Reproducible research software development using Python (ML example)

Software environment

  • Software install instructions

Episodes

  • Example project: 2D classification task using a nearest-neighbor predictor
  • Introduction to version control with Git and GitHub
    • Motivation
    • Forking, cloning, and browsing
    • Creating branches and commits
    • Merging changes and contributing to the project
    • Conflict resolution
    • Practical advice: How much Git is necessary?
    • Optional: How to turn your project to a Git repo and share it
  • Where to start with documentation
  • Collaborative version control and code review
  • Reproducible environments and dependencies
  • Notebooks and version control
  • Other useful tooling for notebooks
  • Sharing notebooks
  • Tools and useful practices
  • Profiling
  • Automated testing
  • Concepts in refactoring and modular code design
  • How to parallelize independent tasks using workflows (example: Snakemake)
  • Choosing a software license
  • How to publish your code
  • Creating a Python package and deploying it to PyPI

Reference

  • PDF version
  • Credit
  • All lessons
  • CodeRefinery
  • Reusing
Reproducible research software development using Python (ML example)
  • Introduction to version control with Git and GitHub
  • Edit on GitHub

Introduction to version control with Git and GitHub

  • Motivation
  • Forking, cloning, and browsing
  • Creating branches and commits
  • Merging changes and contributing to the project
  • Conflict resolution
  • Practical advice: How much Git is necessary?
  • Optional: How to turn your project to a Git repo and share it
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