Proper building by github pages

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: bundler
+    directory: /
+    schedule:
+      interval: daily
+    allow:
+      - dependency-type: direct

.github/workflows/ci_docs.yml

@@ -0,0 +1,22 @@
+name: CI_DOCS
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+      - name: Build with Jekyll
+        run: bundle exec jekyll build

.github/workflows/pages.yml

@@ -0,0 +1,71 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches:
+      - "main"
+    paths:
+      -"docs/**"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+          working-directory: '${{ github.workspace }}/docs'
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: "docs/_site/"
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

docs/.gitignore

@@ -1,5 +1,8 @@
-_site
-.sass-cache
-.jekyll-cache
+# Ignore the default location of the built site, and caches and metadata generated by Jekyll
+_site/
+.sass-cache/
+.jekyll-cache/
 .jekyll-metadata
-vendor
+# Ignore folders generated by Bundler
+.bundle/
+vendor/

docs/Gemfile

@@ -1,36 +1,7 @@
-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", "~> 4.3.2"
-# This is the default theme for new Jekyll sites. You may change this to anything you like.
-#gem "minima", "~> 2.5"
-gem "just-the-docs"
-# 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", "~> 228", group: :jekyll_plugins
-# If you have any plugins, put them here!
-group :jekyll_plugins do
-  gem "jekyll-feed", "~> 0.12"
-end
+source 'https://rubygems.org'
 
-# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
-# and associated library.
-platforms :mingw, :x64_mingw, :mswin, :jruby do
-  gem "tzinfo", ">= 1", "< 3"
-  gem "tzinfo-data"
-end
+gem "jekyll", "~> 4.3.3" # installed by `gem jekyll`
+# gem "webrick"        # required when using Ruby >= 3 and Jekyll <= 4.2.2
 
-# Performance-booster for watching directories on Windows
-gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
-
-# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
-# do not have a Java counterpart.
-gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]
-
-gem "webrick", "~> 1.8"
+gem "just-the-docs", "0.7.0" # pinned to the current release
+# gem "just-the-docs"        # always download the latest release

docs/_config.yml

@@ -1,58 +1,14 @@
-# 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: scATAC Fragment Tools
 email: seppe.dewinter@kuleuven.be
 description: >- # this means to ignore newlines until "baseurl:"
   Tools for working with scATAC-seq fragment files.
 url: "https://aertslab.github.io/scatac_fragment_files" # the base hostname & protocol for your site, e.g. http://example.com
 
-aux_links: # remove if you don't want this link to appear on your pages
-  Template Repository: https://aertslab.github.io/scatac_fragment_files
+aux_links:
+  Template Repository: https://github.com/just-the-docs/just-the-docs-template
 
 # Build settings
 theme: just-the-docs
-plugins:
-  - jekyll-feed
-  - just-the-docs
-
-
-# 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/
 
 callouts:
   warning: