lab-materials

Instructions and other materials related to the afternoon labs in the Biostatistics-courses

Repository Structure

This repository is organized as monorepo to support multiple courses:

. 
├── courses/
│   ├── course-1/          # First biostatistics course
│   │   ├── chapters/      # Course content chapters
│   │   ├── labs/          # Lab exercises
│   │   ├── _quarto.yml    # Course-specific config
│   │   └── index.qmd      # Course landing page
│   ├── course-2/          # Second biostatistics course
│   └── course-3/          # Third biostatistics course
├── index.qmd             # Landing page source
└── _quarto.yml           # Root configuration

Rendering the Website

Render All Content

From the repository root:

# Render landing page
quarto render index.qmd

# Render Course 1
quarto render courses/course-1

# Render Course 2  
quarto render courses/course-2

# Render Course 3
quarto render courses/course-3

# (and so on for additional courses)

Render a Single Course

From the repository root:

quarto render courses/course-1

Adding a New Course

1. Create a feature branch (e.g. add-course-3).
2. Create directory courses/course-3/ with needed subfolders (chapters/, labs/).
3. Copy _quarto.yml from an existing course; update title/sidebar (keep freeze: auto).
4. Add index.qmd plus at least one chapter and one lab file (placeholders fine).
5. Render locally: quarto render courses/course-3 (creates courses/course-3/docs/ and _freeze/).
6. Verify _freeze/ exists; commit new course files including _freeze/.
7. Update root index.qmd to link to the new course.
8. Push branch and open a PR. The PR build will render the new course automatically (workflow loops over courses/course-*).
9. Merge PR into main; deployment publishes /course-3/.
10. To refresh computations later: quarto render courses/course-3 --execute-refresh and commit updated _freeze/.

Deployment

This repository deploys to its own GitHub Pages site at:

https://biostatistics-psychiatry.github.io/lab-materials/

CI/CD Workflow Overview

• Pull Requests (PRs): Build runs rendering all courses for status checks. No deployment occurs.
• Merging PRs into main: Build renders once, assembles a unified _site/ directory, uploads a Pages artifact, then the deploy-pages action publishes it.
• Assembly: _site/ is created fresh each run (first step removes any previous _site). Contents copied:
  • Root rendered docs/ (landing page)
  • Each course's rendered docs/ into _site/course-1/, _site/course-2/, etc.
• _site/ is never committed, it only exists inside the workflow runner.

Freeze & Computation

This project uses freeze: auto to cache R computations. This means:

• First render: R code executes and results are cached in _freeze/
• Subsequent renders: Cached results are used (no R execution needed)
• GitHub Actions: Only renders HTML from frozen content (no R required)
  • Render before pushing: If you add a new chunk or modify code, run a normal render first so the cache populates, then commit any changes under courses/course-*/_freeze/ before pushing.

Local Full-Site Preview

To mimic the CI page assembly, use the helper script:

bash scripts/preview-full-site.sh

Then visit http://localhost:8000 to inspect the complete project. The script renders all courses, assembles _site/, and serves it with Python.