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ENVIRONMENT_SETUP.md

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Environment Setup Guide

This document explains how to set up the development environment for working with and reproducing notebook publications.

Setup the code environment

This repository uses conda to manage the computational and build environment. If you don't have it installed (check with conda --version), you can find operating system-specific instructions for installing miniconda here.

When you're ready, run the following commands to create and activate the environment. Replace [REPO-NAME] with your repository name.

conda env create -n [REPO-NAME] --file env.yml
conda activate [REPO-NAME]

(As you introduce dependencies to your publication, or if you already have your full set of dependencies, add them to env.yml with the version pinned.)

Now, install any internal packages in the repository:

pip install -e .

And finally, install the pre-commit hooks. This is optional but recommended:

pre-commit install

Test your installation with make preview. Your pub will open up in your browser.

Afterwards, create a branch to work on (don't commit to main directly).

Pub Development

When working with Jupyter notebooks:

  1. Edit index.ipynb as your main publication file
  2. Use make preview to see changes in real-time
  3. Run make execute before committing to update _freeze/ with execution results

Other Commands

The Makefile provides several useful commands for development:

  • make lint: Run linting checks using ruff
  • make format: Automatically format code using ruff
  • make pre-commit: Run all pre-commit hooks
  • make test: Run pytest tests, if they exist
  • make bump-version: Update version number