USyd NCI Gadi guide

Contributing to this repository

1. Do not under any circumstances commit to the main branch without review by someone else;
2. Fork the repository, make and test changes, then put in a pull request
3. If you are not sure how to do something, ask for help.

File location

• Store index.qmd, setup.qmd files in the root directory
• Store markdown lessons (.qmd or .md) in the notebooks folder
• Store figures in a figs folder

How to contribute to the guide

You can choose to work either locally or on your Nimbus VM to make changes to this guide. Please work in VS code to easily edit the markdown files. No changes are to be made to the html files directly.

Grab a copy of the repository by cloning it to your local machine or Nimbus VM:

git clone https://github.com/Sydney-Informatics-Hub/ANZAC_neurogenetics_Gadi_guide.git

1. Edit index.qmd to change the main landing page. This is a markdown file.
2. Edit or create setup.qmd to change the Setup instruction pages. Same - basically a md file.
3. Edit _quarto.yml to reorder/rename/remove/replace the dropdown menu options.
4. Add additional *.qmd files to the root dir to have them converted to html files (and add them to _quarto.yml to make them navigable), if you'd like.
5. Add any figures to figs/ and give them a descriptive name.

You can browse the result locally by exploring the html files created (note: sometimes figures display locally but not on web and the other way around too) by running:

quarto preview

Once you've made changes to the materials, run the following on the commandline:

quarto render
# First time you create the file, add them to be tracked by github, e.g.
git add docs/*
git commit -am "your comments"
git push origin main 

This repository has been set up to auto publish updates using a github action in .github/workflows/quarto_render_publish.yml. Once you push changes to main, you should see the updates on the website within a couple of minutes.

Themes, Aesthetic and Branding

If you'd like to use a more generic and possibly neutral theme, go to the _quarto.yaml and change the format section to:

format:
  html:
   toc: true
   theme:
      light: flatly
      dark: darkly
   css: styles.scss
   code-link: true
   code-fold: false

If you'd like to change to the USYD Masterbrand Ochre, go to the _quarto.yaml and change the format section to:

format:
  html:
    theme: simplex
    css: [lesson.css, bootstrap-icons.css]
    toc: true
    code-overflow: wrap
    highlight-style: github