Tutorial

This tutorial shows you how to build a python package with the minimum components for a clean and well engineered package. In this tutorial, you will learn how to setup a project, how to build and implement unit tests, how to create documentation, and how to publish your tool to bioconda and PyPI.

In this tutorial, we will build a simple project that plots mapping quality distribution from an input bam file. Below is a sample plot that our tool produces:

Tutorial Outline

• Prerequisites
  • Requirements
  • Creating a conda environment
  • Getting the code
• Project Setup
  • Basic Directory Structure
  • Setup.py
  • Scripts
  • Unit tests
  • Documentation
  • Other Important Files
  • Next Steps
• Command Line Scripts
• Unit tests and Continuous Integration
  • Continuous Integration with Travis
• Uploading your package to PyPI
  • Building your package
  • Uploading to PyPI
  • Tagging a release on GitHub
• Adding your Package to Bioconda
• Project Documentation
  • Building documentation locally
  • Autogenerating API Documentation
  • Adding documentation to readthedocs
• Summary
  • Resources

Let’s get started!