The Sphinx documentation in a repository is automatically compiled as 'html' and deployed, by means of the gh-pages branch, with this GitHub Actions to GitHub Pages. The user has only to be sure that the repository accomplishes a couple of requirements.

In summary, this GitHub action does the following:

• Takes the author and SHA id of the trigger action (push or pull request) to be consistent along the action.
• Creates a new gh-pages branch if this is not already in the repository.
• Compiles the sphinx documentation in the directory and branch specified by the user.
• Pushes the output html documentation to the gh-pages branch.

This GitHub Action was developed by the Computational Biology and Drug Design Research Unit -UIBCDF- at the Mexico City Children's Hospital Federico Gómez (see also Contributers). Other GitHub Actions can be found at the UIBCDF GitHub site.

There is no need to have a gh-pages branch already in the repository. This action will create it for you. But once this GitHub action runned for first time, make sure that GitHub Pages is taking the web source code from the branch gh-pages. In the github repository go to 'Settings -> Pages -> Source' and check that no other branch is selected as source.

The compilation of your sphinx documentation requires dependencies that can be solved with a temporary conda environment. Make sure that the repository has a Yaml file with the details to make this environment (see the section "Documentation conda environment").

To include this GitHub Action, create a YAML file (named sphinx_docs_to_gh_pages.yaml, for instance) with the following content in the directory .github/workflows of your repository:

name: Sphinx docs to gh-pages

on:
  push:
    branches:
      - main

# workflow_dispatch:        # Un comment line if you also want to trigger action manually

jobs:
  sphinx_docs_to_gh-pages:
    runs-on: ubuntu-latest
    name: Sphinx docs to gh-pages
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - name: Make conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          python-version: 3.10    # Python version to build the html sphinx documentation
          environment-file: devtools/conda-envs/docs_env.yaml    # Path to the documentation conda environment
          auto-update-conda: false
          auto-activate-base: false
          show-channel-urls: true
      - name: Installing the library
        shell: bash -l {0}
        run: |
          python setup.py install
      - name: Running the Sphinx to gh-pages Action
        uses: uibcdf/[email protected]
        with:
          branch: main
          dir_docs: docs
          sphinx-apidoc-opts: '--separate -o . ../'
          sphinx-apidoc-exclude: '../*setup* ../*.ipynb'
          sphinx-opts: ''

Two things need to be known to run the GitHub Actions without further work: the meaning of the input parameters and the YAML file to make a temporary Conda environment where the sphinx documentation can be compiled.

These are the input parameters of the action:

They are placed in the last lines of the above workflow example file:

      - name: Running the Sphinx to gh-pages Action
        uses: uibcdf/[email protected]
          with:
            branch: main
            dir_docs: docs
            sphinx-opts: ''
            sphinx-apidoc-opts: '--separate -o . ../'
            sphinx-apidoc-exclude: '../*.ipynb'

In case your sphinx documentation is placed in a directory named 'docs' in the 'main' branch to be compiled with no further options, you can do without the section with:.

The Sphinx documentation will need specific libraries and packages to be compiled. There are a few options to achieving this, one is to create a Conda environment in which to build the documentation. Alternatively if your package includes the [options.extras_require] docs section you can install these.

They can be specified in a Conda environment file. This way, a temporary enviroment can be made and activated to compile the documentation with all dependencies satisfied. Write a file in the repository with the following content:

name: docs

channels:

  - conda-forge
  - defaults

dependencies:

  # Write here all dependencies to compile the sphinx documentation.
  # This list is just an example
  - python=3.10
  - sphinx
  - sphinx_rtd_theme
  - sphinxcontrib-bibtex
  - nbsphinx
  - recommonmark
  - sphinx-markdown-tables

And replace the value of the workflow input parameter environment-file: with the right path to your documentation conda enviroment file. In the case of the above example ('devtools/conda-envs/docs_env.yaml'):

jobs:
  sphinx_docs_to_gh-pages:
    steps:
      - name: Make conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          # Replace with the path to your documentation conda enviroment file
          environment-file: devtools/conda-envs/docs_env.yaml

Many Python packages use setuptools for configuring installation via the setup.cfg file. One section of this is the [options.extras_require] where packages not required for running the package but used in testing or building documentation can be listed. To list your documentation build requirements add the following to your setup.cfg

[options.extras_require]

docs =
  sphinx<5.0
  myst_parser
  pydata_sphinx_theme
  sphinx_markdown_tables
  sphinx_rtd_theme
  sphinxcontrib-mermaid

Then in your sphinx_docx_to_gh_pages.yaml that you have created under the .github/workflows/ directory replace the step with -name Make conda environment (see above example) with the following steps which will setup the specified Python version and then install the docs requirements listed in your setup.cfg.

jobs:
  sphinx_docs_to_gh-pages:
    steps:
      - name: Setup Python
        uses: actions/setup-python@v2
        with:
          python-version: 3.10
      - name: Installing the Documentation requirements
        run: |
          pip3 install .[docs]

This GitHub Action was developed to solve a need of the UIBCDF. And to be used, additionally, as an example of house-made GitHub Action for researchers and students in this lab.

Other tools you can find in the market doing these same tasks are mentioned below. We recognize and thank the work of their developers. Many of those GitHub Actions were used by us to learn how to set up our own one.

If you think that your GitHub Action should be mentioned here, fell free to PR with a new line.

• sphinx-pages
• spinx-action
• action-sphinx-composite

• gh-pages-action
• github-pages-deploy-action
• GitHub-Pages-deploy
• create-ghpages-ifnotexists
• simple-github-pages-deploy-action
• gh-pages-action
• ghaction-github-pages
• actions-gh-pages

• github-push-action

• pages
• spinx-pages

• GitHub Pages
• GitHub Actions
• Sphinx
• YAML