Reproducibility Checklist: Software

[aidan-axiom]

Extra resources:

• OHW23 Joseph Gum's presentation
• Software Best Practices, Valentina Staneva's presentation

• Is your software publicly available?

  
  - Make sure all code stored locally is pushed to GitHub. You can use git diff to compare the differences.
  
• Is your software under version control?

  
  - You can use git tags and GitHub releases to mark important versions.
  
• Can your software run on different operating systems?

  
  - Test among the team members with different OS.
  - Use Github Actions to test on different OS.
  
• Is it easy to install all the dependencies for your software?

  
  - Is the one file that can encompass all dependencies (requirements.txt, conda env, or mamba env`)?
  - If not, can you provide the users with a pre-built environment (Docker)?
  
• Does your software have a license?

  
  - Choose Your License
  
• Does your software use other software: are their licenses compatible with yours?

  
  - Read about copy-left licenses, such as GPL.
  
• Do you have a way to test whether adding new code features or library updates preserves the software’s functionality?

  
  - As you are testing whether the code works, store those tests and integrate the with continuous integration framework (like GitHub Actions) so they are run automatically.
  
• Is it obvious from the folder structure where the code is and what it is doing?

  
  - Reorganize your folders/files so that new users can find content quickly (get inspired from the Cookiecutter Folder Structure)
  - add .gitignore file so you do not add unnecessary files from the repo
  - use git rm to remove files which you have already added. Never use git add . to avoid this
  
• Does your code follow good style practices and conventions?

  
  Follow general guidance for good code style.
  - Check and select the style conventions for your language.
  - Install an automatic style checker for your editor.
• Do you have a lot of repetitive code?

  
  - Move repetitive code into functions.
  - Move repetitive functions out of notebooks and put them into a module.
  - Organize modules into a package, so it is installable.
• Do you guide how new users can contribute to your repo?

  
  - Make a contributer's guide