Coding for Reproducible Research (CfRR) Courses

This repository contains the Coding for Reproducible Research (CfRR) training programme materials from the University of Exeter. The content is published as a Jupyter Book website and is also usable locally (e.g., to run notebooks or preview changes before opening a pull request).

• Website: https://coding-for-reproducible-research.github.io/CfRR_Courses/home_page.html
• Contact: codingforreproducibleresearch@exeter.ac.uk

Repository layout

Content is organized as a Jupyter Book (see _config.yml and _toc.yml), with notebooks/markdown grouped by programme area:

• home_page.md: Jupyter Book homepage content.
• cfrr_program_details/: Programme-level pages (e.g., About, Code of Conduct, how to use the site).
• course_homepages/: Course-category overview pages (Python, R, Unix/Linux, etc.).
• programme_information/: Workshop information pages (outlines/details for each workshop).
• individual_modules/: Core teaching materials for each module (notebooks, markdown, images).
• individual_modules/section_landing_pages/: Per-module landing pages (objectives, prerequisites, overview).
• short_courses/: Short/special-topic materials.
• where_is_my_understanding/: Self-assessment quiz materials.
• pathways/: Notebooks/content describing relationships between courses (e.g., pathway visualizations).
• data/: Shared data used to generate parts of the site (e.g., workshop schedule and pathway graphs).
• resources/: Shared resources referenced across materials.
• R_functions/, julia_functions/: Language-specific helper functions used in materials.
• _static/, _templates/: Jupyter Book static assets and template overrides.
• .github/workflows/: CI workflows (build, deploy, accessibility checks).

Key repo files:

• _config.yml: Jupyter Book configuration.
• _toc.yml: Jupyter Book table of contents.
• pyproject.toml: Python dependencies used in CI to build the book.
• requirements.in: A lightweight dependency list (kept for convenience; CI uses pyproject.toml).
• CITATION.cff, references.bib: Citation metadata and bibliographic references.

Finding the source file for a webpage

If you are browsing the published website and want to edit the corresponding source (.md or .ipynb) locally, you can usually map from the URL path to the repo path:

1. Take the part of the URL after CfRR_Courses/ and remove the .html suffix.
2. Look for a matching source file in the repo with the same path and either a .md or .ipynb extension.

Examples:

• Website page .../home_page.html → home_page.md
• Website page .../contributing/contributing.html → contributing/contributing.md (or .ipynb if that page is a notebook)
• Website page .../pathways/related_courses.html → pathways/related_courses.ipynb

If you cannot find an exact match (some pages are generated/renamed), _toc.yml is the source of truth for what files are included in the book and in what structure.

Getting started

Browse online

For most users, browsing the published website is the easiest way to use the materials:

https://coding-for-reproducible-research.github.io/CfRR_Courses/home_page.html

Run locally (Poetry, matches CI)

CI builds use Python 3.11, so using Python 3.11 locally is recommended as well.

1. Clone the repo:

git clone https://github.com/coding-for-reproducible-research/CfRR_Courses.git
cd CfRR_Courses

2. Install dependencies with Poetry:

poetry install

3. Launch JupyterLab to interact with notebooks:

poetry run jupyter lab

Notes:

• Poetry installs from pyproject.toml (the same source used in GitHub Actions).
• If you prefer an activated shell instead of prefixing commands with poetry run, use poetry shell.

Secret scanning before commits

This repository includes a Gitleaks pre-commit hook for catching accidental credentials before they are committed. Install pre-commit, then enable the hook:

pre-commit install

To scan the repository manually:

pre-commit run gitleaks --all-files

Build and preview the website

Build the Jupyter Book:

poetry run jupyter-book build .

The generated static site is written to _build/html/. To preview locally:

poetry run python -m http.server --directory _build/html 8000

Then open http://localhost:8000/ in your browser.

Contributing

Contributions are welcome. See contributing/ for contribution guidelines and course-development notes. The contributing section is also published here:

https://coding-for-reproducible-research.github.io/CfRR_Courses/contributing/contributing.html

License

There is no single license that applies to the entire repository. Each module typically includes its own LICENSE.txt under individual_modules/<module_name>/.

CI and deployment

This project uses GitHub Actions to build, test, and deploy the website:

• .github/workflows/build-book.yml: builds the book on pull requests to main.
• .github/workflows/deploy-book.yml: builds and deploys _build/html to GitHub Pages on pushes to main (and on a schedule).
• .github/workflows/accessibility*.yml: builds the book and runs accessibility checks (see above).
• .github/workflows/secret-scanning.yml: runs Gitleaks and posts a PR comment with redacted secret-scanning results.

The build and deploy workflows also scan generated _build/ log files after the Jupyter Book build. Repository administrators should enable GitHub secret scanning and push protection in the repository's code security settings where available.