Summary and Setup

This session teaches researchers how to convert their software into packages, making it easier for other researchers to use it. In addition, packaged software promotes standardization, reproducibility, and increased research impact through wider adoption due to being more accessible. The episodes in this session cover the full end-to-end process of taking existing code, adding the required metadata, and publishing to central repositories for both R and Python.

Summary

Packaging your software is one of the most important steps in a software project to make it both findable and accessible. This course will provide you with an understanding of why and when packaging is useful, how to structure packages, and take you through each step of the packaging process. Examples will be provided in both Python and R.

Software Setup

Python

Python can be downloaded from the official website, versions 3.11 or newer are recommended. uv will be used to manage dependencies and create the package skeleton as it consolidates a lot of functionality that is distributed amongst multiple first party packages. Installation instructions are available on the website.

R

RStudio can be installed from Posit’s website, which also has links to install R. Some additional tools will be needed for Windows and Mac users to build packages: Windows users will need to install Rtools for Windows users, while Mac users will need to setup Xcode then run installed the Command Line Tools via Preferences->Downloads.

Terminal

A terminal interface will also be required, listed below are the recommended ones for each OS. Although terminal commands aren’t an explicit part of the lesson if you are unfamiliar with them guidance will be available during the session. This carpentries lesson is also a good starting place to learn.

Use Command Prompt or PowerShell.

  • Located in Start Menu, or by typing “cmd” or “powershell” in the search bar.
  • Basic commands: dir (list files), cd (change directory), cls (clear screen).
  • To confirm if Python is available, type python --version in Command Prompt or PowerShell.
  • If Python is correctly installed, you should see the correct version number printed in your terminal.

Use Terminal.app.

  • Located in Applications → Utilities → Terminal, or open using Cmd+Space and type “Terminal”.
  • Basic commands: ls (list files), cd (change directory), clear (clear screen).
  • To confirm if Python is available, type python3 --version in your terminal.
  • On some macOS installations python may refer to Python 2, so you can use python3 to be specific. Commands throughout the course will use python, but please use python3 if you need to. If it’s correctly installed, you should see the correct version number printed in your terminal.

Use Terminal

  • Open with Ctrl+Alt+T or find it in application menu (often called “Terminal”, or GNOME Terminal”).
  • Basic commands: ls (list files), cd (change directory), clear (clear screen).
  • To confirm if Python is available, type python3 --version in your terminal.
  • On some distributions, python may refer to Python 2, so you can use python3 to be specific. Commands throughout the course will use python, but please use python3 if you need to. If it’s correctly installed, you should see the correct version number printed in your terminal.