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Gen-AI Assisted Scientific Software Research Development

This is a sample lesson for training on using generative AI tools to assist scientific research software development. It is a test of a new software carpentry plugin that provides agents and skills to create a lesson plan following the software carpentry pedagogical approach.

Rendering the Lesson

This lesson is built with MyST and Jupyter Book 2.0. The recommended way to manage the environment and build the book is via Pixi.

Prerequisites

Install Pixi by following the instructions at https://pixi.sh/latest/#installation.

Set up the environment

From the repository root, install all dependencies defined in pixi.toml:

pixi install

This creates an isolated environment with Python, MyST, and any other lesson dependencies.

Build the HTML book

pixi run build

The rendered site will be written to _build/html/. Open _build/html/index.html in a browser to preview it locally.

Live preview with hot reload

pixi run preview

This starts a local development server and watches for file changes, rebuilding automatically.

Adding dependencies

If an episode requires additional Python packages (e.g. numpy, pandas), add them to the [dependencies] section of pixi.toml and re-run pixi install.

Repository Structure

Path Description
episodes/ Lesson episode source files (Markdown)
index.md Book landing page
myst.yml MyST / Jupyter Book configuration and table of contents
pixi.toml Pixi environment and task definitions
pixi.lock Locked dependency versions for reproducibility
outline/ Lesson planning materials
_build/ Build output — not committed to version control

License

This lesson is released under the CC-BY-4.0 license.

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