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https://github.com/uibcdf/action-sphinx-docs-to-gh-pages

GitHub Action: The sphinx documentation in a repository is compiled and deployed to GitHub Pages through the gh-pages branch.
https://github.com/uibcdf/action-sphinx-docs-to-gh-pages

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GitHub Action: The sphinx documentation in a repository is compiled and deployed to GitHub Pages through the gh-pages branch.

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# action-sphinx-docs-to-gh-pages

[![Open Source Love](https://badges.frapsoft.com/os/v2/open-source.svg?v=103)](https://github.com/ellerbrock/open-source-badges/)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)



The [Sphinx](https://www.sphinx-doc.org/en/master/) documentation in a repository is automatically compiled as 'html'

and deployed, by means of the `gh-pages` branch, with this [GitHub Actions](https://github.com/features/actions) to

[GitHub Pages](https://pages.github.com/). The user has only to be sure that the repository accomplishes [a couple of

requirements](#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](https://www.uibcdf.org/) (see also

[Contributers](https://github.com/uibcdf/action-sphinx-docs-to-gh-pages/graphs/contributors)). Other GitHub Actions can

be found at [the UIBCDF GitHub site](https://github.com/search?q=topic%3Agithub-actions+org%3Auibcdf&type=Repositories).



## Requirements



### GitHub Pages taking the source from the branch gh-pages



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.



### A YAML file to create a conda environment with docs compilation dependencies



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"](#Documentation-conda-environment)).



## How to use it



To include this GitHub Action, create a [YAML](https://yaml.org/) file (named `sphinx_docs_to_gh_pages.yaml`, for instance)

with the following content in the directory `.github/workflows` of your repository:



```yaml

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.



### Input parameters



These are the input parameters of the action:



| Input parameters        | Description                                                                                         | Default value    |

|-------------------------|-----------------------------------------------------------------------------------------------------|------------------|

| `branch`                | Name of the branch where the sphinx documentation is located                                        | `main`           |

| `branch-checkout-args`  | Arguments to pass to `git checkout`: `git checkout ${checkout-args} "${branch}"`                    | ''               |

| `dir_docs`              | Path where the sphinx documentation is located                                                      | `docs`           |

| `sphinx-apidoc`         | With sphinx-apidoc                                                                                  | true             |

| `sphinx-apidoc-exclude` | With sphinx-apidoc                                                                                  | `*setup* tests*` |

| `sphinx-apidoc-opts`    | Options for sphinx-apidoc (default outputs to dir_docs and searches for modules one level up)       | '-o . ../'       |

| `sphinx-opts`           | Compilation options for sphinx-build                                                                | ''               |



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



```yaml

      - 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:`.



### Documentation Requirements



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](https://docs.conda.io/en/latest/) environment in which to build the

documentation. Alternatively if your package includes the `[options.extras_require] docs` section you can install these.



#### Conda environment



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:



```yaml

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](#How-to-use-it) ('devtools/conda-envs/docs\_env.yaml'):



```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

```



#### `setup.cfg`



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`



``` 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`.



``` yaml

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]

```



## Other tools like this one



This GitHub Action was developed to solve a need of the [UIBCDF]((https://www.uibcdf.org/)). 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



* [sphinx-pages](https://github.com/seanzhengw/sphinx-pages)

* [spinx-action](https://github.com/ammaraskar/sphinx-action)

* [action-sphinx-composite](https://github.com/rickstaa/action-sphinx-composite)



### GitHub Pages



* [gh-pages-action](https://github.com/axetroy/gh-pages-action)

* [github-pages-deploy-action](https://github.com/JamesIves/github-pages-deploy-action)

* [GitHub-Pages-deploy](https://github.com/Cecilapp/GitHub-Pages-deploy)

* [create-ghpages-ifnotexists](https://github.com/ChristopherDavenport/create-ghpages-ifnotexists)

* [simple-github-pages-deploy-action](https://github.com/rdarida/simple-github-pages-deploy-action)

* [gh-pages-action](https://github.com/axetroy/gh-pages-action)

* [ghaction-github-pages](https://github.com/crazy-max/ghaction-github-pages)

* [actions-gh-pages](https://github.com/peaceiris/actions-gh-pages)



### GitHub Push



* [github-push-action](https://github.com/ad-m/github-push-action)



### Shinx + GitHub Pages



* [pages](https://github.com/sphinx-notes/pages)

* [spinx-pages](https://github.com/seanzhengw/sphinx-pages)



## Links



* [GitHub Pages](https://pages.github.com/)

* [GitHub Actions](https://github.com/features/actions)

* [Sphinx](https://www.sphinx-doc.org/en/master/)

* [YAML](https://yaml.org/)