snakemake-logger-plugin-rich

Snakemake Logger Plugin: Rich

Note: This plugin is currently in development and may not be fully stable. Use at your own discretion and report any issues to the repository's issue tracker.

Introduction

A logging plugin for Snakemake that utilizes rich for enhanced terminal styling and progress bars.

Usage

• Install via pip:

  pip install snakemake-logger-plugin-rich
  

• Run Snakemake with the --logger rich option:

  snakemake --logger rich
  

Development

This project uses pixi for environment management.

Setting up the development environment

• Fork the repository

• Clone the repository:

  git clone https://github.com/<your-username>/snakemake-logger-plugin-rich.git
  cd snakemake-logger-plugin-rich
  

• Install dependencies using pixi:

  pixi install
  

• Activate the development environment:

  pixi shell -e dev
  

Available development tasks

Run these commands with pixi run:

• Demo: pixi run demo [snakefile] - Runs a complete demo workflow and cleans up afterward. Uses demo/Snakefile by default, or specify a custom Snakefile path
• Run Demo: pixi run run-demo [snakefile] - Runs a demonstration Snakemake workflow using the plugin. Uses demo/Snakefile by default, or specify a custom Snakefile path
• Dry Run: pixi run dryrun [snakefile] - Performs a dry run of the demo workflow. Uses demo/Snakefile by default, or specify a custom Snakefile path
• Clean Demo: pixi run clean-demo - Cleans up demo output files
• Quality Control: pixi run qc - Runs formatting, linting, and type checking
• Format: pixi run format - Format code with ruff
• Lint: pixi run lint - Lint code with ruff
• Lint Fix: pixi run lint-fix - Lint and auto-fix code with ruff
• Type Check: pixi run type-check - Type check with mypy

Testing the plugin

To test the plugin with the demo workflow:

pixi run demo

Or to run just the demo workflow without cleanup:

pixi run run-demo

To test with a custom Snakefile:

pixi run demo path/to/your/Snakefile