Summary and Schedule

This is a new lesson built with The Carpentries Workbench.

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

This lesson will teach you how to manage software projects with the popular version control system Git.

The example project will assume a basic understanding of either Python or R, and learners are expected to be comfortable using simple commands in a Bash shell.

The lesson assumes learners are working with a Linux style shell (i.e. zsh on MacOS or GitBash on Windows) inside the VS Code IDE.

It is important that students complete these setup tasks before the workshop.

Environment Management with Conda

Discussion

Details

In this workshop we will use conda to manage Python environments and install packages.

Our preferred flavour of conda is provided by Miniforge3, but you could also use Miniconda.

After installing miniforge you will use conda from within the GitBash shell to manage environments and software instalation. See “Installing Git” below.

  1. Install the latest version of Miniforge3
  2. Open the miniforge prompt app and run the command conda init bash
  1. Install the latest version of Miniforge3

Note: Select the “x86_64” for Intel processors, or “Arm64” for Apple Silicon chips.

Check installation:

  • Open the Terminal app.
  • Check for (base) prefix in your prompt.
  • Run conda --version

Installing Git

Windows users will need to install GitBash which is a linux-like terminal that comes pre-installed with Git.

You will use conda from within the GitBash shell to manage environments and software instalation.

  1. Install GitBash

Windows checks:

  • Open the GitBash terminal app.
  • Check for (base) prefix in your prompt.
  • If (base) is not present, open the “miniforge prompt” app and run conda init bash
  • Open a new GitBash terminal session.
  • Run conda --version
  • Run git --version

Open the Terminal app and run git --version. You may be prompted to install git.

Note: You may be prompted to install Xcode which will take some time.

Configure Git

If you are setting up Git for the first time, you will need to set your user name and email.

IMPORTANT:

  • You must use same email as your github account.
  • You should use an email address that you will always have access to (not a work or university address).

BASH 

git config --global user.name "Alfredo Linguini"
git config --global user.email "a.linguini@gmail.com"

Please use your own name and email address instead of Alfredo’s. And make sure you use the same email associated with your GitHub account.

We will also set the default editor as nano.

BASH 

git config --global core.editor "nano -w"

Setup Github

Create a GitHub account

Create a new account at GitHub.com if you do not have one.

Again, use an email address that you will always have access to (not a work or university address).

Configure SSH access

If you do not have ssh set up for git create a new ssh key and add the key to your github account.

Note: On windows you should do this from the GitBash shell.

To confirm that your key is correctly configured run:

BASH 

ssh -T git@github.com

VS Code setup

VS Code is a popular Interactive Development Environment (IDE) that we will use to edit our project.

Follow the VS Code installation instructions here.

If you are on Windows, also follow the steps below:

  1. Open VS Code and set GitBash as default terminal.
  2. From the View menu select Command Palette --> Terminal: Select Default Profile.
  3. Then select GitBash as the default profile.