2  Command Line

beginner
basics
command line
Summary

In this session, we will explore the concept of the command line and discover some commands that work well alongside Git.

Learning Objectives

💡 You can navigate directories using the command line
💡 You can use shortcuts like the tilde or dots to navigate your file system
💡 You can explain the difference between absolute and relative paths
💡 You can use arguments and flags to modify command-line commands
💡 You understand the concept of wild cards (*) and can use it for system navigation

Take the quiz!

2.1 Why using Git from the command line?

You are most likely used to interacting with programs on your computer through graphical user interfaces (GUIs) where you can select options through graphical icons and visual indicators using the computer mouse. However, computers have historically been controlled through text-based commands typed into command-line interfaces (CLIs) using the computer keyboard. To this day, the command line has persisted as a reliable (and sometimes the only) way to interact effectively with computer programs. Similarly, even though many GUIs for Git exist (for an overview, see the chapter on Graphical User Interfaces), Git is fundamentally a command-line tool. This is why comfort with the command line is a good basis for learning Git.

General advantages of the command line include:

  1. Longevity: The command line has stood the test of time, remaining relevant and widely used even as new technologies emerge.
  2. Power: The command line is a robust and powerful tool, enabling users to accomplish intricate tasks efficiently.
  3. Simplicity: With just a few keystrokes or lines of code, the command line empowers users to execute complex tasks effortlessly.
  4. Task Automation: The command line allows users to automate repetitive tasks, saving time and effort in performing them manually.
  5. Flexibility: Knowing how to use Git from the command line, allows you to use Git on every device.
  6. Workflow Integration: Users can seamlessly combine smaller tasks into larger, more potent workflows, enhancing productivity and efficiency.
  7. Comprehensive Feature Set: The command line interface provides access to the complete range of Git features, offering more extensive functionality compared to graphical user interfaces (GUIs).
  8. Extensive Online Support: When looking for help or troubleshooting Git-related issues online, you will often find valuable assistance in the form of command line instructions. Platforms like Stack Overflow frequently provide guidance and solutions based on command line usage.

2.2 Terminology

Before we begin with the basics of the command line, let’s start by defining some key terms that you will frequently encounter throughout this book:

A file is an unit of digital data storage that can contain a variety of information, such as text, images or even programs. It is identified by a unique name and a file extension, which indicates the file’s format or type (for example, file.txt). Files are organized within a file system, allowing users to create, access, modify, and delete them.

A folder is a container used in file systems to store and organize files and other folders. Folders provide a hierarchical structure that allows users to group and manage files, making it easier to locate and navigate through data.

A directory is a more technical term, while folder is a user-friendly term for the same concept. In practice, the two terms are often used interchangeably and many operating systems have adopted the term “folder”.

The command-line interface (CLI) is a text-based way to interact with computer programs. Specifically, the term “command line” refers to the interface where users input text commands to communicate with the computer. Most people primarily use a Graphical User Interface (GUI) to work with programs on their computer, but historically, text-based interfaces were more common. Often, the GUI can only access a limited set of features available through the CLI and some programs don’t even have a GUI and can only be used through the command line. For many years, the command line was the primary way to interact with computers. This text-based interaction allows to perform various tasks, from running programs to managing files and directories.

The terminal, short for “terminal emulator”, is the application or program that you open on your computer to access the command-line interface. Terminals were used to connect to mainframe computers in the early days of computing. The terminal program creates a window in which you can type commands and see the output from these commands.

The shell is a software that interprets the commands you type into the terminal. It acts as a layer between you and the operating system. The shell processes the commands and communicates with the computer’s operating system to execute them. It allows you to perform various tasks that your operating system offers, such as managing files, running and stopping programs, and changing system settings, all through text commands. Examples of popular shells include Bash on Linux and macOS, and PowerShell on Windows.

In combination, in a typical scenario, you would open a terminal (the window), use the shell within that terminal to understand and process your commands, and interact with your computer through the command line interface provided by the terminal. That being said, the terms “shell”, “command line”, “command-line interface (CLI)”, and “terminal” are often used interchangeably and roughly refer to the same thing: a simple window showing a prompt and a blinking cursor (see Figure 2.1). In movies, when people hack into computers, they often type rapidly in this window.

Figure 2.1: The command line (Bourne shell interaction in Version 7 Unix). License: CC0, Source: Wikimedia Commons

As briefly described in the section on terminology, the default “programming language” of the command line is a version of the Shell. Examples of popular shells include Bash on Linux and macOS, and PowerShell on Windows. The program Git for Windows provides a Bash emulation that is used to run Git from the command line which generally behaves like Bash in Linux and macOS environments.

2.3 Finding the command line

This section helps you finding the command line on your operating system. Click on the tab for your operating system or computer environment for detailed information.

Figure 2.2: Logo of the Git Bash program on Windows (Source: Git for Windows on GitHub)

By default, Windows operating systems do not come with a pre-installed Unix Shell program. In this guide, we recommend using an emulator provided by Git for Windows, which grants you access to both the Bash shell and Git commands.

For an installation guide, you can check out the chapters on Installation and Setup. Once you have installed Git for Windows, you can open a terminal by launching the program called “Git Bash” from the Windows start menu.

Figure 2.3: Icon of the Terminal program on macOS (Source: Wikimedia Commons, License: Public Domain)

You can access your default shell through the Terminal program (see the icon in Figure 2.3) that can be found within the Utilities folder: There are (at least) three different ways to get there:

  1. In the Finder, go to Applications > Utilities > Terminal.app
  2. In the Finder, select the Go menu > Utilities > Terminal.app
  3. Activate the Mac Spotlight search function, type Terminal in the search bar, and press the Enter key.

You may want to keep the Terminal in your Dock to find it more easily.

On new Apple computers, especially those running recent versions of macOS, you might have to allow the Terminal access to certain files and folders after your initial commands. If a prompt appears asking for permission, you will need to confirm it to continue using Terminal with access to these files.

On an Apple computer running macOS Mojave or earlier versions, the default Unix Shell is Bash. Unix is a family of operating systems serving as the basis for Linux and macOS with the inclusion of a command line interface (or Unix Shell) as a key feature. For a Mac computer operating on macOS Catalina or later releases, the default Unix Shell is Zsh. Bash and Zsh are both programs, which are command-line interfaces for interacting with an operating system. Zsh is often considered better than Bash for its more advanced features and improved scripting capabilities. It also has extensive community-contributed plugins and themes. However, the change to Zsh was not a drastic shift for most users, since there a few practical differences.

To verify if your machine is configured to use a shell other than Bash, you can type the following command in your Terminal window (you will learn about the command that is used here, echo, in this chapter):

Code
echo $SHELL

If the output is /bin/bash or a similar path, it means your default shell is set to Bash. This is the most common shell on Unix-based systems, including macOS.

If the output is /bin/zsh or a similar path, it means your default shell is set to Zsh.

If the output is a different path, it indicates that your shell is configured to use a different shell program. If your machine is configured to use a shell other than Bash, you can switch to Bash by opening a terminal and typing bash.

  1. In the upper-left corner of your screen, click on the logo.
  2. Select “About This Mac”: A dropdown menu will appear. Choose “About This Mac”.
  3. View the macOS Version: In the “About This Mac” window, you will see information about your Mac, including the macOS version. The version number will be listed under the “Overview” tab. For example, it might say “macOS Big Sur” or “macOS Monterey”, along with the version number (for example, “Version 11.4”).

For example, you can check out Oh My Zsh.

Oh My Zsh is a delightful, open source, community-driven framework for managing your Zsh configuration. It comes bundled with thousands of helpful functions, helpers, plugins, themes,

In addition, if you want to add syntax highlighting (similar to the code chunks in this book), check out zsh-syntax-highlighting.

To open a fresh terminal window on Linux, you can usually use a keyboard shortcut, which often involves pressing Ctrl + Alt + T simultaneously. If this shortcut does not work, you can find the terminal application in your system’s applications menu and click on it to open a new window. Additionally, if you are already in a graphical environment, right-clicking on the desktop or within a file manager may offer an option to open a terminal in the current location.

If it is not possible for you to access a command line interface using your personal computer, you can use a remote solution with JupyterHub. JupyterHub is a web-based platform that allows multiple users to access an interactive computing environment on a shared server.

If you are a student at University of Hamburg, you can access a remote environment, using your university login credentials here:

https://code.min.uni-hamburg.de

Simply click on the link and log in.

Once you are logged in, you should be able to view the remote environment and create files using different programs like , Python or Java .

Figure 2.4: Screenshot of JupyterHub, showing the start screen.

If you scroll down in the “launcher” window, there should be the option to open a terminal window. Your remote environment will be mostly empty, but you can move around and manage files just like you could on your own computer.

Figure 2.5: Screenshot of JupyterHub, showing the terminal.

2.4 Opening the command line

When you open the shell, you’ll see a prompt that tells you that the shell is ready for input. Your terminal interface will usually show a message similar to the following prompt:

Output
$

In the shell, the prompt is usually represented by the symbol $ but it can look a bit different sometimes. In our examples, we will use $ as the prompt. The important thing to remember is to not type the prompt, $, itself when entering commands. Only type the command that comes after the $ prompt. For this reason, we remove the $ prompt from all code examples in this guide. Also, remember to press the Enter key after typing a command to execute it.

After the prompt, you’ll see a text cursor that shows where you can type. The cursor can be a flashing or solid block, or it can be an underscore or a pipe symbol. You may have seen a similar cursor in a text editing program.

Keep in mind that your prompt may look slightly different. Usually, in popular shell environments, your username and the host name appear before the $ symbol. For example, your prompt might look like this:

Output
wittkuhn@lip-osx-005509:~$

2.6 Clean and efficient command line

In this section, we provide some tips and tricks to help you become more efficient when using the command line and execute commands cleanly.

2.6.1 Autocompletion

While using the command line, instead of typing out the full command or path, you can press the key to automatically complete the rest of the command. Begin typing a command or the initial letters of a file or directory, for example:

Code
cd ~/Doc

Once you’ve typed a portion of the command or path, press the key. The command-line interface will attempt to auto-complete the command or path based on what matches your input. In this case for example:

Code
cd ~/Documents/

If there are multiple possibilities, pressing again will cycle through the available options. Auto-completion also works for system commands. For example, typing ls (you will find out more about this command below) and pressing might complete it to ls -l or ls -a. Auto-completion also works for the Git commands that will be introduced in the following chapters of this book.

2.6.2 Command history

Using the Up and Down arrow keys on your keyboard allows you to quickly access and reuse commands without retyping them.

After executing one or multiple commands, pressing the Up arrow key retrieves the most recent command. If you’ve navigated back using the Up arrow, pressing the Down arrow key moves you forward through the command history. You can continue to press Up and Down to cycle through the executed commands. To execute a command, hit Enter, or you can edit it as needed before execution.

The main benefit of this is time efficiency. Instead of typing out the entire command, especially for lengthy or complex commands, you can retrieve and modify previous commands quickly. It also minimizes the chances of introducing typos or syntax errors when reusing commands. And it’s also the reason why the up arrow key is among the earliest that needs replacement on software developers’ keyboards.

2.6.3 Clearing the command line

The clear command is used to clear the content of your terminal, providing a clean and empty slate. It helps improve visibility by removing previous commands, outputs, and clutter from your terminal window.

To clear the content of the terminal screen, type and execute the clear command:

Code
clear

Press Enter and the terminal screen will be cleared, leaving only a new prompt at the top of the window. After using clear, you can continue working in a fresh and uncluttered terminal window.

2.6.4 Saving command line history

When you exit the command line, your command history is not automatically saved by default. To review the commands you’ve used, you can use the history command, which works on both macOS and Windows (when using Git Bash).

If you’re interested in keeping your command history for documentation or learning purposes, you can easily save either your current session’s history or the entire history stored by your terminal to a text file using the following command:

Code
history > history.txt

This command will capture your entire command history and save it to a file named history.txt in your current directory. You can then view this file directly from the command line or through your usual file viewer.

2.7 List files and folders

The ls command is used to list the files and folders in a specified directory or the current working directory. If you run this command, you will see the contents of your current working directory.

Code
ls
Click here to see the output of the ls executed in the project directory of this guide.
CITATION.cff
LICENSE
Makefile
README.md
_affiliations.yml
_authors.yml
_book
_courses.yml
_extensions
_metadata.yml
_quarto.yml
_variables.yml
chapters
cheatsheet.json
chicago-author-date-note.csl
contents-listing.json
contents.html
contents.qmd
custom.scss
exercises
functions.R
github-buttons.html
index.html
index.qmd
misc
objectives
plausible.html
references.bib
renv
renv.lock
site_libs
static
version-control-book.Rproj

However, the ls command provides various options, such as flags and arguments, to enhance its functionality beyond simple file listing. To provide additional instructions to a command, we can pass flags and arguments by typing them after the command name.

2.7.1 List files in a specific directory

To list files in a specific folder (relative to the current working directory), we use the ls command followed by the name of the folder. For example, we can list the contents of the chapters folder in the project directory of this guide. In this case, chapters is a so-called “argument” to the ls command.

Code
ls chapters
Click here to see the output of this command executed in the project directory of this guide.
branches.qmd
command-line.qmd
command-line.rmarkdown
first-steps-git.qmd
github-advanced.qmd
gui.qmd
installation.qmd
intro-version-control.html
intro-version-control.qmd
issues.qmd
project-management.qmd
remotes-intro.qmd
rewriting-history.qmd
setup.qmd
tags-and-releases.qmd

2.7.2 Listing hidden files

Hidden files, often starting with a dot (.) in their names, are files that remain mostly hidden from the regular view in GUIs. They can serve different purposes, such as storing configuration settings, sensitive data, or temporary files. Hidden files can be accessed through the command line or by changing settings in the file manager to make them visible.

Be cautios when modifying hidden files!

It’s important to be cautious when modifying or deleting hidden files, as they can impact the proper functioning of the operating system and applications. This is also typically the reason why these files are hidden. Only listing hidden files (as explained in this section) does not modify them, so it’s generally safe to execute the ls -a command to view hidden files.

To view hidden files, we can use the -a (for “all”) flag in the ls command:

Code
ls -a
Click here to see the output of ls -a executed in the project directory of this guide.
.
..
.Renviron
.Rprofile
.all-contributorsrc
.codespellrc
.git
.github
.gitignore
.quarto
.zenodo.json
CITATION.cff
LICENSE
Makefile
README.md
_affiliations.yml
_authors.yml
_book
_courses.yml
_extensions
_metadata.yml
_quarto.yml
_variables.yml
chapters
cheatsheet.json
chicago-author-date-note.csl
contents-listing.json
contents.html
contents.qmd
custom.scss
exercises
functions.R
github-buttons.html
index.html
index.qmd
misc
objectives
plausible.html
references.bib
renv
renv.lock
site_libs
static
version-control-book.Rproj

To list only hidden files, see the command in Tip 2.2.

To list only hidden files, you can run the following command:

Code
ls -d .?*

The -d (or --directory) flag lists directory entries instead of contents and does not dereference symbolic links. The .?* argument will only state hidden files.

Click here to see the output of ls -d .?* executed in the project directory of this guide.
..
.Renviron
.Rprofile
.all-contributorsrc
.codespellrc
.git
.github
.gitignore
.quarto
.zenodo.json

2.7.3 What is the difference between a flag and an argument?

The difference between a flag and an argument is that a flag is used to modify the behavior of a command, while an argument provides additional input or information to the command.

2.7.3.1 What is a flag?

A flag is typically a single character or a combination of characters preceded by a hyphen (-) or double hyphen (--). It is used to enable or disable specific options or features of a command. Flags are optional and are used to customize the behavior of the command.

2.7.3.2 What is an argument?

An argument is the actual input or information that is passed to a command to perform a specific action. It can be a value, a file name, a directory path, or any other data required by the command to complete its task. Arguments are often positioned after the command and any flags, and they can be mandatory or optional depending on the command’s requirements.

2.7.3.3 Multiple single-letter flags

You can combine multiple single-letter flags by using a single dash. For example, to instruct the ls command to list all files (including hidden files) in a long format that is easy to read for humans, you can use the following combination of flags:

Code
ls -alh
Click here to see the output of ls -alh executed in the project directory of this guide.
total 336K
drwxr-xr-x 14 runner docker 4.0K Jul 15 17:45 .
drwxr-xr-x  3 runner docker 4.0K Jul 15 17:36 ..
-rw-r--r--  1 runner docker   36 Jul 15 17:36 .Renviron
-rw-r--r--  1 runner docker   48 Jul 15 17:36 .Rprofile
-rw-r--r--  1 runner docker 2.1K Jul 15 17:36 .all-contributorsrc
-rw-r--r--  1 runner docker   76 Jul 15 17:36 .codespellrc
drwxr-xr-x  8 runner docker 4.0K Jul 15 17:44 .git
drwxr-xr-x  3 runner docker 4.0K Jul 15 17:36 .github
-rw-r--r--  1 runner docker   90 Jul 15 17:36 .gitignore
drwxr-xr-x  7 runner docker 4.0K Jul 15 17:45 .quarto
-rw-r--r--  1 runner docker  925 Jul 15 17:36 .zenodo.json
-rw-r--r--  1 runner docker  992 Jul 15 17:36 CITATION.cff
-rw-r--r--  1 runner docker  20K Jul 15 17:36 LICENSE
-rw-r--r--  1 runner docker  517 Jul 15 17:36 Makefile
-rw-r--r--  1 runner docker 7.5K Jul 15 17:36 README.md
-rw-r--r--  1 runner docker  935 Jul 15 17:36 _affiliations.yml
-rw-r--r--  1 runner docker  641 Jul 15 17:36 _authors.yml
drwxr-xr-x  2 runner docker 4.0K Jul 15 17:44 _book
-rw-r--r--  1 runner docker  939 Jul 15 17:36 _courses.yml
drwxr-xr-x  3 runner docker 4.0K Jul 15 17:36 _extensions
-rw-r--r--  1 runner docker   86 Jul 15 17:36 _metadata.yml
-rw-r--r--  1 runner docker 3.4K Jul 15 17:36 _quarto.yml
-rw-r--r--  1 runner docker 2.6K Jul 15 17:36 _variables.yml
drwxr-xr-x  2 runner docker 4.0K Jul 15 17:45 chapters
-rw-r--r--  1 runner docker 6.1K Jul 15 17:36 cheatsheet.json
-rw-r--r--  1 runner docker  23K Jul 15 17:36 chicago-author-date-note.csl
-rw-r--r--  1 runner docker  470 Jul 15 17:45 contents-listing.json
-rw-r--r--  1 runner docker  53K Jul 15 17:45 contents.html
-rw-r--r--  1 runner docker  636 Jul 15 17:36 contents.qmd
-rw-r--r--  1 runner docker  265 Jul 15 17:36 custom.scss
drwxr-xr-x  2 runner docker 4.0K Jul 15 17:36 exercises
-rw-r--r--  1 runner docker 2.4K Jul 15 17:36 functions.R
-rw-r--r--  1 runner docker  145 Jul 15 17:36 github-buttons.html
-rw-r--r--  1 runner docker  44K Jul 15 17:44 index.html
-rw-r--r--  1 runner docker 6.6K Jul 15 17:36 index.qmd
drwxr-xr-x  2 runner docker 4.0K Jul 15 17:45 misc
drwxr-xr-x  2 runner docker 4.0K Jul 15 17:36 objectives
-rw-r--r--  1 runner docker  118 Jul 15 17:36 plausible.html
-rw-r--r--  1 runner docker  12K Jul 15 17:36 references.bib
drwxr-xr-x  4 runner docker 4.0K Jul 15 17:38 renv
-rw-r--r--  1 runner docker  16K Jul 15 17:36 renv.lock
drwxr-xr-x  9 runner docker 4.0K Jul 15 17:45 site_libs
drwxr-xr-x  2 runner docker 4.0K Jul 15 17:44 static
-rw-r--r--  1 runner docker  211 Jul 15 17:36 version-control-book.Rproj

2.7.3.4 Getting help

Getting help with commands can differ between operating systems. See the instructions for Windows and macOS below.

If you want to know what flags and arguments a command supports, most commands provide usage information when you use the flag --help. For example, you can use the ls command together with the --help flag:

Code
ls --help

This will list all possible flags you can use together with the ls command.

On macOS you can not use the --help flag. Instead you can use the man command, in combination with your desired command. This will display the manual page for a specified command. You can navigate through the manual pages using the arrow keys, and you can exit by pressing q. For example:

Code
man ls

2.8 Manipulating the file system

The command line offers commands for creating, moving, and deleting folders and files.

2.8.1 Creating a folder

Let’s use the command line to create a new project folder as an example: To make a directory, we’ll use the mkdir command.

Be aware where you are creating new directories!

When creating new directories, consider their location carefully. If you are experimenting, consider deleting the newly created directories afterwards to avoid clutter.

The path of the directory we want to create is given as an argument to the command. If we want to create a directory in the current folder, we just need to use its name, as the path is assumed to be relative. For example, to create a new folder for your favorite recipes, we can use the following command:

Code
mkdir recipes

Make sure that the project folder is present by using the ls command, and then move into it by using the cd command.

Code
cd recipes

2.8.2 Creating multiple folders

Next, we will proceed to create multiple additional folders within the recipes project folder. The mkdir command allows us to create multiple directories simultaneously by providing multiple arguments, each representing a separate folder. For example, we might create the following three folders:

Code
mkdir vegetarian vegan glutenfree

2.8.3 Creating files

Let’s create some files in the recipes project folder. To do this, you can use your favorite text editor or the command line. In the command line, you can use the touch command to create a new empty file. The file doesn’t need to contain anything. For example, to create an empty file called recipes.txt, we can use the following command:

Code
touch recipes.txt

2.8.4 Opening files

To open files, you can use your preferred text editor but also the command line. On the command line, you can use the start command on Windows (using Git Bash) or the open command on macOS. These commands will open the specified file in the default application associated with the file type.

Code
start recipes.txt
Code
open recipes.txt

2.8.5 Writing short text into files

The echo command can be used to write text to a file, directly from the command line. Using echo in combination with >> adds content to an existing file. For example, to add text to the recipes.txt file using the command line:

Code
echo "This is a list of all my favorite recipes." >> recipes.txt 

This adds the provided text to the existing content of recipes.txt.

Difference between using >> or > with echo when writing short text into files

When you use the command echo "Git is cool" >> file.txt, it will append the text “Git is cool” to the end of the file file.txt. If the file does not exist, it will be created and the text “Git is cool” will be added. If the file already contains other text, the “Git is cool” text will be added after the existing text at the end of the file.

On the other hand, when you use the command echo "Git is cool" > file.txt, it will write the text “Git is cool” to a file named file.txt. If the file already exists, it will overwrite its contents with the new text “Git is cool”.

2.8.6 Viewing file content

If you want to quickly view the content of a file without opening it, you can do so in the command line using the cat command. To display the content of a file, simply use cat followed by the file name. For example:

Code
cat recipes.txt 

This command will output the entire content of the recipes.txt file to the terminal.

Click here to see the output of the cat command applied to the .gitignore file in the project directory of this guide.
/.quarto/
/_book/
.Rproj.user
/env/
.Rhistory
static
/.luarc.json
.DS_Store
*.html
*.ipynb

2.8.7 Moving folders and files

Let’s say we want to move the recipes.txt file to the /vegan subfolder. We can use the mv command to move files and folders. The mv command requires two arguments: the first is the files or folders to be moved, and the second is the path where they should be moved. To move the recipes.txt file to the /vegan subfolder, the command would look like this:

Code
mv recipes.txt vegan

2.8.7.1 Moving files to the parent directory

Let’s assume that you moved the recipes.txt file to the /vegan subfolder, as shown above. Now let’s move the recipes.txt file back to the parent recipes folder. To do this, you can first cd into the /vegan subfolder and then use the .. shortcut (for details on .., see the section above) in combination with the mv command:

Code
mv recipes.txt ..

2.8.8 Renaming files and folders

Suppose we don’t like the folder name vegan because recipes.txt actually contains recipes with meat. We can use the mv command to rename files and folders by moving them to a different location in the file system, for example meat, like this:

Code
mv vegan meat

2.8.9 Wildcards

Now let’s learn how to use so-called wildcards to perform actions on multiple files or folders at the same time. A wildcard is denoted by the symbol *, and it helps us select file system arguments that match certain patterns. For example, suppose we wish to display a list of all files of a certain file type (here, all files with the .yml file extension) in the current directory:

Code
ls -alh *.yml
Click here to see the output of the ls -alh *.yml command executed in the project directory of this guide.
-rw-r--r-- 1 runner docker  935 Jul 15 17:36 _affiliations.yml
-rw-r--r-- 1 runner docker  641 Jul 15 17:36 _authors.yml
-rw-r--r-- 1 runner docker  939 Jul 15 17:36 _courses.yml
-rw-r--r-- 1 runner docker   86 Jul 15 17:36 _metadata.yml
-rw-r--r-- 1 runner docker 3.4K Jul 15 17:36 _quarto.yml
-rw-r--r-- 1 runner docker 2.6K Jul 15 17:36 _variables.yml

The first column (-rw-r--r--) represents the file permissions. In Unix-like systems, it shows who can read, write, or execute the file. In this case, the files are readable and writable by the owner (rw-), readable by the group (r--), and readable by others (r--).

The second column (1) indicates the number of hard links to the file.

The third column (runner) is the username of the file’s owner. Here, the username is runner because the this online guide is build automatically on GitHub using GitHub Actions and runner refers to the computing environment where the build process is executed. If you would build the book on your computer, it would show your username.

The fourth column (docker) is the group associated with the file. Here, the group name is docker which again refers to the computing environment where this online guide is built.

The fifth column shows the size of the file. In this case there are just small textfiles included with the sizes ranging from 97B to 3.0K.

The next column (for example, Jan 18 20:39) display the date and time when the file was last modified.

The last column (for example, _affiliations.yml etc.) shows the name of each file.

By using the wildcard *, we can generate a list of all files ending with .yml. Similarly, we can apply the wildcard at the end of a path to match items starting with a specific letter, such as folders beginning with i:

Code
ls -alh i*
Click here to see the output of the command ls -alh i* executed in the project directory of this guide.
-rw-r--r-- 1 runner docker  44K Jul 15 17:44 index.html
-rw-r--r-- 1 runner docker 6.6K Jul 15 17:36 index.qmd

2.8.10 Removing files and folders

To delete files and folders, you can use the rm command. Provide the path of the files or folders that you want to delete as the argument. However, if you want to remove a folder, you need to include the -r (or --recursive) flag.

Warning: Be careful when using the rm command!

When you use the rm command to delete files, they are removed entirely (!!!) from your system and cannot be retrieved from a “Recycle Bin” or “Trash” as when you delete files using the file browser!

For example, to remove the glutenfree folder, you would use the following command:

Code
rm -r glutenfree

2.8.11 Combining commands

Combining commands in the command-line using semicolons ; is a way to execute multiple commands sequentially on a single line. Each command is separated by a semicolon, and they are executed one after the other, regardless of the success or failure of the previous command.

For example, let’s say you want to (1) create a new directory, (2) move into that directory, and then (3) list the files in that directory, all in one go. You can use semicolons to combine these commands like this:

Code
mkdir new_directory ; cd new_directory ; ls

This will (1) create a new directory called new_directory, (2) change the current working directory to new_directory and (3) list the files in this new directory.

2.9 Summary

In this lesson, we have achieved the following:

  1. We clarified some of the technical terms associated with the command line.
  2. We explored the components of command-line commands: paths, arguments, and flags.
  3. We gained knowledge about relative and absolute paths, including convenient shortcuts like ~, . and ...
  4. We experienced the functionality of wildcards.
  5. We acquired familiarity with several essential shell commands.

It’s important to note that what we covered here only scratches the surface of what can be accomplished using the shell. The primary aim was to provide useful concepts that help when learning Git. If you’re interested in delving deeper, you may find a more comprehensive introduction at one of the following resources.

Figure 2.6: “Hackerman” meme found on Reddit.com

2.10 Acknowledgements & further reading

We would like to express our gratitude to the following resources, which have been essential in shaping this chapter. We recommend these references for further reading:

Authors Title Website License Source
Millman et al. (2018) Teaching Computational Reproducibility for Neuroimaging CC BY 4.0. Website:
Milligan and Baker (2014) Introduction to the Bash Command Line NA NA NA
McBain (2019) Git for Scientists CC BY-SA 4.0
Capes et al. (2023) swcarpentry/shell-novice: Software Carpentry: the UNIX shell CC BY 4.0

2.11 Cheatsheet

Command Description
pwd Displays the path of the current working directory
cd <PATH> Changes the current working directory to <PATH>
cd ~ Changes the current working directory to the user’s home directory
cd .. Moves up one folder
cd ../.. Moves up two folders
clear Clears the contents of your command line window
ls Lists files and folders in the current working directory
ls <PATH> Lists files and folders in <PATH>
ls -a Lists all files (including hidden files) in the current working directory
ls -alh Lists all files in a long format that is easy to read for humans
[Command] --help Displays all possible flags for a specific command (on Windows)
man [Command] Displays all possible flags for a specific command (on macOS)
mkdir <FOLDER> Creates a new folder called <FOLDER>
mkdir <FOLDER1> <FOLDER2> Creates two separate folders called <FOLDER1> and <FOLDER2>
touch <FILE> Creates a new empty file called <FILE>
open <FILE> Opens the file called <FILE> (on macOS)
start <FILE> Opens the file called <FILE> (on Windows)
echo "example text" >> file.txt Writes “example text” into file.txt
cat <FILE> Displays the content of <FILE>
mv FILE.txt <FOLDER> Move FILE.txt into <FOLDER>
mv <FOLDER_OLD> <FOLDER_NEW> Renames <FOLDER_OLD> to <FOLDER_NEW>
ls -alh *.csv Uses a wildcard to list all .csv files in the current working directory
rm -r <FOLDER> Removes the folder <FOLDER>
history Display the command history of the current terminal session
history > history.txt Saves the entire command history to a file named history.txt
history >> history.txt Adds the entire command history to the end of the file named history.txt