Matt Dray (@mattdray)
These are likely to be your most commonly-used bash commands. These will be useful when you start using the command line for version-control with Git.
||Print working directory|
||List folder contents|
||Make directory (folder)|
||Create a file|
||Open Nano editor|
||Open a file in its default program|
||Move a file|
||Remove (delete) a file|
||Manual for a command|
New Year’s R-solution
People shared recently on Twitter their R goals for 2019 (see Maëlle Salmon’s post). Some of them referenced the use of Git and GitHub (see Jason Baik’s scraped dataset) for version-control of their projects.
It wasn’t that long ago that I began working with Git and GitHub (see my history on my GitHub profile). Now seems a good time to record what I learnt and maybe someone else will find it useful, or suggest better approaches.
I’m splitting this into two posts: one introducing the basics of the command line – a useful first step – and one about a basic Git workflow.
In these posts I assume that you:
- have little-to-no understanding of the command line and Git commands, but some experience of coding
- want to version control your R project
- intend to store your version-controlled files in the cloud with GitHub
- want to interact with Git via the command line, rather than with a Graphical User Interface (GUI)
- are using a Mac, writing in bash and will access the command line via Terminal
These are relatively narrow constraints, but there will likely be some overlap with your particular configuration.
The command line
Our goal is to start writing Git commands at the command line. Before we get to Git, we need to know what the command line is and get some experience of working there.
You probably interact with your computer primarily via a Graphical User Interface (GUI) composed of windows and visual representations of files and folders, and probably use a mouse to do this.
But there’s another way: you can write text commands directly to your computer to manipulate files and folders. One benefit is that you can save and re-execute commands in a script, which is much more reproducible than an unkown series of mouse-based interactions.
What language are we going to use to communicate? We’ll be writing in our computer’s default scripting langage, called bash. In this post we’ll be looking at a few basic commands.
Open the Terminal application (tap command and space to search for it). Terminal acts as a Command Line Interface (CLI): a place where you can chat with your machine.
Terminal is a simple application where you type commands and execute them. You’re presented with the prompt, which is the form
<computer name>:<current directory> <user>$. For example:
The prompt will appear each time your computer is awaiting an instruction. You just need to write your command after the
$ and hit enter.
Where are we?
The commands we input are going to affect the current folder we’re in, or other files and folders relative to it.
Where are you when you start Terminal? The prompt helps you orient yourself: see the
<current directory> bit of
<computer name>:<current directory> <user>$.
When you start, the prompt will show the tilde
~ by default. This is a shortcut symbol for your ‘home’ directory, which on a Mac will be set to the path
We can prove this by typing
pwd at the prompt and hitting the enter key.
bros:~ luigi$ pwd /Users/luigi
This command prints the path for the current working directory. The folder we’re working in at any given moment is called ‘the working directory’.
Look around with
We can look at the contents of our current working directory with
ls, which means ‘list the files’.
bros:~ luigi$ ls Applications Desktop Documents Downloads Movies Music Pictures plumbing-invoice.txt
It holds some folders and a text file. This command is analagous to double-clicking a folder to open it and look inside.
We can go one better: we can add ‘flags’ to the command. These are arguments prefixed with a hyphen that change the command’s default behaviour. We’re going to ask for all the files and folders (some are hidden!) with
-a and also we’ll use
-p to append the folders with a forward slash to make them more obvious.
bros:~ luigi$ ls -a -p ./ ../ .luigi-profile .gameboy-horror-token .poltergust-key Applications/ Desktop/ Documents/ Downloads/ Movies/ Music/ Pictures/ plumbing-invoice.txt
So now can see all the files, including the hidden ones. Hidden files are often settings or profiles for various programs, or tokens stored for API access. One example of a hidden file for R is an .Rprofile.
You can see a description of the command and the list of available flags using the
man command. For example, try
man ls to learn about the list command. Sometimes the contents of the man file don’t fit the screen; keep hitting return until the bottom, or tap
q to quit.
Create/edit a file with
Let’s create a file in our current working directory with the
touch command and then convince ourselves it’s there by listing the folder contents. I’m choosing to write a Markdown file with the
.md extension, but you could just as easily have specified a
.txt text file, for example.
bros:Documents luigi$ touch mushroom-top3.md bros:Documents luigi$ ls -p coin-balance/ mushroom-top3.md monty-mole-fanfic.txt moustache-wiggle.gif plumbing/ star-locations/
Okay great, but the file is empty. How do we write something in it? Well, you could use
open characters.md at the prompt to open the file in your default text editor (TextEdit or something), but we can also write text from within Terminal itself. Perhaps the simplest way is to use the Nano editor, which you can think of as a text editor built into Terminal.
You just need to type
nano <file name>.
bros:important-notes luigi$ nano mushroom-top3.md
The prompt will disappear and you’ll see a header saying
File: characters.md. You’re now editing this file with Nano. Start typing.
# Mushroom Kingdom Top Threes ## The best 1. **Luigi** 2. Baby Luigi 3. Daisy ## The worst 1. Red Luigi 2. Waluigi 3. King Boo
Notice the options at the bottom of the window. We can exit Nano with
^X (control and X keys). You’ll be asked if you want to save; hit
Y for yes. Then you’ll be asked for a
File name to write: characters.md. You can edit the name or hit enter to confirm. The content is now saved.
Create a folder with mkdir
As well as files, the command
mkdir <folder name> will create a new folder in our current working directory. We can switch to the new folder with
cd and can again convince ourselves by looking at the
bros:Documents luigi$ mkdir new-games-starring-luigi bros:Documents luigi$ cd bros:new-games-starring-luigi luigi$ pwd /Users/luigi/Documents/important-notes bros:new-games-starring-luigi luigi$ ls bros:new-games-starring-luigi luigi$
ls on an empty directory will return nothing.
Move your files with
Let’s say we have a rogue text file in our home directory (
~) that should really be in a subfolder of
Documents/. The command
mv allows us to move it. It’s like dragging and dropping a file from one folder into another.
You can specify this in the form
mv <filepath> <filepath> to move files to and from any path, or or navigate with
cd to the folder containing the file and use the form
mv <file> <filepath>). The code below does the latter, using
ls to move between folders and show where the file is.
bros:Documents luigi$ cd ~ bros:~ luigi$ ls Applications Desktop Documents Downloads Movies Music Pictures plumbing-invoice.txt bros:~ luigi$ mv plumbing-invoice.txt ~/Documents/important-notes/plumbing bros:~ luigi$ ls Applications Desktop Documents Downloads Movies Music Pictures bros:~ luigi$ cd /Documents/plumbing/important-notes/plumbing bros:plumbing luigi$ ls overalls.jpg plumbing-invoice.txt tighten-warp-pipes.txt
While we’re in this folder, we might want to prune our files a bit. You can remove files with the
bros:plumbing luigi$ ls overalls.jpg plumbing-invoice.txt tighten-warp-pipes.txt bros:plumbing luigi$ rm tighten-warp-pipes.txt bros:plumbing luigi$ ls overalls.jpg plumbing-invoice.txt
Well done for reaching the finish. So we should have enough knowledge now to navigate and manipulate folders. This will be extremely helpful when we start using Git commands at the command line in part two of the ‘Git going’ series.