Merge branch 'master' of git.fmrib.ox.ac.uk:open-science/community/Open-WIN-Community

.devcontainer/Dockerfile

+# [Choice] Debian OS version (use bullseye on local arm64/Apple Silicon): bullseye, buster
+ARG VARIANT=bullseye
+FROM mcr.microsoft.com/vscode/devcontainers/jekyll:0-${VARIANT}
+
+# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
+ARG NODE_VERSION="none"
+RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1
\ No newline at end of file

.devcontainer/base.Dockerfile

+# [Choice] Debian OS version (use 2.7-bullseye on local arm64/Apple Silicon): 2.7-bullseye, 2.7-buster
+ARG VARIANT=2.7-bullseye
+FROM mcr.microsoft.com/vscode/devcontainers/ruby:${VARIANT}
+COPY library-scripts/meta.env /usr/local/etc/vscode-dev-containers
+
+# ENV Variables required by Jekyll
+ENV LANG=en_US.UTF-8 \
+    LANGUAGE=en_US:en \
+    TZ=Etc/UTC \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    LANGUAGE=en_US
+
+# Install bundler, latest jekyll, and github-pages for older jekyll
+RUN gem install bundler jekyll github-pages
+
+# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
+ARG NODE_VERSION="none"
+RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

.devcontainer/devcontainer.json

+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.224.2/containers/jekyll
+{
+  "name": "Just the docs",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "args": {
+      // Update 'VARIANT' to pick a Debian OS version: bullseye, buster
+      // Use bullseye when on local arm64/Apple Silicon.
+      "VARIANT": "bullseye",
+      // Enable Node.js: pick the latest LTS version
+      "NODE_VERSION": "lts/*"
+    }
+  },
+
+  // Set *default* container specific settings.json values on container create.
+  "settings": {},
+
+  // Add the IDs of extensions you want installed when the container is created.
+  "extensions": ["GitHub.vscode-pull-request-github"],
+
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  "forwardPorts": [
+    // Jekyll server
+    4000,
+    // Live reload server
+    35729
+  ],
+
+  // Use 'postCreateCommand' to run commands after the container is created.
+  "postCreateCommand": "sh .devcontainer/post-create.sh",
+
+  // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+  "remoteUser": "vscode"
+}

.devcontainer/post-create.sh

+#!/bin/sh
+
+# Install the version of Bundler.
+if [ -f Gemfile.lock ] && grep "BUNDLED WITH" Gemfile.lock > /dev/null; then
+    cat Gemfile.lock | tail -n 2 | grep -C2 "BUNDLED WITH" | tail -n 1 | xargs gem install bundler -v
+fi
+
+# If there's a Gemfile, then run `bundle install`
+# It's assumed that the Gemfile will install Jekyll too
+if [ -f Gemfile ]; then
+    bundle install
+fi

.github/ISSUE_TEMPLATE/config.yml

 blank_issues_enabled: false
 contact_links:
   - name: Ask a question
-    url: https://github.com/pmarsceill/just-the-docs/discussions
+    url: https://github.com/just-the-docs/just-the-docs/discussions
     about: Ask questions and discuss with other community members

.github/dependabot.yml

+version: 2
+updates:
+- package-ecosystem: npm
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "10:00"
+  open-pull-requests-limit: 10
+- package-ecosystem: bundler
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "10:00"
+  open-pull-requests-limit: 10

.github/release-drafter.yml

 references:
   - v+
-  - master
-name-template: 'v$RESOLVED_VERSION 🌈'
-tag-template: 'v$RESOLVED_VERSION'
+  - main
+name-template: "v$RESOLVED_VERSION 🌈"
+tag-template: "v$RESOLVED_VERSION"
 categories:
-  - title: '🚀 Features'
+  - title: "🚀 Features"
     labels:
-      - 'feature'
-      - 'enhancement'
-  - title: '🐛 Bug Fixes'
+      - "feature"
+      - "enhancement"
+  - title: "🐛 Bug Fixes"
     labels:
-      - 'fix'
-      - 'bugfix'
-      - 'bug'
-  - title: '🧰 Maintenance'
-    label: 
-      - 'chore'
-      - 'dependencies'
-change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+      - "fix"
+      - "bugfix"
+      - "bug"
+  - title: "🧰 Maintenance"
+    label:
+      - "chore"
+      - "dependencies"
+change-template: "- $TITLE @$AUTHOR (#$NUMBER)"
 version-resolver:
   major:
     labels:
-      - 'next-major-release'
+      - "next-major-release"
   minor:
     labels:
-      - 'next-minor-release'
+      - "next-minor-release"
   patch:
     labels:
-      - 'patch'
+      - "patch"
   default: minor
 template: |
   ## Changes

.github/workflows/ci-master.yml

-on: 
-  push:
-    branches:
-    - master
-
-name: Master branch CI
-
-jobs:
-
-  jekyll-latest:
-    name: Build Jekyll site (latest)
-    runs-on: ubuntu-latest
-    steps:
-
-    - uses: actions/checkout@master
-
-    - name: Build the site in the jekyll/builder container
-      run: |
-        docker run --rm \
-        --volume="${{ github.workspace }}:/srv/jekyll" \
-        jekyll/builder:latest /bin/bash -c "gem install bundler && chmod -R 777 /srv/jekyll && bundle install && bundle exec jekyll build && bundle exec rake search:init"
-  jekyll-3-8-5:
-    name: Build Jekyll site (v3.8.5)
-    runs-on: ubuntu-latest
-    steps:
-
-    - uses: actions/checkout@master
-
-    - name: Build the site in the jekyll/builder container
-      run: |
-        docker run --rm \
-        --volume="${{ github.workspace }}:/srv/jekyll" \
-        jekyll/builder:3.8.5 /bin/bash -c "gem install bundler && chmod -R 777 /srv/jekyll && bundle install && bundle exec jekyll build && bundle exec rake search:init"
-  assets:
-    name: Format and test CSS and JS
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Use Node.js 12.x
-      uses: actions/setup-node@v1
-      with:
-        node-version: '12.x'
-    - run: npm install
-    - run: npm test

.github/workflows/ci.yml

-on: [pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+      - 'v**'
 
 name: CI
 
 jobs:
-
-  jekyll-latest:
-    name: Build Jekyll site (latest)
-    runs-on: ubuntu-latest
-    steps:
-
-    - uses: actions/checkout@v2
-
-    - name: Build the site in the jekyll/builder container
-      run: |
-        docker run --rm \
-        --volume="${{ github.workspace }}:/srv/jekyll" \
-        jekyll/builder:latest /bin/bash -c "gem install bundler && chmod -R 777 /srv/jekyll && bundle install && bundle exec jekyll build && bundle exec rake search:init"
-
-  jekyll-3-8-5:
-    name: Build Jekyll site (v3.8.5)
+  jekyll-build:
+    name: Build Jekyll site
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        jekyll-version: [3.9, 4.3]
     steps:
-
-    - uses: actions/checkout@v2
-
-    - name: Build the site in the jekyll/builder container
-      run: |
-        docker run --rm \
-        --volume="${{ github.workspace }}:/srv/jekyll" \
-        jekyll/builder:3.8.5 /bin/bash -c "gem install bundler && chmod -R 777 /srv/jekyll && bundle install && bundle exec jekyll build && bundle exec rake search:init"
+    - 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: false
+    - name: Bundle Install
+      run: bundle install
+    - name: Install Jekyll ${{ matrix.jekyll-version }}
+      run: gem install jekyll -v ${{ matrix.jekyll-version }}
+    - name: Init Search
+      run: bundle exec rake search:init
+    - name: Build Site
+      run: bundle exec jekyll build
 
   assets:
     name: Test CSS and JS
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        node-version: [18.x]
+
     steps:
-    - uses: actions/checkout@v2
-    - name: Use Node.js 12.x
+    - uses: actions/checkout@v3
+    - name: Use Node.js ${{ matrix.node-version }}
       uses: actions/setup-node@v1
       with:
-        node-version: '12.x'
+        node-version: ${{ matrix.node-version }}
     - run: npm install
     - run: npm test

.github/workflows/deploy.yml

+# 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"]
+
+  # 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
+    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: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v2
+      - 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
+
+  # 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@v1

.github/workflows/publish-gem.yml

@@ -9,11 +9,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Ruby 2.6
+    - uses: actions/checkout@v3
+    - name: Set up Ruby 3.1
       uses: actions/setup-ruby@v1
       with:
-        ruby-version: 2.6.x
+        ruby-version: 3.1
 
     - name: Publish to GPR
       run: |

.github/workflows/update_jekyll-anchor-heading.yml

+name: Update Vendor plugin - jekyll-anchor-headings
+on:
+  # schedule:
+  #   # once per week
+  #   - cron: "0 15 * * 0"
+  workflow_dispatch:
+jobs:
+  update-deps:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Get latest release information
+        id: latest-release
+        uses: pozetroninc/github-action-get-latest-release@master
+        with:
+          owner: allejo
+          repo: jekyll-anchor-headings
+          excludes: prerelease, draft
+
+      - name: Update jekyll-anchor-headings
+        id: update
+        uses: suisei-cn/actions-download-file@v1.3.0
+        with:
+          url: "https://github.com/allejo/jekyll-anchor-headings/releases/download/${{ steps.latest-release.outputs.release }}/anchor_headings.html"
+          target: _includes/vendor/
+
+      - name: Create PR
+        uses: peter-evans/create-pull-request@v4
+        with:
+          commit-message: "chore[dependency]: Update `jekyll-anchor-headings` to `${{ steps.latest-release.outputs.release }}`"
+          title: "auto: Update `jekyll-anchor-headings` to `${{ steps.latest-release.outputs.release }}`"
+          body: |
+            Update `jekyll-anchor-headings` to `${{ steps.latest-release.outputs.release }}`
+            This is an automated pull request.
+          branch: update/vendor/jekyll-anchor-headings
+          delete-branch: true
+          labels: |
+            kind/update
+            area/dependency
+          add-paths: |
+            _includes/vendor/anchor_headings.html
+          token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -7,3 +7,4 @@ _site
 Gemfile.lock
 node_modules
 *.icloud
+.DS_Store

.gitlab-ci.yml

 image: ruby
 
 before_script:
-  - gem install bundler:2.1.4
-  
+  - gem install bundler:2.3.26
+
 pages:
   script:
-    - bundle _2.1.4_ install
+    - bundle _2.3.26_ install
     - bundle exec jekyll build -d public
   tags:
     - docker

.prettierignore

@@ -7,3 +7,4 @@ assets/css/just-the-docs-dark.scss
 assets/js/vendor/lunr.min.js
 assets/js/search-data.json
 assets/js/just-the-docs.js
+*.md

.prettierrc

@@ -4,5 +4,4 @@
   "singleQuote": false,
   "tabWidth": 2,
   "trailingComma": "es5"
-}
-
+}
\ No newline at end of file

.stylelintrc.json

@@ -5,9 +5,16 @@
     "assets/css/just-the-docs-dark.scss",
     "_sass/vendor/**/*.scss"
   ],
-  "extends": ["stylelint-config-primer", "stylelint-config-prettier"],
+  "extends": [
+    "stylelint-config-standard-scss",
+    "stylelint-config-prettier-scss"
+  ],
   "plugins": ["stylelint-prettier"],
   "rules": {
-    "prettier/prettier": true
+    "prettier/prettier": true,
+    "alpha-value-notation": null,
+    "color-function-notation": null,
+    "no-descending-specificity": null,
+    "scss/no-global-function-names": null
   }
 }

.vscode/tasks.json

+{
+  // See https://go.microsoft.com/fwlink/?LinkId=733558
+  // for the documentation about the tasks.json format
+  "version": "2.0.0",
+  "tasks": [
+    {
+      "label": "Serve",
+      "type": "shell",
+      "command": "bundle exec jekyll serve --livereload",
+      "group": {
+        "kind": "test",
+        "isDefault": true
+      },
+      "isBackground": true
+    },
+    {
+      "label": "Build",
+      "type": "shell",
+      "command": "bundle exec jekyll build",
+      "group": {
+        "kind": "build",
+        "isDefault": true
+      }
+    }
+  ]
+}

404.html

@@ -8,4 +8,4 @@ search_exclude: true
 
 <h1>Page not found</h1>
 
-<p>The page you requested could not be found. Try using the navigation {% if site.search_enabled != false %}or search {% endif %}to find what you're looking for or go to this <a href="{{ '/' | absolute_url }}">site's home page</a>.</p>
+<p>The page you requested could not be found. Try using the navigation {% if site.search_enabled != false %}or search {% endif %}to find what you're looking for or go to this <a href="{{ '/' | relative_url }}">site's home page</a>.</p>