Scientific Wiki Template

How to use this template

This guide outlines the basic steps to set up, configure, and publish your own version of this Scientific Wiki.

1. Fork and Initialize

First, fork this repository to your own GitHub account.

Forking the template

Once this is done, you will have the base template files in your new repository:

Initial repository files

To enable website hosting, you need to create an empty branch called gh-pages. Then, navigate to your repository settings, go to the GitHub Pages section, and select the gh-pages branch as your build and deployment source:

GitHub Pages setup

2. Configure Your Wiki

The main configuration for the website is handled inside the _quarto.yml file. You can customize this file to change the site’s title, logo, navigation sidebar, and bibliography settings:

website:
  title: "Scientific Wiki Template"
  search: true
  sidebar:
    style: "docked"
    logo: "img/logo/logo.png"
    contents:
      - href: index.qmd
        text: "Home"
      - section: "Topics"
        contents:
        - section: "Examples"
          contents:
          - auto: "doc/Examples/*.qmd"
        - section: "Physics"
          contents:
          - auto: "doc/Physics/*.qmd"
      - href: https://github.com/MKReyesH/ScientificWiki
        text: "GitHub Project"
      - href: about.qmd

bibliography: bib/references.bib
csl: bib/journal-of-cosmology-and-astroparticle-physics.csl

You can manage references by adding .bib files to the bib/ folder. You can also change the citation style by updating the csl file path. Quarto supports many Zotero styles, which can be found at the Zotero Style Repository.

Bibliography files

3. Add Content

To add new pages to the wiki, simply create new plain text files (with .qmd extension) inside the doc/ folder. The system will automatically recognize the files and add them to the sidebar. The sidebar reproduces the exact folder structure inside the doc/ folder, so you can create drop-down menus simply by placing files inside sub-folders:

Documentation folder structure

All content files must be plain text file using the .qmd extension and must be written using Quarto Markdown syntax. For a detailed guide on native formatting, please see the Quarto Markdown Guide.

Moreover, anticipating that a lot of scientific content is already written in LaTeX, this template also includes (limited) compatibility for simple LaTeX structures. The commands that are safe to use in the .qmd files are explained in the Allowed LaTeX Syntax Guide. For more complex structures like figures or tables, native Markdown syntax must be used.

4. Commit changes and Deploy

Every time you commit changes to your repository, GitHub Actions will automatically take care of the deployment phase. The updated webpage will be built and pushed to the gh-pages branch, going live online in just a few minutes.