Summary and Setup

This is a new lesson built with The Carpentries Workbench.

Please follow the steps below and install the required software before the scheduled workshop.

Software Setup

We use VS Code for general coding. Make sure to install VS Code for your operating system following the instructions below:

Discussion

Windows users

If you are a Windows user, you may also need WSL, the Windows Subsystem for Linux. WSL will allow you to use the Terminal from within VS Code and to execute UNIX style commands.

Follow the official instructions here.

After installing WSL, you will also need to install GitBash.

After installing GitBash, change the default Terminal executable on VS Code:

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

✅ You’re all set to use VS Code with GitBash on Windows.

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.

Your Linux distribution likely comes with Git. If not, click here and follow the instructions.

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

Environment management with conda

For certain workshops, you may need to install conda, an open-source software and package management system. This is usually necessary when working with Python code.

Our preferred flavour of conda is miniforge, but you could also use miniconda.

Click here and follow the miniforge installation instructions for your OS.