diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..ff1a325 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,8 @@ +version: 2 +updates: + - package-ecosystem: bundler + directory: / + schedule: + interval: daily + allow: + - dependency-type: direct diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml new file mode 100644 index 0000000..9ca81e8 --- /dev/null +++ b/.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 diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml new file mode 100644 index 0000000..f5b7460 --- /dev/null +++ b/.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 diff --git a/docs/.gitignore b/docs/.gitignore index f40fbd8..601da72 100644 --- a/docs/.gitignore +++ b/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/ diff --git a/docs/Gemfile b/docs/Gemfile index 8546ffb..3aec09b 100644 --- a/docs/Gemfile +++ b/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 diff --git a/docs/_config.yml b/docs/_config.yml index 7155209..f4155b0 100644 --- a/docs/_config.yml +++ b/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: