouge (~> 3.0)
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safe_yaml (~> 1.0)
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terminal-table (~> 2.0)
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jekyll-feed (0.15.1)
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jekyll (>= 3.7, < 5.0)
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jekyll-sass-converter (2.1.0)
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sassc (> 2.0.1, < 3.0)
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jekyll-seo-tag (2.7.1)
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jekyll (>= 3.8, < 5.0)
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jekyll-theme-simplex (0.9.8.15)
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jekyll (~> 4.0)
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jekyll-watch (2.2.1)
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listen (~> 3.0)
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kramdown (2.3.1)
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rexml
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kramdown-parser-gfm (1.1.0)
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kramdown (~> 2.0)
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liquid (4.0.3)
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listen (3.6.0)
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rb-fsevent (~> 0.10, >= 0.10.3)
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rb-inotify (~> 0.9, >= 0.9.10)
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mercenary (0.4.0)
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minima (2.5.1)
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jekyll (>= 3.5, < 5.0)
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jekyll-feed (~> 0.9)
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jekyll-seo-tag (~> 2.1)
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pathutil (0.16.2)
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forwardable-extended (~> 2.6)
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public_suffix (4.0.6)
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rb-fsevent (0.11.0)
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rb-inotify (0.10.1)
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ffi (~> 1.0)
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rexml (3.2.5)
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rouge (3.26.0)
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safe_yaml (1.0.5)
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sassc (2.4.0-x64-mingw32)
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ffi (~> 1.9)
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terminal-table (2.0.0)
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unicode-display_width (~> 1.1, >= 1.1.1)
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thread_safe (0.3.6)
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tzinfo (1.2.9)
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thread_safe (~> 0.1)
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tzinfo-data (1.2021.1)
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tzinfo (>= 1.0.0)
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unicode-display_width (1.7.0)
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wdm (0.1.1)
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webrick (1.7.0)
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PLATFORMS
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x64-mingw32
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DEPENDENCIES
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jekyll (~> 4.2.0)
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jekyll-feed (~> 0.12)
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jekyll-theme-simplex
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minima (~> 2.5)
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tzinfo (~> 1.2)
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tzinfo-data
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wdm (~> 0.1.1)
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webrick (~> 1.7)
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BUNDLED WITH
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2.2.25

‎README.md

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# openbiolink.github.io
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## Use all Themes on gh pages
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https://www.moncefbelyamani.com/making-github-pages-work-with-latest-jekyll/
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## Generate doc for loader and evaluator
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from src folder run ```pdoc --html openbiolink/obl2021/obl2021.py --force```

‎_config.yml

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# Welcome to Jekyll!
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#
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# This config file is meant for settings that affect your whole blog, values
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# which you are expected to set up once and rarely edit after that. If you find
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# yourself editing this file very often, consider using Jekyll's data files
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# feature for the data you need to update frequently.
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#
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# For technical reasons, this file is *NOT* reloaded automatically when you use
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# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
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#
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# If you need help with YAML syntax, here are some quick references for you:
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# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
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# https://learnxinyminutes.com/docs/yaml/
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#
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# Site settings
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# These are used to personalize your new site. If you look in the HTML files,
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# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
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# You can create any custom variable you would like, and they will be accessible
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# in the templates via {{ site.myvariable }}.
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title: OpenBioLink2021 Challenge
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email: [email protected]
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description: >- # this means to ignore newlines until "baseurl:"
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Hello, this is an demo of the jekyll theme simplex.
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Here you can check out all the features of the theme.
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To try this theme, have a look at the Github.
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# Build settings
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plugins:
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- jekyll-feed
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# Exclude from processing.
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# The following items will not be processed, by default.
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# Any item listed under the `exclude:` key here will be automatically added to
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# the internal "default list".
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#
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# Excluded items can be processed by explicitly listing the directories or
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# their entries' file path in the `include:` list.
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#
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# exclude:
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# - .sass-cache/
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# - .jekyll-cache/
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# - gemfiles/
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# - Gemfile
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# - Gemfile.lock
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# - node_modules/
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# - vendor/bundle/
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# - vendor/cache/
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# - vendor/gems/
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# - vendor/ruby/
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logo_img: /assets/img/logo2021-transp.png
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copyright: © Simon Ott 2021, <a href="/attributions.html">Icon attributions</a> #Your copyright.
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collections:
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category:
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output: true
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authors:
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output: false
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defaults:
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-
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scope:
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path: ""
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type: category
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values:
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layout: "category"

‎_data/nav.yaml

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- title: Challenge
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url:
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icon: assets/img/icons/goal.svg
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- title: Dataset
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url: dataset
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icon: assets/img/icons/biomedicine.svg
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- title: Participation
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url: participation/
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icon: assets/img/icons/rocket.svg
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- title: Rules
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url: rules/
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icon: assets/img/icons/guideline.svg
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- title: Team
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url: team/
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icon: assets/img/icons/team.svg

‎_includes/footer.html

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<footer class="footer">
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<section class="footer__about">
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<p class="footer__about__copyright">{{ site.copyright }}</p>
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{% if site.copyright != nil %}
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<span class="divider">·</span>
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{% endif %}
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<span class="footer__about__theme"><p>theme</p><a id="simplex-logo" href="https://github.com/andreondra/jekyll-theme-simplex" target="_blank"><img alt="Simplex theme logo" src="{{ site.url }}/assets/img/icons/simplex_logo.svg"/></a><p>by <a href="https://ondrej.golasowski.com/">golas</a></p></span>
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</section>
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</footer>

‎_includes/head.html

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<link rel="stylesheet" href="{{ site.url }}/assets/fonts/fonts.css"/>
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<link rel="stylesheet" href="{{ site.url }}/assets/style.css"/>
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<link rel="stylesheet" href="{{ site.url }}/assets/js/lity.min.css"/>
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{% if site.favicon != nil %}
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<link rel='shortcut icon' type='image/x-icon' href='{{ site.favicon }}' />
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{% endif %}
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<meta property="og:site_name" content="{{ site.title }}" />
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<meta
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property="og:title"
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content="
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{% if page.title != nil %}
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{{page.title}}
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{% else %}
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{{site.title}}
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{% endif %}
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"
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/>
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{% if page.og_description != nil %}
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<meta property="og:description" content="{{ page.og_description }}" />
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{% endif %}
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<meta property="og:url" content="{{ site.url }}/{{ page.url }}" />
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{% if page.og_type != nil %}
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<meta property="og:type" content="{{ page.og_type }}" />
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{% else %}
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<meta property="og:type" content="article" />
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{% endif %}
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{% if page.og_image != nil %}
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<meta property="og:image" content="{{ site.url }}/{{ page.og_image }}" />
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<meta property="og:image:secure_url" content="{{ site.url }}/{{ page.og_image }}" />
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{% endif %}
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{% if page.fb_app_id != nil %}
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<meta property="fb:app_id" content="{{ page.fb_app_id }}" />
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{% else if site.fb_app_id != nil %}
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<meta property="fb:app_id" content="{{ site.fb_app_id }}" />
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{% endif %}
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<title>
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{% if page.title != nil %}
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{{page.title}}
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{% else %}
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{{site.title}}
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{% endif %}
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</title>

‎_includes/header.html

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<header class="header">
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<!-- particles.js container -->
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<div id="particles-js" class="particles"></div>
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<!-- scripts -->
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/particles.min.js"></script>
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<script>
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particlesJS.load('particles-js', '/assets/particles.json', function() {
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console.log('particles.js loaded - callback');
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});
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</script>
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<section class="logo">
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<a href="{{ site.url }}/" class="logo__link">
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{% if site.logo_img != nil %}
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<h1 style="display: none;">{{ site.title }}</h1>
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<img class="logo__link__img" src="{{site.logo_img}}" />
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{% else %}
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<h1>{{ site.title }}</h1>
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{% endif %}
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</a>
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</section>
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<button id="menuToggle">
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<div></div>
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<div></div>
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<div></div>
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</button>
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<nav class="menu">
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{% include nav.html nav=site.data.nav %}
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</nav>
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</header>

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