davetang / cookiemonster

Cookiecutter templates

Table of Contents

• Cookiecutter templates
  • Script template
  • WDL workflow template
  • Python3 Virtual Environment
  • R Markdown documents
  • GitHub README
  • New project

Cookiecutter templates

Cookiecutter is a templating tool; you use it to generate new files based on a template that you or someone else has already defined. For example, let's say you wanted to write a new Python script. Instead of starting from scratch, you define a template with some code snippets you commonly use, like some usage code; this is actually my new_script template. Then you run cookiecutter with the template, answer some questions, and the new file/s will be generated according to what you answered. That's it!

Install cookiecutter using pip.

pip install cookiecutter

Script template

Generate a new Bash, R, Perl, Python, or Ruby template script that accepts positional and optional command line arguments.

cookiecutter new_script

Or run cookiecutter using the template on GitHub by using the --directory option.

cookiecutter https://github.com/davetang/cookiemonster --directory=new_script
# project_name [Parse file]: parse_file
# project_slug [parse_file]:
# project_short_description [A one-sentence description of the project]: Testing
# name [Dave Tang]:
# year [2023]:
# Select language:
# 1 - Bash
# 2 - R
# 3 - Perl
# 4 - Python
# 5 - Ruby
# Choose from 1, 2, 3, 4, 5 [1]:
# script_name [parse.sh]:

The new script (parse.sh by default) will be created with the provided details.

tree --charset ascii parse_file/
# parse_file/
# |-- parse.sh
# `-- README.md
# 
# 0 directories, 2 files

head parse_file/parse.sh
# #!/usr/bin/env bash
# #
# # Written by Dave Tang
# # Year 2023
# #
# set -euo pipefail
# 
# alpha=unset
# beta=unset
# gamma=unset

WDL workflow template

Generate a new WDL workflow.

cookiecutter wdl_workflow

Python3 Virtual Environment

Generate a helper script used for creating a Python3 virtual environment for installing tools, etc.

cookiecutter venv

R Markdown documents

Generate a template R Markdown document that outputs a Markdown document or PowerPoint document. The template also generates a script for rendering the R Markdown document.

cookiecutter rmd_to_pptx
cookiecutter rmd_to_md

GitHub README

To use this template, first make a GitHub repo on github.com. The project slug needs to match the repo name you chose on GitHub. The template will generate a Quarto document that will be rendered automatically into README.md by GitHub Actions when you push to GitHub.

cookiecutter github_readme

New project

As per my blog post.

cookiecutter new_project