bhklab-project-template 0.9.0

A simple CLI tool to create new BHKLab projects from a template

Project Template for BHKLab Projects

Table of Contents

• How this works
• Project Overview
• Requirements
• Usage
  • using pixi
  • using uv
  • using copier
• Documentation
  • Meeting Notes
  • Status
  • Troubleshooting
• Issues
• Contributors

How this works

This project uses the copier tool to maintain a standardized project template that follows the general structure of BHKLab repositories.

Copier facilitates the management of project templates by using jinja2 templating for file/directory names and content in the template.

Project Overview

The BHKLab project template aims to provide:

• Simple project setup with pixi, mkdocs, and basic DMP folder structure
• Support for reproducible research with proper documentation
• GitHub integrations and standardized workflow

Requirements

1: Make sure you have the pixi tool installed.

Visit the pixi documentation

The following two commands should work:

pixi exec gh --help

pixi exec bhklab-project-template --help

2: Make sure you have logged in to GitHub CLI.

pixi exec gh auth login --hostname 'github.com' --git-protocol https

Follow the instructions to authenticate with your GitHub account.

[!WARNING] Make sure you have been added to our lab organization(s) before proceeding!

Usage

Run the following command to create a new project. Replace <PROJECT_NAME> with the name of your project.

using pixi

pixi exec bhklab-project-template <PROJECT_NAME>

• i.e gdcs-drug-combo would create a directory called gdcs-drug-combo

pixi exec bhklab-project-template gdcs-drug-combo

using uv

uv run -m bhklab_project_template <PROJECT_NAME>

using copier

pixi exec copier copy --trust gh:bhklab/bhklab-project-template <PROJECT_NAME>

• This will create a new directory with the name of your project and copy the template files into it.

Documentation

• Meeting Notes
• Status
• Troubleshooting

Issues

Please report any issues with the template to the bhklab/bhklab-project-template.

Contributors

• Jermiah Joseph (@jjjermiah)