Ctrl+K

Setup

Setup#

Installing Git#

Please follow the instructions bellow to install and setting up Git.

Linux#

Check if git is available on your machine by running

git --version

The above command returns the git version (if available).

If git is not already available on your machine you can try to install it via your distribution package manager (e.g. apt-get or yum), for example:

sudo apt-get install git

or

sudo yum install git

MacOS#

The XCode command line tools come with Git so no need to do anything more, as long as you can run the following in your terminal:

git --version

Windows#

Install the GitHub Desktop Client. This comes with both a GUI client as well as the Git Bash terminal client which we will use during the course. In some instances Git Bash may need to be installed separately. In order to use conda with Git Bash follow the instructions here

You’ll know it has worked when you can open a Git Bash terminal (the window should have a title that starts with MINGW32) and get the Git version by running

git --version

Setting up Git#

Is Git available?#

Check if git is available on your machine by running

git --version

If git is not available you can follow instructions here to install git in your machine.

Basic configurations#

When we use Git on a new computer for the first time, we need to configure a few things. Below are a few examples of configurations we will set as we get started with Git:

  • our name and email address,

  • to colorize our output,

  • what our preferred text editor is,

  • and that we want to use these settings globally (i.e. for every project)

User info#

On a command line, Git commands are written as git verb, where verb is what we actually want to do. So here is how Jane sets up her new laptop:

git config --global user.name "Jane Smith"

git config --global user.email "jane.smith@university.ac.uk"

Note

You need to do this only once if you pass the --global option. If you want to override this with a different name or email address for specific projects, you can run the command without the --global option when you’re in that project.

Please use your own name and email address instead of Jane’s. Later on in this workshop, we’ll be setting up an account on Github so make sure you use the same email address. We recommend that you use your institutional email address.

You can check that they have been set correctly by running

git config user.name

git config user.email

Colours#

git config --global color.ui "auto"

Text editor#

Jane also has to set her favourite text editor, following this table:

Editor

Configuration command

Atom

$ git config --global core.editor "atom --wait"

nano

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

BBEdit (Mac, with command line tools)

$ git config --global core.editor "edit -w"

Sublime Text (Mac)

$ git config --global core.editor "subl -n -w"

Sublime Text (Win, 32-bit install)

$ git config --global core.editor "'c:/program files (x86)/sublime text 3/sublime_text.exe' -w"

Sublime Text (Win, 64-bit install)

$ git config --global core.editor "'c:/program files/sublime text 3/sublime_text.exe' -w"

Notepad++ (Win, 32-bit install)

$ git config --global core.editor "'c:/program files (x86)/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"

Notepad++ (Win, 64-bit install)

$ git config --global core.editor "'c:/program files/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"

Kate (Linux)

$ git config --global core.editor "kate"

Gedit (Linux)

$ git config --global core.editor "gedit --wait --new-window"

Scratch (Linux)

$ git config --global core.editor "scratch-text-editor"

emacs

$ git config --global core.editor "emacs"

vim

$ git config --global core.editor "vim"

VS Code

$ git config --global core.editor "code --wait"

It is possible to reconfigure the text editor for Git whenever you want to change it.

Default Git branch naming#

Source file changes are associated with a branch. For new learners in this lesson, it’s enough to know that branches exist, and this lesson uses one branch.

By default, Git will create a branch called master when you create a new repository with git init (as explained in the next Episode). This term evokes the racist practice of human slavery and the software development community has moved to adopt more inclusive language.

In 2020, most Git code hosting services transitioned to using main as the default branch. As an example, any new repository that is opened in GitHub and GitLab default to main. However, Git has not yet made the same change. As a result, local repositories must be manually configured have the same main branch name as most cloud services.

To set main as your local default branch:

git config --global init.defaultBranch main

Note that if this value is unset in your local Git configuration, the init.defaultBranch value defaults to master.

Check your configurations#

git config --list

Need help?#

Always remember that if you forget the subcommands or options of a git command, you can access the relevant list of options typing git <command> -h, e.g.:

git config -h

or access the corresponding Git manual by typing git <command> --help, e.g.:

git config --help

More generally, you can get the list of available git commands and further resources of the Git manual typing:

git help

Additional references#

Installing Anaconda#

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of the scientific packages we use in the lesson individually can be a bit cumbersome, and therefore recommend the all-in-one installer Anaconda.

Windows#

  1. Open https://www.anaconda.com/products/individual in your web browser.

  2. Download the Anaconda Python 3 installer for Windows.

  3. Double-click the executable and install Python 3 using the recommended settings. Make sure that Register Anaconda as my default Python 3.x option is checked – it should be in the latest version of Anaconda.

  4. Verify the installation: click Start, search and select Anaconda Prompt from the menu. A window should pop up where you can now type commands such as checking your Conda installation with:

conda --help

MacOS#

  1. Visit https://www.anaconda.com/products/individual in your web browser.

  2. Download the Anaconda Python 3 installer for macOS. These instructions assume that you use the graphical installer .pkg file.

  3. Follow the Anaconda Python 3 installation instructions. Make sure that the install location is set to “Install only for me” so Anaconda will install its files locally, relative to your home directory. Installing the software for all users tends to create problems in the long run and should be avoided.

  4. Verify the installation: click the Launchpad icon in the Dock, type Terminal in the search field, then click Terminal. A window should pop up where you can now type commands such as checking your conda installation with:

conda --help

Linux#

  1. Open https://www.anaconda.com/products/individual in your web browser.

  2. Download the Anaconda Python 3 installer for Linux.

  3. Install Anaconda using all of the defaults for installation.

    • Open a terminal window.

    • Navigate to the folder where you downloaded the installer.

    • Type bash Anaconda3- and press Tab. The name of the file you just downloaded should appear.

    • Press Return

    • Follow the text-only prompts. When the license agreement appears (a colon will be present at the bottom of the screen) press Spacebar until you see the bottom of the text. Type yes and press Return to approve the license. Press Return again to approve the default location for the files. Type yes and press Return to prepend Anaconda to your PATH (this makes the Anaconda distribution your user’s default Python).

  4. Verify the installation: this depends a bit on your Linux distribution, but often you will have an Applications listing in which you can select a Terminal icon you can click. A window should pop up where you can now type commands such as checking your conda installation with

conda --help
Contents