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Tessa Pierce

NSF Postdoc in dib-lab at UC Davis

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I need to edit some documentation for our workflow projects dammit and elvers. These docs are set up in mkdocs, which I love for it’s simplicity: I can write all my documentation in markdown, and mkdocs will take care of formatting and building html for web display. Thanks to Charles Reid for getting the lab on mkdocs a few years ago and for building us a custom theme back in 2018!

GitHub Actions can now be used to automate the manual part of building and deploying mkdocs documentation: time to set this up.

Looks like we can start from GitHub Actions for GitHub Pages. Since dammit and elvers are both project repositories, I’ll just go through the project instructions.

First, add a workflow file: .github/workflows/gh-pages.yml that contains the build and deploy instructions.

This particular file works with the material theme:

name: build and deploy mkdocs to github pages
on:
  push:
    branches:
      - master
jobs:
  deploy:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
        with:
          submodules: "recursive" 
          fetch-depth: 0       # Fetch all history for .GitInfo and .Lastmod
      - name: Setup Python
        uses: actions/setup-python@v1
        with:
          python-version: '3.7'
          architecture: 'x64'
      - name: Install dependencies
        run: |
          python3 -m pip install --upgrade pip     # install pip
          python3 -m pip install mkdocs            # install mkdocs 
          python3 -m pip install mkdocs-material   # install material theme
      - name: Build site
        run: mkdocs build
      - name: Deploy
        uses: peaceiris/actions-gh-pages@v3
        with:
          github_token: $
          publish_dir: ./site

Commit, push, and watch the magic happen. Commit a change to your documentation to double check that your site builds properly.

And… Done! Wow, I really thought there would be more to this - happy to report that something that went faster than expected.

The gh-actions file (containing the code above) can be found here; the site builds to http://dib-lab.github.io/dammit.

The mkdocs.yml file for the documentation website is here, also reproduced below:

site_name: dammit
site_url: http://dib-lab.github.io/dammit
repo_name: dammit
repo_url: https://github.com/dib-lab/dammit
edit_uri: ""

copyright: 'Copyright &copy; 2020 <a href="http://ivory.idyll.org/lab/">Lab for Data Intensive Biology</a> at UC Davis'

# change directory names here
docs_dir: doc
site_dir: site

theme:
  name: material

  # pretty colors! see https://squidfunk.github.io/mkdocs-material/getting-started/#primary-colors
  palette:
    primary: 'green'
    accent: 'purple'
  
  # fun logos! see https://material.io/icons/
  icon:
    logo: material/dns

  font:
    text: 'Roboto'
    code: 'Roboto Mono'

# give a title for each page
nav:
  - 'Home': 'index.md'
  - 'About': 'about.md'
  - 'Installation':
    - 'Requirements': 'system_requirements.md'
    - 'Bioconda': 'install.md'
  - 'Databases':
    - 'Basic Usage': 'database-usage.md'
    - 'About the Databases': 'database-about.md'
    - 'Advanced Database Handling': 'database-advanced.md'
  - 'Tutorial': 'tutorial.md'
  - 'For developers':
    - 'Notes for developers': 'dev_notes.md'