Strukturbiologi

Repository for course notes for Strukturbiologi at the Department of Molecular Biology & Genetics at Aarhus University.

Installation

The site is build using Quarto a Markdown-based publishing system and uses git for version control with the remote repository hosted on Github.com.

Git

To work on the site locally you will need to clone the repository, you can do so for a HTTPS setup with

git clone https://github.com/au-mbg/structural_biology.git

or for SSH (requires setting up an SSH key, which can be a little tricky) with

git clone https://github.com/au-mbg/structural_biology.git

This requires having git installed, if you do not then you can first install pixi like described below and then use that to install git.

Pixi

Pixi is a package manager that can install all the required programs to render the site.

The first step is to install pixi this can be installed on MacOS and Linux with the command

curl -fsSL https://pixi.sh/install.sh | sh

On Windows it can be installed either through the installer available from the pixi website or with the command

powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"

After the installation finishes you will need to open a new terminal for the pixi-command to be available.

Installing git with pixi

If you do not have git installed, you can use pixi to install git, like so

pixi global install git

After this open a new terminal/shell and git will be available.

Then the git clone commands listed above will work.

git authentication

To help with git setup you can run

pixi run github-auth

This will ask a few questions and eventually open a browser to login to github. You will only need to do this once per machine.

Basic git operations

Before making any updates it's a good idea to make sure you have the latest version

git pull

When you've made an update you can run

git status

This will list all the files that have been changed, for example

On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   course_notes/exercises/te_01_i_gang_med_pymol.qmd

no changes added to commit (use "git add" and/or "git commit -a")

Then you add the files you want to commit

git add course_notes/exercises/te_01_i_gang_med_pymol.qmd

Write a commit message

git commit -m "Update the exercises for the first TØ session."

And then push to the remote

git push

For slightly more detailed instructions see git - the simple guide.

Using pixi for site rendering

With pixi installed the site can be rendered or previewed using the commands

• pixi run preview exercise: Opens a live preview of the student facing version of the site.
• pixi run preview solution: Opens a live preview of the instructor facing version of the site.
• pixi run render-all: Renders the entire site (not live).
• pixi run clean: Cleans up any site artifacts.

Manual installation

If instead opting to not use pixi this requires installing

• quarto: See Quarto Get Started
• A Python 3.12 environment with appropriate packages.

This installation path is not recommended unless you're comfortable tinkering a bit.

Publishing

The site is automatically rendered and published when commits are pushed to the main-branch of the repository.

This is configured through Github Actions, see publish.yml.

Authoring

For authoring instructions see AUTHORING.md