Introduction

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• What is version control and why should I use it?

Objectives

• Understand the benefits of an automated version control system.

• Understand the basics of how automated version control systems work.

• Explain how the shell relates to the keyboard, the screen, the operating system, and users’ programs.

We’ll start by exploring how version control can be used to keep track of what one person did and when. Even if you aren’t collaborating with other people, automated version control is much better than this situation:

“Piled Higher and Deeper” by Jorge Cham, http://www.phdcomics.com

We’ve all been in this situation before: it seems ridiculous to have multiple nearly-identical versions of the same document. Some word processors let us deal with this a little better, such as Microsoft Word’s Track Changes, Google Docs’ version history, or LibreOffice’s Recording and Displaying Changes.

Version control systems start with a base version of the document and then record changes you make each step of the way. You can think of it as a recording of your progress: you can rewind to start at the base document and play back each change you made, eventually arriving at your more recent version.

Once you think of changes as separate from the document itself, you can then think about “playing back” different sets of changes on the base document, ultimately resulting in different versions of that document. For example, two users can make independent sets of changes on the same document.

Unless multiple users make changes to the same section of the document - a conflict - you can incorporate two sets of changes into the same base document.

A version control system is a tool that keeps track of these changes for us, effectively creating different versions of our files. It allows us to decide which changes will be made to the next version (each record of these changes is called a commit), and keeps useful metadata about them. The complete history of commits for a particular project and their metadata make up a repository. Repositories can be kept in sync across different computers, facilitating collaboration among different people.

To build this workshop’s website, we often have multiple people working on the site independantly. Here is a snapshot of the history of changes, or commits, which we have implemented on this website. You will notice multiple people are involved, and they each include a comment on what changes are being made.

Taking a closer look at one of these commits, we can see what exactly has been edited. The line of content which has been changed is marked in red, and the new line of content is marked in green.

The Long History of Version Control Systems

Automated version control systems are nothing new. Tools like RCS, CVS, or Subversion have been around since the early 1980s and are used by many large companies. However, many of these are now considered legacy systems (i.e., outdated) due to various limitations in their capabilities. More modern systems, such as Git and Mercurial, are distributed, meaning that they do not need a centralized server to host the repository. These modern systems also include powerful merging tools that make it possible for multiple authors to work on the same files concurrently.

Paper Writing

• Imagine you drafted an excellent paragraph for a paper you are writing, but later ruin it. How would you retrieve the excellent version of your conclusion? Is it even possible?

• Imagine you have 5 co-authors. How would you manage the changes and comments they make to your paper? If you use LibreOffice Writer or Microsoft Word, what happens if you accept changes made using the Track Changes option? Do you have a history of those changes?

Solution

• Recovering the excellent version is only possible if you created a copy of the old version of the paper. The danger of losing good versions often leads to the problematic workflow illustrated in the PhD Comics cartoon at the top of this page.

• Collaborative writing with traditional word processors is cumbersome. Either every collaborator has to work on a document sequentially (slowing down the process of writing), or you have to send out a version to all collaborators and manually merge their comments into your document. The ‘track changes’ or ‘record changes’ option can highlight changes for you and simplifies merging, but as soon as you accept changes you will lose their history. You will then no longer know who suggested that change, why it was suggested, or when it was merged into the rest of the document. Even online word processors like Google Docs or Microsoft Office Online do not fully resolve these problems.

The Shell

Git is a command line tool, so we’ll start the workshop with an introduction to working with “the shell”. The shell is a program where users can type commands. With the shell, it’s possible to invoke complicated programs like climate modeling software or simple commands that create an empty directory with only one line of code. The most popular Unix shell is Bash (the Bourne Again SHell — so-called because it’s derived from a shell written by Stephen Bourne). Bash is the default shell on most modern implementations of Unix and in most packages that provide Unix-like tools for Windows.

Using the shell will take some effort and some time to learn. While a GUI presents you with choices to select, CLI choices are not automatically presented to you, so you must learn a few commands like new vocabulary in a language you’re studying. However, unlike a spoken language, a small number of “words” (i.e. commands) gets you a long way, and we’ll cover those essential few today.

The grammar of a shell allows you to combine existing tools into powerful pipelines and handle large volumes of data automatically. Sequences of commands can be written into a script, improving the reproducibility of workflows.

In addition, the command line is often the easiest way to interact with remote machines and supercomputers. Familiarity with the shell is near essential to run a variety of specialized tools and resources including high-performance computing systems. As clusters and cloud computing systems become more popular for scientific data crunching, being able to interact with the shell is becoming a necessary skill. We can build on the command-line skills covered here to tackle a wide range of scientific questions and computational challenges.

Let’s get started.

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

$

The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show the prompt as $ . Most importantly: when typing commands, either from these lessons or from other sources, do not type the prompt, only the commands that follow it. Also note that after you type a command, you have to press the Enter key to execute it.

Changing your prompt

Your prompt may be super long (containing your username, computer name, etc.). To change your prompt type in:

$ export PS1= ">"

This will last as long as the length of your shell session.

The prompt is followed by a text cursor, a character that indicates the position where your typing will appear. The cursor is usually a flashing or solid block, but it can also be an underscore or a pipe. You may have seen it in a text editor program, for example.

So let’s try our first command, ls which is short for listing. This command will list the contents of the current directory:

$ ls

Desktop     Downloads   Movies      Pictures
Documents   Library     Music       Public

Command not found

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:

$ ks

ks: command not found

This might happen if the command was mis-typed or if the program corresponding to that command is not installed.

Key Points

• Version control is like an unlimited ‘undo’.

• Version control also allows many people to work in parallel.

• A shell is a program whose primary purpose is to read commands and run other programs.

Shell: Navigating Files and Directories

Overview

Teaching: 30 min
Exercises: 10 min

Questions

• How can I move around on my computer?

• How can I see what files and directories I have?

• How can I specify the location of a file or directory on my computer?

Objectives

• Explain the similarities and differences between a file and a directory.

• Translate an absolute path into a relative path and vice versa.

• Construct absolute and relative paths that identify specific files and directories.

• Use options and arguments to change the behaviour of a shell command.

• Demonstrate the use of tab completion and explain its advantages.

The part of the operating system responsible for managing files and directories is called the file system. It organizes our data into files, which hold information, and directories (also called ‘folders’), which hold files or other directories.

Several commands are frequently used to create, inspect, rename, and delete files and directories. To start exploring them, we’ll go to our open shell window.

First, let’s find out where we are by running a command called pwd (which stands for ‘print working directory’). Directories are like places — at any time while we are using the shell, we are in exactly one place called our current working directory. Commands mostly read and write files in the current working directory, i.e. ‘here’, so knowing where you are before running a command is important. pwd shows you where you are:

$ pwd

/Users/nelle

Here, the computer’s response is /Users/nelle, which is Nelle’s home directory:

Home Directory Variation

The home directory path will look different on different operating systems. On Linux, it may look like /home/nelle, and on Windows, it will be similar to C:\Documents and Settings\nelle or C:\Users\nelle. (Note that it may look slightly different for different versions of Windows.) In future examples, we’ve used Mac output as the default - Linux and Windows output may differ slightly but should be generally similar.

We will also assume that your pwd command returns your user’s home directory. If pwd returns something different, you may need to navigate there using cd or some commands in this lesson will not work as written. See Exploring Other Directories for more details on the cd command.

To understand what a ‘home directory’ is, let’s have a look at how the file system as a whole is organized. For the sake of this example, we’ll be illustrating the filesystem on our scientist Nelle’s computer. After this illustration, you’ll be learning commands to explore your own filesystem, which will be constructed in a similar way, but not be exactly identical.

On Nelle’s computer, the filesystem looks like this:

At the top is the root directory that holds everything else. We refer to it using a slash character, /, on its own; this character is the leading slash in /Users/nelle.

Inside that directory are several other directories: bin (which is where some built-in programs are stored), data (for miscellaneous data files), Users (where users’ personal directories are located), tmp (for temporary files that don’t need to be stored long-term), and so on.

We know that our current working directory /Users/nelle is stored inside /Users because /Users is the first part of its name. Similarly, we know that /Users is stored inside the root directory / because its name begins with /.

Slashes

Notice that there are two meanings for the / character. When it appears at the front of a file or directory name, it refers to the root directory. When it appears inside a path, it’s just a separator.

Underneath /Users, we find one directory for each user with an account on Nelle’s machine, her colleagues imhotep and larry.

The user imhotep’s files are stored in /Users/imhotep, user larry’s in /Users/larry, and Nelle’s in /Users/nelle. Nelle is the user in our examples here; therefore, we get /Users/nelle as our home directory. Typically, when you open a new command prompt, you will be in your home directory to start.

Now let’s learn the command that will let us see the contents of our own filesystem. We can see what’s in our home directory by running ls:

$ ls

Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

(Again, your results may be slightly different depending on your operating system and how you have customized your filesystem.)

ls prints the names of the files and directories in the current directory. We can make its output more comprehensible by using the -F option which tells ls to classify the output by adding a marker to file and directory names to indicate what they are:

• a trailing / indicates that this is a directory
• @ indicates a link
• * indicates an executable

Depending on your shell’s default settings, the shell might also use colors to indicate whether each entry is a file or directory.

$ ls -F

Applications/ Documents/    Library/      Music/        Public/
Desktop/      Downloads/    Movies/       Pictures/

Here, we can see that the home directory contains only sub-directories. Any names in the output that don’t have a classification symbol are files in the current working directory.

Clearing your terminal

If your screen gets too cluttered, you can clear your terminal using the clear command. You can still access previous commands using ↑ and ↓ to move line-by-line, or by scrolling in your terminal.

Getting help

ls has lots of other options. There are two common ways to find out how to use a command and what options it accepts — depending on your environment, you might find that only one of these ways works:

1. We can pass a --help option to any command (available on Linux and Git Bash), for example:

    $ ls --help
   

2. We can read its manual with man (available on Linux and macOS):

    $ man ls
   

We’ll describe both ways next.

Help for built-in commands

Some commands are built in to the Bash shell, rather than existing as separate programs on the filesystem. One example is the cd (change directory) command. If you get a message like No manual entry for cd, try help cd instead. The help command is how you get usage information for Bash built-ins.

The --help option

Most bash commands and programs that people have written to be run from within bash, support a --help option that displays more information on how to use the command or program.

$ ls --help

Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if neither -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options, too.
  -a, --all                  do not ignore entries starting with .
  -A, --almost-all           do not list implied . and ..
      --author               with -l, print the author of each file
  -b, --escape               print C-style escapes for nongraphic characters
      --block-size=SIZE      scale sizes by SIZE before printing them; e.g.,
                               '--block-size=M' prints sizes in units of
                               1,048,576 bytes; see SIZE format below
  -B, --ignore-backups       do not list implied entries ending with ~
  -c                         with -lt: sort by, and show, ctime (time of last
                               modification of file status information);
                               with -l: show ctime and sort by name;
                               otherwise: sort by ctime, newest first
  -C                         list entries by columns
      --color[=WHEN]         colorize the output; WHEN can be 'always' (default
                               if omitted), 'auto', or 'never'; more info below
  -d, --directory            list directories themselves, not their contents
  -D, --dired                generate output designed for Emacs' dired mode
  -f                         do not sort, enable -aU, disable -ls --color
  -F, --classify             append indicator (one of */=>@|) to entries
...        ...        ...

Unsupported command-line options

If you try to use an option that is not supported, ls and other commands will usually print an error message similar to:

$ ls -j

ls: invalid option -- 'j'
Try 'ls --help' for more information.

The man command

The other way to learn about ls is to type

$ man ls

This command will turn your terminal into a page with a description of the ls command and its options.

To navigate through the man pages, you may use ↑ and ↓ to move line-by-line, or try B and Spacebar to skip up and down by a full page. To search for a character or word in the man pages, use / followed by the character or word you are searching for. Sometimes a search will result in multiple hits. If so, you can move between hits using N (for moving forward) and Shift+N (for moving backward).

To quit the man pages, press Q.

Manual pages on the web

Of course, there is a third way to access help for commands: searching the internet via your web browser. When using internet search, including the phrase unix man page in your search query will help to find relevant results.

GNU provides links to its manuals including the core GNU utilities, which covers many commands introduced within this lesson.

Exploring More ls Options

You can also use two options at the same time. What does the command ls do when used with the -l option? What about if you use both the -l and the -h option?

Some of its output is about properties that we do not cover in this lesson (such as file permissions and ownership), but the rest should be useful nevertheless.

Solution

The -l option makes ls use a long listing format, showing not only the file/directory names but also additional information, such as the file size and the time of its last modification. If you use both the -h option and the -l option, this makes the file size ‘human readable’, i.e. displaying something like 5.3K instead of 5369.

Listing in Reverse Chronological Order

By default, ls lists the contents of a directory in alphabetical order by name. The command ls -t lists items by time of last change instead of alphabetically. The command ls -r lists the contents of a directory in reverse order. Which file is displayed last when you combine the -t and -r options? Hint: You may need to use the -l option to see the last changed dates.

Solution

The most recently changed file is listed last when using -rt. This can be very useful for finding your most recent edits or checking to see if a new output file was written.

Exploring Other Directories

Not only can we use ls on the current working directory, but we can use it to list the contents of a different directory. Let’s take a look at our Desktop directory by running ls -F Desktop, i.e., the command ls with the -F option and the [argument][Arguments] Desktop. The argument Desktop tells ls that we want a listing of something other than our current working directory:

$ ls -F Desktop

shell-lesson-data/

Note that if a directory named Desktop does not exist in your current working directory, this command will return an error. Typically, a Desktop directory exists in your home directory, which we assume is the current working directory of your bash shell.

Your output should be a list of all the files and sub-directories in your Desktop directory, including the shell-lesson-data directory you downloaded at the setup for this lesson. (On most systems, the contents of the Desktop directory in the shell will show up as icons in a graphical user interface behind all the open windows. See if this is the case for you.)

Organizing things hierarchically helps us keep track of our work. While it’s possible to put hundreds of files in our home directory just as it’s possible to pile hundreds of printed papers on our desk, it’s much easier to find things when they’ve been organized into sensibly-named subdirectories.

Now that we know the shell-lesson-data directory is located in our Desktop directory, we can do two things.

First, using the same strategy as before, we can look at its contents by passing a directory name to ls:

$ ls -F Desktop/shell-lesson-data

exercise-data/  north-pacific-gyre/

Second, we can actually change our location to a different directory, so we are no longer located in our home directory.

The command to change locations is cd followed by a directory name to change our working directory. cd stands for ‘change directory’, which is a bit misleading. The command doesn’t change the directory; it changes the shell’s current working directory. In other words it changes the shell’s settings for what directory we are in. The cd command is akin to double-clicking a folder in a graphical interface to get into that folder.

Let’s say we want to move into the exercise-data directory we saw above. We can use the following series of commands to get there:

$ cd Desktop
$ cd shell-lesson-data
$ cd exercise-data

These commands will move us from our home directory into our Desktop directory, then into the shell-lesson-data directory, then into the exercise-data directory. You will notice that cd doesn’t print anything. This is normal. Many shell commands will not output anything to the screen when successfully executed. But if we run pwd after it, we can see that we are now in /Users/nelle/Desktop/shell-lesson-data/exercise-data.

If we run ls -F without arguments now, it lists the contents of /Users/nelle/Desktop/shell-lesson-data/exercise-data, because that’s where we now are:

$ pwd

/Users/nelle/Desktop/shell-lesson-data/exercise-data

$ ls -F

animal-counts/  creatures/  numbers.txt  alkanes/  writing/

We now know how to go down the directory tree (i.e. how to go into a subdirectory), but how do we go up (i.e. how do we leave a directory and go into its parent directory)? We might try the following:

$ cd shell-lesson-data

-bash: cd: shell-lesson-data: No such file or directory

But we get an error! Why is this?

With our methods so far, cd can only see sub-directories inside your current directory. There are different ways to see directories above your current location; we’ll start with the simplest.

There is a shortcut in the shell to move up one directory level. It works as follows:

$ cd ..

.. is a special directory name meaning “the directory containing this one”, or more succinctly, the parent of the current directory. Sure enough, if we run pwd after running cd .., we’re back in /Users/nelle/Desktop/shell-lesson-data:

$ pwd

/Users/nelle/Desktop/shell-lesson-data

The special directory .. doesn’t usually show up when we run ls. If we want to display it, we can add the -a option to ls -F:

$ ls -F -a

./  ../  exercise-data/  north-pacific-gyre/

-a stands for ‘show all’ (including hidden files); it forces ls to show us file and directory names that begin with ., such as .. (which, if we’re in /Users/nelle, refers to the /Users directory). As you can see, it also displays another special directory that’s just called ., which means ‘the current working directory’. It may seem redundant to have a name for it, but we’ll see some uses for it soon.

Note that in most command line tools, multiple options can be combined with a single - and no spaces between the options; ls -F -a is equivalent to ls -Fa.

Other Hidden Files

In addition to the hidden directories .. and ., you may also see a file called .bash_profile. This file usually contains shell configuration settings. You may also see other files and directories beginning with .. These are usually files and directories that are used to configure different programs on your computer. The prefix . is used to prevent these configuration files from cluttering the terminal when a standard ls command is used.

These three commands are the basic commands for navigating the filesystem on your computer: pwd, ls, and cd. Let’s explore some variations on those commands. What happens if you type cd on its own, without giving a directory?

$ cd

How can you check what happened? pwd gives us the answer!

$ pwd

/Users/nelle

It turns out that cd without an argument will return you to your home directory, which is great if you’ve got lost in your own filesystem.

Let’s try returning to the exercise-data directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to exercise-data in one step:

$ cd Desktop/shell-lesson-data/exercise-data

Check that we’ve moved to the right place by running pwd and ls -F.

If we want to move up one level from the data directory, we could use cd ... But there is another way to move to any directory, regardless of your current location.

So far, when specifying directory names, or even a directory path (as above), we have been using relative paths. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.

This allows us to move to our shell-lesson-data directory from anywhere on the filesystem (including from inside exercise-data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to shell-lesson-data.

$ pwd

/Users/nelle/Desktop/shell-lesson-data/exercise-data

$ cd /Users/nelle/Desktop/shell-lesson-data

Run pwd and ls -F to ensure that we’re in the directory we expect.

Two More Shortcuts

The shell interprets a tilde (~) character at the start of a path to mean “the current user’s home directory”. For example, if Nelle’s home directory is /Users/nelle, then ~/data is equivalent to /Users/nelle/data. This only works if it is the first character in the path; here/there/~/elsewhere is not here/there/Users/nelle/elsewhere.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between two directories – i.e. if you execute cd - twice, you end up back in the starting directory.

The difference between cd .. and cd - is that the former brings you up, while the latter brings you back.

---

Try it! First navigate to ~/Desktop/shell-lesson-data (you should already be there).

$ cd ~/Desktop/shell-lesson-data

Then cd into the exercise-data/creatures directory

$ cd exercise-data/creatures

Now if you run

$ cd -

you’ll see you’re back in ~/Desktop/shell-lesson-data. Run cd - again and you’re back in ~/Desktop/shell-lesson-data/exercise-data/creatures

Absolute vs Relative Paths

Starting from /Users/amanda/data, which of the following commands could Amanda use to navigate to her home directory, which is /Users/amanda?

1. cd .
2. cd /
3. cd /home/amanda
4. cd ../..
5. cd ~
6. cd home
7. cd ~/data/..
8. cd
9. cd ..

Solution

1. No: . stands for the current directory.
2. No: / stands for the root directory.
3. No: Amanda’s home directory is /Users/amanda.
4. No: this command goes up two levels, i.e. ends in /Users.
5. Yes: ~ stands for the user’s home directory, in this case /Users/amanda.
6. No: this command would navigate into a directory home in the current directory if it exists.
7. Yes: unnecessarily complicated, but correct.
8. Yes: shortcut to go back to the user’s home directory.
9. Yes: goes up one level.

Relative Path Resolution

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls -F ../backup display?

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original/ pnas_final/ pnas_sub/

Solution

1. No: there is a directory backup in /Users.
2. No: this is the content of Users/thing/backup, but with .., we asked for one level further up.
3. No: see previous explanation.
4. Yes: ../backup/ refers to /Users/backup/.

ls Reading Comprehension

Using the filesystem diagram below, if pwd displays /Users/backup, and -r tells ls to display things in reverse order, what command(s) will result in the following output:

pnas_sub/ pnas_final/ original/

1. ls pwd
2. ls -r -F
3. ls -r -F /Users/backup

Solution

1. No: pwd is not the name of a directory.
2. Yes: ls without directory argument lists files and directories in the current directory.
3. Yes: uses the absolute path explicitly.

General Syntax of a Shell Command

We have now encountered commands, options, and arguments, but it is perhaps useful to formalise some terminology.

Consider the command below as a general example of a command, which we will dissect into its component parts:

$ ls -F /

ls is the command, with an option -F and an argument /. We’ve already encountered options which either start with a single dash (-) or two dashes (--), and they change the behavior of a command. [Arguments] tell the command what to operate on (e.g. files and directories). Sometimes options and arguments are referred to as parameters. A command can be called with more than one option and more than one argument, but a command doesn’t always require an argument or an option.

You might sometimes see options being referred to as switches or flags, especially for options that take no argument. In this lesson we will stick with using the term option.

Each part is separated by spaces. If you omit the space between ls and -F the shell will look for a command called ls-F, which doesn’t exist. Also, capitalization can be important. For example, ls -s will display the size of files and directories alongside the names, while ls -S will sort the files and directories by size, as shown below:

$ cd ~/Desktop/shell-lesson-data
$ ls -s exercise-data

total 28
 4 animal-counts   4 creatures  12 numbers.txt   4 alkanes   4 writing

Note that the sizes returned by ls -s are in blocks. As these are defined differently for different operating systems, you may not obtain the same figures as in the example.

$ ls -S exercise-data

animal-counts  creatures  alkanes  writing  numbers.txt

Putting all that together, our command ls -F / above gives us a listing of files and directories in the root directory /. An example of the output you might get from the above command is given below:

$ ls -F /

Applications/         System/
Library/              Users/
Network/              Volumes/

Key Points

• The file system is responsible for managing information on the disk.

• Information is stored in files, which are stored in directories (folders).

• Directories can also store other directories, which then form a directory tree.

• pwd prints the user’s current working directory.

• ls [path] prints a listing of a specific file or directory; ls on its own lists the current working directory.

• cd [path] changes the current working directory.

• Most commands take options that begin with a single -.

• Directory names in a path are separated with / on Unix, but \ on Windows.

• / on its own is the root directory of the whole file system.

• An absolute path specifies a location from the root of the file system.

• A relative path specifies a location starting from the current location.

• . on its own means ‘the current directory’; .. means ‘the directory above the current one’.

Shell: Working With Files and Directories

Overview

Teaching: 30 min
Exercises: 20 min

Questions

• How can I create, copy, and delete files and directories?

• How can I edit files?

Objectives

• Create a directory hierarchy that matches a given diagram.

• Create files in that hierarchy using an editor or by copying and renaming existing files.

• Delete, copy and move specified files and/or directories.

Creating directories

We now know how to explore files and directories, but how do we create them in the first place?

In this episode we will learn about creating and moving files and directories, using the exercise-data/writing directory as an example.

Step one: see where we are and what we already have

We should still be in the shell-lesson-data directory on the Desktop, which we can check using:

$ pwd

/Users/nelle/Desktop/shell-lesson-data

Next we’ll move to the exercise-data/writing directory and see what it contains:

$ cd exercise-data/writing/

$ ls -F

haiku.txt  LittleWomen.txt

Create a directory

Let’s create a new directory called thesis using the command mkdir thesis (which has no output):

$ mkdir thesis

As you might guess from its name, mkdir means ‘make directory’. Since thesis is a relative path (i.e., does not have a leading slash, like /what/ever/thesis), the new directory is created in the current working directory:

$ ls -F

haiku.txt  LittleWomen.txt  thesis/

Since we’ve just created the thesis directory, there’s nothing in it yet:

$ ls -F thesis

Note that mkdir is not limited to creating single directories one at a time. The -p option allows mkdir to create a directory with nested subdirectories in a single operation:

$ mkdir -p ../project/data ../project/results

The -R option to the ls command will list all nested subdirectories within a directory. Let’s use ls -FR to recursively list the new directory hierarchy we just created in the project directory:

$ ls -FR ../project

../project/:
data/  results/

../project/data:

../project/results:

Two ways of doing the same thing

Using the shell to create a directory is no different than using a file explorer. If you open the current directory using your operating system’s graphical file explorer, the thesis directory will appear there too. While the shell and the file explorer are two different ways of interacting with the files, the files and directories themselves are the same.

Good names for files and directories

Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files and directories.

1. Don’t use spaces.

   Spaces can make a name more meaningful, but since spaces are used to separate arguments on the command line it is better to avoid them in names of files and directories. You can use - or _ instead (e.g. north-pacific-gyre/ rather than north pacific gyre/). To test this out, try typing mkdir north pacific gyreand see what directory (or directories!) are made when you check with ls -F.

2. Don’t begin the name with - (dash).

   Commands treat names starting with - as options.

3. Stick with letters, numbers, . (period or ‘full stop’), - (dash) and _ (underscore).

   Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.

If you need to refer to names of files or directories that have spaces or other special characters, you should surround the name in quotes ("").

Create a text file

Let’s change our working directory to thesis using cd, then run a text editor called Nano to create a file called draft.txt:

$ cd thesis
$ nano draft.txt

Which Editor?

When we say, ‘nano is a text editor’ we really do mean ‘text’. It can only work with plain character data, not tables, images, or any other human-friendly media. We use it in examples because it is one of the least complex text editors. However, because of this trait, it may not be powerful enough or flexible enough for the work you need to do after this workshop. On Unix systems (such as Linux and macOS), many programmers use Emacs or Vim (both of which require more time to learn), or a graphical editor such as Gedit or VScode. On Windows, you may wish to use Notepad++. Windows also has a built-in editor called notepad that can be run from the command line in the same way as nano for the purposes of this lesson.

No matter what editor you use, you will need to know where it searches for and saves files. If you start it from the shell, it will (probably) use your current working directory as its default location. If you use your computer’s start menu, it may want to save files in your Desktop or Documents directory instead. You can change this by navigating to another directory the first time you ‘Save As…’

Let’s type in a few lines of text.

Once we’re happy with our text, we can press Ctrl+O (press the Ctrl or Control key and, while holding it down, press the O key) to write our data to disk. We will be asked to provide a name for the file that will contain our text. Press Return to accept the suggested default of draft.txt.

Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.

Control, Ctrl, or ^ Key

The Control key is also called the ‘Ctrl’ key. There are various ways in which using the Control key may be described. For example, you may see an instruction to press the Control key and, while holding it down, press the X key, described as any of:

• Control-X
• Control+X
• Ctrl-X
• Ctrl+X
• ^X
• C-x

In nano, along the bottom of the screen you’ll see ^G Get Help ^O WriteOut. This means that you can use Control-G to get help and Control-O to save your file.

nano doesn’t leave any output on the screen after it exits, but ls now shows that we have created a file called draft.txt:

$ ls

draft.txt

Creating Files a Different Way

We have seen how to create text files using the nano editor. Now, try the following command:

$ touch my_file.txt

1. What did the touch command do? When you look at your current directory using the GUI file explorer, does the file show up?

2. Use ls -l to inspect the files. How large is my_file.txt?

3. When might you want to create a file this way?

Solution

1. The touch command generates a new file called my_file.txt in your current directory. You can observe this newly generated file by typing ls at the command line prompt. my_file.txt can also be viewed in your GUI file explorer.

2. When you inspect the file with ls -l, note that the size of my_file.txt is 0 bytes. In other words, it contains no data. If you open my_file.txt using your text editor it is blank.

3. Some programs do not generate output files themselves, but instead require that empty files have already been generated. When the program is run, it searches for an existing file to populate with its output. The touch command allows you to efficiently generate a blank text file to be used by such programs.

To avoid confusion later on, we suggest removing the file you’ve just created before proceeding with the rest of the episode, otherwise future outputs may vary from those given in the lesson. To do this, use the following command:

$ rm my_file.txt

What’s In A Name?

You may have noticed that all of Nelle’s files are named ‘something dot something’, and in this part of the lesson, we always used the extension .txt. This is just a convention; we can call a file mythesis or almost anything else we want. However, most people use two-part names most of the time to help them (and their programs) tell different kinds of files apart. The second part of such a name is called the filename extension and indicates what type of data the file holds: .txt signals a plain text file, .pdf indicates a PDF document, .cfg is a configuration file full of parameters for some program or other, .png is a PNG image, and so on.

This is just a convention, albeit an important one. Files merely contain bytes; it’s up to us and our programs to interpret those bytes according to the rules for plain text files, PDF documents, configuration files, images, and so on.

Naming a PNG image of a whale as whale.mp3 doesn’t somehow magically turn it into a recording of whale song, though it might cause the operating system to associate the file with a music player program. In this case, if someone double-clicked whale.mp3 in a file explorer program,the music player will automatically (and erroneously) attempt to open the whale.mp3 file.

Moving files and directories

Returning to the shell-lesson-data/exercise-data/writing directory,

$ cd ~/Desktop/shell-lesson-data/exercise-data/writing

In our thesis directory we have a file draft.txt which isn’t a particularly informative name, so let’s change the file’s name using mv, which is short for ‘move’:

$ mv thesis/draft.txt thesis/quotes.txt

The first argument tells mv what we’re ‘moving’, while the second is where it’s to go. In this case, we’re moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as renaming the file. Sure enough, ls shows us that thesis now contains one file called quotes.txt:

$ ls thesis

quotes.txt

One must be careful when specifying the target file name, since mv will silently overwrite any existing file with the same name, which could lead to data loss. By default, mv will not ask for confirmation before overwriting files. However, an additional option, mv -i (or mv --interactive), will cause mv to request such confirmation.

Note that mv also works on directories.

Let’s move quotes.txt into the current working directory. We use mv once again, but this time we’ll use just the name of a directory as the second argument to tell mv that we want to keep the filename but put the file somewhere new. (This is why the command is called ‘move’.) In this case, the directory name we use is the special directory name . that we mentioned earlier.

$ mv thesis/quotes.txt .

The effect is to move the file from the directory it was in to the current working directory. ls now shows us that thesis is empty:

$ ls thesis

$

Alternatively, we can confirm the file quotes.txt is no longer present in the thesis directory by explicitly trying to list it:

$ ls thesis/quotes.txt

ls: cannot access 'thesis/quotes.txt': No such file or directory

ls with a filename or directory as an argument only lists the requested file or directory. If the file given as the argument doesn’t exist, the shell returns an error as we saw above. We can use this to see that quotes.txt is now present in our current directory:

$ ls quotes.txt

quotes.txt

Moving Files to a new folder

After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder. The files should have been placed in the raw folder.

$ ls -F
 analyzed/ raw/
$ ls -F analyzed
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed

Fill in the blanks to move these files to the raw/ folder (i.e. the one she forgot to put them in)

$ mv sucrose.dat maltose.dat ____/____

Solution

$ mv sucrose.dat maltose.dat ../raw

Recall that .. refers to the parent directory (i.e. one above the current directory) and that . refers to the current directory.

Copying files and directories

The cp command works very much like mv, except it copies a file instead of moving it. We can check that it did the right thing using ls with two paths as arguments — like most Unix commands, ls can be given multiple paths at once:

$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt

quotes.txt   thesis/quotations.txt

We can also copy a directory and all its contents by using the recursive option -r, e.g. to back up a directory:

$ cp -r thesis thesis_backup

We can check the result by listing the contents of both the thesis and thesis_backup directory:

$ ls thesis thesis_backup

thesis:
quotations.txt

thesis_backup:
quotations.txt

Renaming Files

Suppose that you created a plain-text file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it statstics.txt

After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so?

1. cp statstics.txt statistics.txt
2. mv statstics.txt statistics.txt
3. mv statstics.txt .
4. cp statstics.txt .

Solution

1. No. While this would create a file with the correct name, the incorrectly named file still exists in the directory and would need to be deleted.
2. Yes, this would work to rename the file.
3. No, the period(.) indicates where to move the file, but does not provide a new file name; identical file names cannot be created.
4. No, the period(.) indicates where to copy the file, but does not provide a new file name; identical file names cannot be created.

Moving and Copying

What is the output of the closing ls command in the sequence shown below?

$ pwd

/Users/jamie/data

$ ls

proteins.dat

$ mkdir recombined
$ mv proteins.dat recombined/
$ cp recombined/proteins.dat ../proteins-saved.dat
$ ls

1. proteins-saved.dat recombined
2. recombined
3. proteins.dat recombined
4. proteins-saved.dat

Solution

We start in the /Users/jamie/data directory, and create a new folder called recombined. The second line moves (mv) the file proteins.dat to the new folder (recombined). The third line makes a copy of the file we just moved. The tricky part here is where the file was copied to. Recall that .. means ‘go up a level’, so the copied file is now in /Users/jamie. Notice that .. is interpreted with respect to the current working directory, not with respect to the location of the file being copied. So, the only thing that will show using ls (in /Users/jamie/data) is the recombined folder.

1. No, see explanation above. proteins-saved.dat is located at /Users/jamie
2. Yes
3. No, see explanation above. proteins.dat is located at /Users/jamie/data/recombined
4. No, see explanation above. proteins-saved.dat is located at /Users/jamie

Removing files and directories

Returning to the shell-lesson-data/exercise-data/writing directory, let’s tidy up this directory by removing the quotes.txt file we created. The Unix command we’ll use for this is rm (short for ‘remove’):

$ rm quotes.txt

We can confirm the file has gone using ls:

$ ls quotes.txt

ls: cannot access 'quotes.txt': No such file or directory

Deleting Is Forever

The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unlinked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.

Using rm Safely

What happens when we execute rm -i thesis_backup/quotations.txt? Why would we want this protection when using rm?

Solution

rm: remove regular file 'thesis_backup/quotations.txt'? y

The -i option will prompt before (every) removal (use Y to confirm deletion or N to keep the file). The Unix shell doesn’t have a trash bin, so all the files removed will disappear forever. By using the -i option, we have the chance to check that we are deleting only the files that we want to remove.

If we try to remove the thesis directory using rm thesis, we get an error message:

$ rm thesis

rm: cannot remove `thesis': Is a directory

This happens because rm by default only works on files, not directories.

rm can remove a directory and all its contents if we use the recursive option -r, and it will do so without any confirmation prompts:

$ rm -r thesis

Given that there is no way to retrieve files deleted using the shell, rm -r should be used with great caution (you might consider adding the interactive option rm -r -i).

Operations with multiple files and directories

Oftentimes one needs to copy or move several files at once. This can be done by providing a list of individual filenames, or specifying a naming pattern using wildcards. Wildcards are special characters that can be used to represent unknown characters or sets of characters when navigating the Unix file system.

Copy with Multiple Filenames

For this exercise, you can test the commands in the shell-lesson-data/exercise-data directory.

In the example below, what does cp do when given several filenames and a directory name?

$ mkdir backup
$ cp creatures/minotaur.dat creatures/unicorn.dat backup/

In the example below, what does cp do when given three or more file names?

$ cd creatures
$ ls -F

basilisk.dat  minotaur.dat  unicorn.dat

$ cp minotaur.dat unicorn.dat basilisk.dat

Solution

If given more than one file name followed by a directory name (i.e. the destination directory must be the last argument), cp copies the files to the named directory.

If given three file names, cp throws an error such as the one below, because it is expecting a directory name as the last argument.

cp: target 'basilisk.dat' is not a directory

Using wildcards for accessing multiple files at once

Wildcards

* is a wildcard, which represents zero or more other characters. Let’s consider the shell-lesson-data/exercise-data/alkanes directory: *.pdb represents ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’. On the other hand, p*.pdb only represents pentane.pdb and propane.pdb, because the ‘p’ at the front can only represent filenames that begin with the letter ‘p’.

? is also a wildcard, but it represents exactly one character. So ?ethane.pdb could represent methane.pdb whereas *ethane.pdb represents both ethane.pdb and methane.pdb.

Wildcards can be used in combination with each other. For example, ???ane.pdb indicates three characters followed by ane.pdb, giving cubane.pdb ethane.pdb octane.pdb.

When the shell sees a wildcard, it expands the wildcard to create a list of matching filenames before running the preceding command. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as an argument to the command as it is. For example, typing ls *.pdf in the alkanes directory (which contains only files with names ending with .pdb) results in an error message that there is no file called *.pdf. However, generally commands like wc and ls see the lists of file names matching these expressions, but not the wildcards themselves. It is the shell, not the other programs, that expands the wildcards.

List filenames matching a pattern

When run in the alkanes directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

1. ls *t*ane.pdb
2. ls *t?ne.*
3. ls *t??ne.pdb
4. ls ethane.*

Solution

The solution is 3.

1. shows all files whose names contain zero or more characters (*) followed by the letter t, then zero or more characters (*) followed by ane.pdb. This gives ethane.pdb methane.pdb octane.pdb pentane.pdb.

2. shows all files whose names start with zero or more characters (*) followed by the letter t, then a single character (?), then ne. followed by zero or more characters (*). This will give us octane.pdb and pentane.pdb but doesn’t match anything which ends in thane.pdb.

3. fixes the problems of option 2 by matching two characters (??) between t and ne. This is the solution.

4. only shows files starting with ethane..

More on Wildcards

Sam has a directory containing calibration data, datasets, and descriptions of the datasets:

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   └── datasets
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    └── all_november_files

Before heading off to another field trip, she wants to back up her data and send some datasets to her colleague Bob. Sam uses the following commands to get the job done:

$ cp *dataset* backup/datasets
$ cp ____calibration____ backup/calibration
$ cp 2015-____-____ send_to_bob/all_november_files/
$ cp ____ send_to_bob/all_datasets_created_on_a_23rd/

Help Sam by filling in the blanks.

The resulting directory structure should look like this

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   │   ├── 2015-10-23-calibration.txt
│   │   ├── 2015-10-26-calibration.txt
│   │   └── 2015-11-23-calibration.txt
│   └── datasets
│       ├── 2015-10-23-dataset1.txt
│       ├── 2015-10-23-dataset2.txt
│       ├── 2015-10-23-dataset_overview.txt
│       ├── 2015-10-26-dataset1.txt
│       ├── 2015-10-26-dataset2.txt
│       ├── 2015-10-26-dataset_overview.txt
│       ├── 2015-11-23-dataset1.txt
│       ├── 2015-11-23-dataset2.txt
│       └── 2015-11-23-dataset_overview.txt
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    │   ├── 2015-10-23-dataset1.txt
    │   ├── 2015-10-23-dataset2.txt
    │   ├── 2015-10-23-dataset_overview.txt
    │   ├── 2015-11-23-dataset1.txt
    │   ├── 2015-11-23-dataset2.txt
    │   └── 2015-11-23-dataset_overview.txt
    └── all_november_files
        ├── 2015-11-23-calibration.txt
        ├── 2015-11-23-dataset1.txt
        ├── 2015-11-23-dataset2.txt
        └── 2015-11-23-dataset_overview.txt

Solution

$ cp *calibration.txt backup/calibration
$ cp 2015-11-* send_to_bob/all_november_files/
$ cp *-23-dataset* send_to_bob/all_datasets_created_on_a_23rd/

Organizing Directories and Files

Jamie is working on a project, and she sees that her files aren’t very well organized:

$ ls -F

analyzed/  fructose.dat    raw/   sucrose.dat

The fructose.dat and sucrose.dat files contain output from her data analysis. What command(s) covered in this lesson does she need to run so that the commands below will produce the output shown?

$ ls -F

analyzed/   raw/

$ ls analyzed

fructose.dat    sucrose.dat

Solution

mv *.dat analyzed

Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The shell will expand *.dat to match all .dat files in the current directory. The mv command then moves the list of .dat files to the ‘analyzed’ directory.

Reproduce a folder structure

You’re starting a new experiment and would like to duplicate the directory structure from your previous experiment so you can add new data.

Assume that the previous experiment is in a folder called 2016-05-18, which contains a data folder that in turn contains folders named raw and processed that contain data files. The goal is to copy the folder structure of the 2016-05-18 folder into a folder called 2016-05-20 so that your final directory structure looks like this:

2016-05-20/
└── data
   ├── processed
   └── raw

Which of the following set of commands would achieve this objective? What would the other commands do?

$ mkdir 2016-05-20
$ mkdir 2016-05-20/data
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20/data/raw

$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ cd data
$ mkdir raw processed

$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20/data/processed

$ mkdir -p 2016-05-20/data/raw
$ mkdir -p 2016-05-20/data/processed

$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ mkdir raw processed

Solution

The first two sets of commands achieve this objective. The first set uses relative paths to create the top-level directory before the subdirectories.

The third set of commands will give an error because the default behavior of mkdir won’t create a subdirectory of a non-existent directory: the intermediate level folders must be created first.

The fourth set of commands achieve this objective. Remember, the -p option, followed by a path of one or more directories, will cause mkdir to create any intermediate subdirectories as required.

The final set of commands generates the ‘raw’ and ‘processed’ directories at the same level as the ‘data’ directory.

Key Points

• cp [old] [new] copies a file.

• mkdir [path] creates a new directory.

• mv [old] [new] moves (renames) a file or directory.

• rm [path] removes (deletes) a file.

• * matches zero or more characters in a filename, so *.txt matches all files ending in .txt.

• ? matches any single character in a filename, so ?.txt matches a.txt but not any.txt.

• Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.

• The shell does not have a trash bin: once something is deleted, it’s really gone.

• Most files’ names are something.extension. The extension isn’t required, and doesn’t guarantee anything, but is normally used to indicate the type of data in the file.

• Depending on the type of work you do, you may need a more powerful text editor than Nano.

Break

Overview

Teaching: min
Exercises: min

Questions

Objectives

Key Points

Setting Up Git

Overview

Teaching: 15 min
Exercises: 0 min

Questions

• How do I get set up to use Git?

Objectives

• Configure git the first time it is used on a computer.

• Understand the meaning of the --global configuration flag.

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,
• what our preferred text editor is,
• and that we want to use these settings globally (i.e. for every project).

On a command line, Git commands are written as git verb options, where verb is what we actually want to do and options is additional optional information which may be needed for the verb. Here is how you can setup your user settings:

$ git config --global user.name "Your Name"
$ git config --global user.email "your.email@ucsb.edu"

Please use your own name and email address instead. This user name and email will be associated with your subsequent Git activity, which means that any changes pushed to GitHub, BitBucket, GitLab or another Git host server after this lesson will include this information.

For this lesson, we will be interacting with GitHub and so the email address used should be the same as the one used when setting up your GitHub account. If you are concerned about privacy, please review GitHub’s instructions for keeping your email address private.

Keeping your email private

If you elect to use a private email address with GitHub, then use that same email address for the user.email value, e.g. username@users.noreply.github.com replacing username with your GitHub one.

Line Endings

As with other keys, when you hit Return on your keyboard, your computer encodes this input as a character. Different operating systems use different character(s) to represent the end of a line. (You may also hear these referred to as newlines or line breaks.) Because Git uses these characters to compare files, it may cause unexpected issues when editing a file on different machines. Though it is beyond the scope of this lesson, you can read more about this issue in the Pro Git book.

You can change the way Git recognizes and encodes line endings using the core.autocrlf command to git config. The following settings are recommended:

On macOS and Linux:

$ git config --global core.autocrlf input

And on Windows:

$ git config --global core.autocrlf true

Git uses a text editor for writing commit messages. The following table describes how to set Git to use various editors you may have installed:

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

Exiting Vim

Note that Vim is the default editor for many programs. If you haven’t used Vim before and wish to exit a session without saving your changes, press Esc then type :q! and hit Return. If you want to save your changes and quit, press Esc then type :wq and hit Return.

Git (2.28+) allows configuration of the name of the branch created when you initialize any new repository. To set it to main (so it matches GitHub), use:

$ git config --global init.defaultBranch main

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 legacy of racialized slavery and many Git users prefer a different name for the default branch.

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.

For versions of Git prior to 2.28, the change can be made on an individual repository level. The command for this is in the next episode. Note that if this value is unset in your local Git configuration, the init.defaultBranch value defaults to master.

The five commands we just ran above only need to be run once: the flag --global tells Git to use the settings for every project, in your user account, on this computer.

You can check your settings at any time:

$ git config --list

You can change your configuration as many times as you want: use the same commands to choose another editor or update your email address.

Proxy

In some networks you need to use a proxy. If this is the case, you may also need to tell Git about the proxy:

$ git config --global http.proxy proxy-url
$ git config --global https.proxy proxy-url

To disable the proxy, use

$ git config --global --unset http.proxy
$ git config --global --unset https.proxy

Git Help and Manual

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

$ git config -h
$ git config --help

While viewing the manual, remember the : is a prompt waiting for commands and you can press Q to exit the manual.

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

$ git help

Key Points

• Use git config with the --global option to configure a user name, email address, editor, and other preferences once per machine.

Creating a Repository

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• Where does Git store information?

Objectives

• Create a local Git repository.

• Describe the purpose of the .git directory.

Once Git is configured, we can start using it. The usage we will demonstrate is making a respository for a personal website. Later, we’ll show how you can publish this site on GitHub pages.

First, let’s create a directory in Desktop folder for our work and then move into that directory:

$ cd ~/Desktop
$ mkdir simple-site
$ cd simple-site

Then we tell Git to make simple-site a repository – a place where Git can store versions of our files:

$ git init

It is important to note that git init will create a repository that includes subdirectories and their files—there is no need to create separate repositories nested within the simple-site repository, whether subdirectories are present from the beginning or added later. Also, note that the creation of the simple-site directory and its initialization as a repository are completely separate processes.

If we use ls to show the directory’s contents, it appears that nothing has changed:

$ ls

But if we add the -a flag to show everything, we can see that Git has created a hidden directory within simple-site called .git:

$ ls -a

.	..	.git

Git uses this special subdirectory to store all the information about the project, including all files and sub-directories located within the project’s directory. If we ever delete the .git subdirectory, we will lose the project’s history.

Next, we will change the default branch to be called main. This might be the default branch depending on your settings and version of git. See the setup episode for more information on this change.

# only necessary if default branch is 'master'
git checkout -b main

Switched to a new branch 'main'

We can check that everything is set up correctly by asking Git to tell us the status of our project:

$ git status

On branch main

No commits yet

nothing to commit (create/copy files and use "git add" to track)

If you are using a different version of git, the exact wording of the output might be slightly different.

Key Points

• git init initializes a repository.

• Git stores all of its repository data in the .git directory.

Tracking Changes

Overview

Teaching: 20 min
Exercises: 0 min

Questions

• How do I record changes in Git?

• How do I check the status of my version control repository?

• How do I record notes about what changes I made and why?

Objectives

• Go through the modify-add-commit cycle for one or more files.

• Explain where information is stored at each stage of that cycle.

• Distinguish between descriptive and non-descriptive commit messages.

Adding files

Let’s create a text file called index.md and add it to our repository. The file will later be converted into a webpage by GitHub pages. We’ll write the file using a syntax called Markdown, which is why we use the .md extensions.

Markdown

Markdown is a language used to simplify writing HTML. Plain text characters like # and * are used in place of HTML tags. These characters are then processed (by GitHub pages) and transformed into HTML tags. As the name Markdown suggests, the language has been trimmed down to a minimum. The most frequently used elements, like headings, paragraphs, lists, tables and basic text formatting (i.e. bold, italic) are part of Markdown. Markdown’s simplified syntax keeps content human-readable.

We’ll use nano to edit the file; you can use whatever editor you like. In particular, this does not have to be the core.editor you set globally earlier. But remember, the bash command to create or edit a new file will depend on the editor you choose (it might not be nano). For a refresher on text editors, check out “Which Editor?” in The Unix Shell lesson.

$ nano index.md

Type a few lines about yourself. (Use the # to create a section header).

# Seth Erickson

I am a data services librarian at UCSB

Let’s first verify that the file was properly created by running the list command (ls):

$ ls

index.md

index.md is a text file, which we can see by running:

$ cat index.md

# Seth Erickson

I am a data services librarian at UCSB

If we check the status of our project again, Git tells us that it’s noticed the new file:

$ git status

On branch main

No commits yet

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	index.md

nothing added to commit but untracked files present (use "git add" to track)

The “untracked files” message means that there’s a file in the directory that Git isn’t keeping track of. We can tell Git to track a file using git add:

$ git add index.md

and then check that the right thing happened:

$ git status

On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)
	new file:   index.md

Git now knows that it’s supposed to keep track of index.md, but it hasn’t recorded these changes as a commit yet. To get it to do that, we need to run one more command:

$ git commit -m "adding initial page content (commit #1)"

[main (root-commit) f14106c] adding initial page content (commit #1)
 1 file changed, 3 insertions(+)
 create mode 100644 index.md

When we run git commit, Git takes everything we have told it to save by using git add and stores a copy permanently inside the special .git directory. This permanent copy is called a commit (or revision) and its short identifier is f14106c. Your commit may have another identifier.

We use the -m flag (for “message”) to record a short, descriptive, and specific comment that will help us remember later on what we did and why. If we just run git commit without the -m option, Git will launch nano (or whatever other editor we configured as core.editor) so that we can write a longer message.

Good commit messages start with a brief (<50 characters) statement about the changes made in the commit. Generally, the message should complete the sentence “If applied, this commit will” . If you want to go into more detail, add a blank line between the summary line and your additional notes. Use this additional space to explain why you made changes and/or what their impact will be.

If we run git status now:

$ git status

On branch main
nothing to commit, working directory clean

it tells us everything is up to date. If we want to know what we’ve done recently, we can ask Git to show us the project’s history using git log:

$ git log

commit f14106cb34f6983fa329168c97042739e4deec77 (HEAD -> main)
Author: Seth Erickson <xxx@yyy.com>
Date:   Mon Apr 24 11:01:07 2023 -0700

    adding initial page content (commit #1)

git log lists all commits made to a repository in reverse chronological order. The listing for each commit includes the commit’s full identifier (which starts with the same characters as the short identifier printed by the git commit command earlier), the commit’s author, when it was created, and the log message Git was given when the commit was created.

Where Are My Changes?

If we run ls at this point, we will still see just one file called index.md. That’s because Git saves information about files’ history in the special .git directory mentioned earlier so that our filesystem doesn’t become cluttered (and so that we can’t accidentally edit or delete an old version).

Now let’s add more to index.md. (Again, we’ll edit with nano and then cat the file to show its contents; you may use a different editor, and don’t need to cat.)

$ nano index.md

Let’s add a list of job responsibilities. (In Markdown, a line beginning with a - and space is converted into an HTML list with bullet points.)

# Seth Erickson

I am a data services librarian at UCSB

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

When we run git status now, it tells us that a file it already knows about has been modified:

$ git status

On branch main
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   index.md

no changes added to commit (use "git add" and/or "git commit -a")

The last line is the key phrase: “no changes added to commit”. We have changed this file, but we haven’t told Git we will want to save those changes (which we do with git add) nor have we saved them (which we do with git commit). So let’s do that now. It is good practice to always review our changes before saving them. We do this using git diff. This shows us the differences between the current state of the file and the most recently saved version:

$ git diff

diff --git a/index.md b/index.md
index 9b284ec..c826feb 100644
--- a/index.md
+++ b/index.md
@@ -1,3 +1,9 @@
 # Seth Erickson
 
 I am a data services librarian at UCSB
+
+My responsibilities include:
+
+- Teaching Carpentry Workshops
+- Helping students learn Git
+

The output is cryptic because it is actually a series of commands for tools like editors and patch telling them how to reconstruct one file given the other. If we break it down into pieces:

1. The first line tells us that Git is producing output similar to the Unix diff command comparing the old and new versions of the file.
2. The second line tells exactly which versions of the file Git is comparing; df0654a and 315bf3a are unique computer-generated labels for those versions.
3. The third and fourth lines once again show the name of the file being changed.
4. The remaining lines are the most interesting, they show us the actual differences and the lines on which they occur. In particular, the + marker in the first column shows where we added a line.

After reviewing our change, it’s time to commit it:

$ git commit -m "add list of responsibilities (commit #2)"

On branch main
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   index.md

no changes added to commit (use "git add" and/or "git commit -a")

Whoops: Git won’t commit because we didn’t use git add first. Let’s fix that:

$ git add index.md
$ git commit -m "add list of responsibilities (commit #2)"

[main bc5ac3e] add list of responsibilities (commit #2)
 1 file changed, 6 insertions(+)

Git insists that we add files to the set we want to commit before actually committing anything. This allows us to commit our changes in stages and capture changes in logical portions rather than only large batches. For example, suppose we’re adding a few citations to relevant research to our thesis. We might want to commit those additions, and the corresponding bibliography entries, but not commit some of our work drafting the conclusion (which we haven’t finished yet).

To allow for this, Git has a special staging area where it keeps track of things that have been added to the current changeset but not yet committed.

Staging Area

If you think of Git as taking snapshots of changes over the life of a project, git add specifies what will go in a snapshot (putting things in the staging area), and git commit then actually takes the snapshot, and makes a permanent record of it (as a commit). If you don’t have anything staged when you type git commit, Git will prompt you to use git commit -a or git commit --all, which is kind of like gathering everyone to take a group photo! However, it’s almost always better to explicitly add things to the staging area, because you might commit changes you forgot you made. (Going back to the group photo simile, you might get an extra with incomplete makeup walking on the stage for the picture because you used -a!) Try to stage things manually, or you might find yourself searching for “git undo commit” more than you would like!

Let’s watch as our changes to a file move from our editor to the staging area and into long-term storage. First, let’s make another change: I’ll fix a typo by adding a period to the bio line.

$ nano index.md

# Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

$ git diff

diff --git a/index.md b/index.md
index c826feb..93d5098 100644
--- a/index.md
+++ b/index.md
@@ -1,6 +1,6 @@
 # Seth Erickson
 
-I am a data services librarian at UCSB
+I am a data services librarian at UCSB.
 
 My responsibilities include:

So far, so good. Now let’s put that change in the staging area and see what git diff reports:

$ git add index.md
$ git diff

There is no output: as far as Git can tell, there’s no difference between what it’s been asked to save permanently and what’s currently in the directory. However, if we do this:

$ git diff --staged

diff --git a/index.md b/index.md
index c826feb..93d5098 100644
--- a/index.md
+++ b/index.md
@@ -1,6 +1,6 @@
 # Seth Erickson
 
-I am a data services librarian at UCSB
+I am a data services librarian at UCSB.
 
 My responsibilities include:

it shows us the difference between the last committed change and what’s in the staging area. Let’s save our changes:

$ git commit -m "fixing a typo (commit #3)"

[main d8dd09e] fixing a typo (commit #3)
 1 file changed, 1 insertion(+), 1 deletion(-)

check our status:

$ git status

On branch main
nothing to commit, working directory clean

and look at the history of what we’ve done so far:

$ git log

commit d8dd09e46f76a9e8560d57bd31ba99059eb27bad (HEAD -> main)
Author: Seth Erickson <...>
Date:   Mon Apr 24 11:19:41 2023 -0700

    fixing a typo (commit #3)

commit bc5ac3ec2412f7e4bfb4da2d7085d3df4cc514ea
Author: Seth Erickson <...>
Date:   Mon Apr 24 11:11:40 2023 -0700

    add list of responsibilities (commit #2)

commit f14106cb34f6983fa329168c97042739e4deec77
Author: Seth Erickson <...>
Date:   Mon Apr 24 11:01:07 2023 -0700

    adding initial page content (commit #1)

Word-based diffing

Sometimes, e.g. in the case of the text documents a line-wise diff is too coarse. That is where the --color-words option of git diff comes in very useful as it highlights the changed words using colors.

Paging the Log

When the output of git log is too long to fit in your screen, git uses a program to split it into pages of the size of your screen. When this “pager” is called, you will notice that the last line in your screen is a :, instead of your usual prompt.

• To get out of the pager, press Q.
• To move to the next page, press Spacebar.
• To search for some_word in all pages, press / and type some_word. Navigate through matches pressing N.

Limit Log Size

To avoid having git log cover your entire terminal screen, you can limit the number of commits that Git lists by using -N, where N is the number of commits that you want to view. For example, if you only want information from the last commit you can use:

$ git log -1

commit d8dd09e46f76a9e8560d57bd31ba99059eb27bad (HEAD -> main)
Author: Seth Erickson <...>
Date:   Mon Apr 24 11:19:41 2023 -0700

    fixing a typo (commit #3)
(END)

You can also reduce the quantity of information using the --oneline option:

$ git log --oneline

d8dd09e (HEAD -> main) fixing a typo (commit #3)
bc5ac3e add list of responsibilities (commit #2)
f14106c adding initial page content (commit #1)

You can also combine the --oneline option with others. One useful combination adds --graph to display the commit history as a text-based graph and to indicate which commits are associated with the current HEAD, the current branch main, or other Git references:

$ git log --oneline --graph

* d8dd09e (HEAD -> main) fixing a typo (commit #3)
* bc5ac3e add list of responsibilities (commit #2)
* f14106c adding initial page content (commit #1)

Directories in Git

Two important facts you should know about directories in Git:

1. Git does not track directories on their own, only files within them.
2. If you can create a directory in your Git repository and populate it with files, you can add all the files in the directory at once.

Create a new directory named images We will be using this directory in the following lessons so please follow along.

$ mkdir images
$ git status
$ git add images
$ git status

Note, our newly created empty directory images does not appear in the list of untracked files even if we explicitly add it (via git add) to our repository. This is the reason why you will sometimes see .gitkeep files in otherwise empty directories. Unlike .gitignore, these files are not special and their sole purpose is to populate a directory so that Git adds it to the repository. In fact, you can name such files anything you like.

Try adding an empty file in our new directory:

$ touch images/.gitkeep
$ git status
$ git add images
$ git status

Before moving on, we will commit these changes.

$ git commit -m "Add images folder"

To recap, when we want to add changes to our repository, we first need to add the changed files to the staging area (git add) and then commit the staged changes to the repository (git commit):

Committing Changes to Git

Which command(s) below would save the changes of myfile.txt to my local Git repository?

1. $ git commit -m "my recent changes"
   

2. $ git init myfile.txt
   $ git commit -m "my recent changes"
   

3. $ git add myfile.txt
   $ git commit -m "my recent changes"
   

4. $ git commit -m myfile.txt "my recent changes"
   

Solution

1. Would only create a commit if files have already been staged.
2. Would try to create a new repository.
3. Is correct: first add the file to the staging area, then commit.
4. Would try to commit a file “my recent changes” with the message myfile.txt.

Committing Multiple Files

The staging area can hold changes from any number of files that you want to commit as a single snapshot. The goals for the rest of this lesson are:

1. Add some text to index.md
2. Create a new file reading-list.md with a list of books you want to read
3. Add changes from both files to the staging area, and commit those changes.

You can add both files to the staging area. We can do that in one line:

$ git add index.md reading-list.md

Or with multiple commands:

$ git add index.md
$ git add reading-list.md

Now the files are ready to commit. You can check that using git status. If you are ready to commit use:

$ git commit -m "update page and add reading list"

[main 86abfdb] add reading list
 2 files changed, 2 insertions(+)
 create mode 100644 reading-list.md

Key Points

• git status shows the status of a repository.

• Files can be stored in a project’s working directory (which users see), the staging area (where the next commit is being built up) and the local repository (where commits are permanently recorded).

• git add puts files in the staging area.

• git commit saves the staged content as a new commit in the local repository.

• Write a commit message that accurately describes your changes.

Exploring History

Overview

Teaching: 25 min
Exercises: 0 min

Questions

• How can I identify old versions of files?

• How do I review my changes?

• How can I recover old versions of files?

Objectives

• Explain what the HEAD of a repository is and how to use it.

• Identify and use Git commit numbers.

• Compare various versions of tracked files.

• Restore old versions of files.

As we saw in the previous episode, we can refer to commits by their identifiers. You can refer to the most recent commit of the working branch by using the identifier HEAD.

To illustrate, let’s make a change to index.md.

$ nano index.md
$ cat index.md

# Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

Contact: <my email>

Now, let’s see what we get.

$ git diff HEAD index.md

diff --git a/index.md b/index.md
index d9f35ba..f9d4112 100644
--- a/index.md
+++ b/index.md
@@ -8,3 +8,5 @@ My responsibilities include:
 - Helping students learn Git
 
 See my [reading list](reading-list.html).
+
+Contact: serickson@ucsb.edu

which is the same as what you would get if you leave out HEAD (try it). The real goodness in all this is when you can refer to previous commits. We do that by adding ~1 (where “~” is “tilde”, pronounced [til-duh]) to refer to the commit one before HEAD.

$ git diff HEAD~1 index.md

If we want to see the differences between older commits we can use git diff again, but with the notation HEAD~1, HEAD~2, and so on, to refer to them:

$ git diff HEAD~2 index.md

diff --git a/index.md b/index.md
index 93d5098..f9d4112 100644
--- a/index.md
+++ b/index.md
@@ -7,3 +7,6 @@ My responsibilities include:
 - Teaching Carpentry Workshops
 - Helping students learn Git
 
+See my [reading list](reading-list.html).
+
+Contact: serickson@ucsb.edu

We could also use git show which shows us what changes we made at an older commit as well as the commit message, rather than the differences between a commit and our working directory that we see by using git diff.

$ git show HEAD~2 index.md

commit d8dd09e46f76a9e8560d57bd31ba99059eb27bad
Author: Seth Erickson <sr.erickson@gmail.com>
Date:   Mon Apr 24 11:19:41 2023 -0700

    fixing a typo (commit #3)

diff --git a/index.md b/index.md
index c826feb..93d5098 100644
--- a/index.md
+++ b/index.md
@@ -1,6 +1,6 @@
 # Seth Erickson
 
-I am a data services librarian at UCSB
+I am a data services librarian at UCSB.
 
 My responsibilities include:

In this way, we can build up a chain of commits. The most recent end of the chain is referred to as HEAD; we can refer to previous commits using the ~ notation, so HEAD~1 means “the previous commit”, while HEAD~123 goes back 123 commits from where we are now.

We can also refer to commits using those long strings of digits and letters that git log displays. These are unique IDs for the changes, and “unique” really does mean unique: every change to any set of files on any computer has a unique 40-character identifier. Our HEAD~2 comment addition was given the ID 7f9e4987af8d390eac5205e9a760e3f72204041c, so let’s try this:

$ git diff d8dd09e46f76a9e8560d57bd31ba99059eb27bad index.md

diff --git a/index.md b/index.md
index 93d5098..f9d4112 100644
--- a/index.md
+++ b/index.md
@@ -7,3 +7,6 @@ My responsibilities include:
 - Teaching Carpentry Workshops
 - Helping students learn Git
 
+See my [reading list](reading-list.html).
+
+Contact: serickson@ucsb.edu

That’s the right answer, but typing out random 40-character strings is annoying, so Git lets us use just the first few characters (typically seven for normal size projects):

$ git diff d8dd09e index.md

diff --git a/index.md b/index.md
index 93d5098..f9d4112 100644
--- a/index.md
+++ b/index.md
@@ -7,3 +7,6 @@ My responsibilities include:
 - Teaching Carpentry Workshops
 - Helping students learn Git
 
+See my [reading list](reading-list.html).
+
+Contact: serickson@ucsb.edu

All right! So we can save changes to files and see what we’ve changed. Now, how can we restore older versions of things? Let’s suppose we change our mind about the last update to index.md (the “ill-considered change”).

git status now tells us that the file has been changed, but those changes haven’t been staged:

$ git status

On branch main
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   index.md

no changes added to commit (use "git add" and/or "git commit -a")

We can put things back the way they were by using git checkout:

$ git checkout HEAD index.md
$ cat index.md

# Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

As you might guess from its name, git checkout checks out (i.e., restores) an old version of a file. In this case, we’re telling Git that we want to recover the version of the file recorded in HEAD, which is the last saved commit. If we want to go back even further, we can use a commit identifier instead:

$ git checkout f14106 index.md

$ cat index.md

$ git status

On branch main
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

    modified:   index.md

Notice that the changes are currently in the staging area. Again, we can put things back the way they were by using git checkout:

$ git checkout HEAD index.md

Don’t Lose Your HEAD

Above we used

$ git checkout f14106 index.md

to revert index.md to its state after the commit f14106. But be careful! The command checkout has other important functionalities and Git will misunderstand your intentions if you are not accurate with the typing. For example, if you forget index.md in the previous command.

$ git checkout f14106

Note: checking out '94456da'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

 git checkout -b <new-branch-name>

HEAD is now at 94456da

The “detached HEAD” is like “look, but don’t touch” here, so you shouldn’t make any changes in this state. After investigating your repo’s past state, reattach your HEAD with git checkout main.

It’s important to remember that we must use the commit number that identifies the state of the repository before the change we’re trying to undo. A common mistake is to use the number of the commit in which we made the change we’re trying to discard. In the example below, we want to retrieve the state from before the most recent commit (HEAD~1), which is commit 94456da:

So, to put it all together, here’s how Git works in cartoon form:

Simplifying the Common Case

If you read the output of git status carefully, you’ll see that it includes this hint:

(use "git checkout -- <file>..." to discard changes in working directory)

As it says, git checkout without a version identifier restores files to the state saved in HEAD. The double dash -- is needed to separate the names of the files being recovered from the command itself: without it, Git would try to use the name of the file as the commit identifier.

The fact that files can be reverted one by one tends to change the way people organize their work. If everything is in one large document, it’s hard (but not impossible) to undo changes to the introduction without also undoing changes made later to the conclusion. If the introduction and conclusion are stored in separate files, on the other hand, moving backward and forward in time becomes much easier.

Recovering Older Versions of a File

Jennifer has made changes to the Python script that she has been working on for weeks, and the modifications she made this morning “broke” the script and it no longer runs. She has spent ~ 1hr trying to fix it, with no luck…

Luckily, she has been keeping track of her project’s versions using Git! Which commands below will let her recover the last committed version of her Python script called data_cruncher.py?

1. $ git checkout HEAD

2. $ git checkout HEAD data_cruncher.py

3. $ git checkout HEAD~1 data_cruncher.py

4. $ git checkout <unique ID of last commit> data_cruncher.py

5. Both 2 and 4

Solution

The answer is (5)-Both 2 and 4.

The checkout command restores files from the repository, overwriting the files in your working directory. Answers 2 and 4 both restore the latest version in the repository of the file data_cruncher.py. Answer 2 uses HEAD to indicate the latest, whereas answer 4 uses the unique ID of the last commit, which is what HEAD means.

Answer 3 gets the version of data_cruncher.py from the commit before HEAD, which is NOT what we wanted.

Answer 1 can be dangerous! Without a filename, git checkout will restore all files in the current directory (and all directories below it) to their state at the commit specified. This command will restore data_cruncher.py to the latest commit version, but it will also restore any other files that are changed to that version, erasing any changes you may have made to those files! As discussed above, you are left in a detached HEAD state, and you don’t want to be there.

Reverting a Commit

Jennifer is collaborating with colleagues on her Python script. She realizes her last commit to the project’s repository contained an error, and wants to undo it. Jennifer wants to undo correctly so everyone in the project’s repository gets the correct change. The command git revert [erroneous commit ID] will create a new commit that reverses the erroneous commit.

The command git revert is different from git checkout [commit ID] because git checkout returns the files not yet committed within the local repository to a previous state, whereas git revert reverses changes committed to the local and project repositories.

Below are the right steps and explanations for Jennifer to use git revert, what is the missing command?

1. ________ # Look at the git history of the project to find the commit ID

2. Copy the ID (the first few characters of the ID, e.g. 0b1d055).

3. git revert [commit ID]

4. Type in the new commit message.

5. Save and close

Solution

The command git log lists project history with commit IDs.

The command git show HEAD shows changes made at the latest commit, and lists the commit ID; however, Jennifer should double-check it is the correct commit, and no one else has committed changes to the repository.

Understanding Workflow and History

What is the output of the last command in

$ cd loops
$ echo "you can loop through lists and sequences" > notes-for-loop.txt
$ git add notes-for-loop.txt
$ echo "You can also nest loops inside another." >> notes-for-loop.txt
$ git commit -m "More notes on loops"
$ git checkout HEAD notes-for-loop.txt
$ cat notes-for-loop.txt #this will print the contents

1. For loops start with `for` and ends with `done`.
   

2. you can loop through lists and sequences
   

3. For loops start with `for` and ends with `done`.
   You can loop through lists and sequences.
   

4. Error because you have changed notes-for-loop.txt without committing the changes
   

Solution

The answer is 2.

The command git add notes-for-loop.txt places the current version of notes-for-loop.txt into the staging area. The changes to the file from the second echo command are only applied to the working copy, not the version in the staging area.

So, when git commit -m "More notes on loops" is executed, the version of notes-for-loop.txt committed to the repository is the one from the staging area and has only one line.

At this time, the working copy still has the second line (and git status will show that the file is modified). However, git checkout HEAD notes-for-loop.txt replaces the working copy with the most recently committed version of notes-for-loop.txt.

So, notes-for-loop.txt will output

 For loops start with `for` and ends with `done`.

Checking Understanding of git diff

Consider this command: git diff HEAD~9 index.md. What do you predict this command will do if you execute it? What happens when you do execute it? Why?

Try another command, git diff [ID] index.md, where [ID] is replaced with the unique identifier for your most recent commit. What do you think will happen, and what does happen?

Getting Rid of Staged Changes

git checkout can be used to restore a previous commit when unstaged changes have been made, but will it also work for changes that have been staged but not committed? Make a change to index.md, add that change, and use git checkout to see if you can remove your change.

Explore and Summarize Histories

Exploring history is an important part of Git, and often it is a challenge to find the right commit ID, especially if the commit is from several months ago.

Imagine the shell-scripts project has more than 50 files. You would like to find a commit that modifies some specific text in index.md. When you type git log, a very long list appeared. How can you narrow down the search?

Recall that the git diff command allows us to explore one specific file, e.g., git diff index.md. We can apply a similar idea here.

$ git log index.md

Unfortunately some of these commit messages are very ambiguous, e.g., update files. How can you search through these files?

Both git diff and git log are very useful and they summarize a different part of the history for you. Is it possible to combine both? Let’s try the following:

$ git log --patch index.md

You should get a long list of output, and you should be able to see both commit messages and the difference between each commit.

Question: What does the following command do?

$ git log --patch HEAD~9 *.txt

Key Points

• git diff displays differences between commits.

• git checkout recovers old versions of files.

Ignoring Things

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• How can I tell Git to ignore files I don’t want to track?

Objectives

• Configure Git to ignore specific files.

• Explain why ignoring files can be useful.

What if we have files that we do not want Git to track for us, like backup files created by our editor or intermediate files created during data analysis? Let’s create a few dummy files:

$ mkdir results
$ touch a.dat b.dat c.dat results/a.out results/b.out

and see what Git says:

$ git status

On branch main
Untracked files:
  (use "git add <file>..." to include in what will be committed)

	a.dat
	b.dat
	c.dat
	results/

nothing added to commit but untracked files present (use "git add" to track)

Putting these files under version control would be a waste of disk space. What’s worse, having them all listed could distract us from changes that actually matter, so let’s tell Git to ignore them.

We do this by creating a file in the root directory of our project called .gitignore:

$ nano .gitignore
$ cat .gitignore

*.dat
results/

These patterns tell Git to ignore any file whose name ends in .dat and everything in the results directory. (If any of these files were already being tracked, Git would continue to track them.)

Once we have created this file, the output of git status is much cleaner:

$ git status

On branch main
Untracked files:
  (use "git add <file>..." to include in what will be committed)

	.gitignore

nothing added to commit but untracked files present (use "git add" to track)

The only thing Git notices now is the newly-created .gitignore file. You might think we wouldn’t want to track it, but everyone we’re sharing our repository with will probably want to ignore the same things that we’re ignoring. Let’s add and commit .gitignore:

$ git add .gitignore
$ git commit -m "Ignore data files and the results folder."
$ git status

On branch main
nothing to commit, working directory clean

As a bonus, using .gitignore helps us avoid accidentally adding to the repository files that we don’t want to track:

$ git add a.dat

The following paths are ignored by one of your .gitignore files:
a.dat
Use -f if you really want to add them.

If we really want to override our ignore settings, we can use git add -f to force Git to add something. For example, git add -f a.dat. We can also always see the status of ignored files if we want:

$ git status --ignored

On branch main
Ignored files:
 (use "git add -f <file>..." to include in what will be committed)

        a.dat
        b.dat
        c.dat
        results/

nothing to commit, working directory clean

Ignoring Nested Files

Given a directory structure that looks like:

results/data
results/plots

How would you ignore only results/plots and not results/data?

Solution

If you only want to ignore the contents of results/plots, you can change your .gitignore to ignore only the /plots/ subfolder by adding the following line to your .gitignore:

results/plots/

This line will ensure only the contents of results/plots is ignored, and not the contents of results/data.

As with most programming issues, there are a few alternative ways that one may ensure this ignore rule is followed. The “Ignoring Nested Files: Variation” exercise has a slightly different directory structure that presents an alternative solution. Further, the discussion page has more detail on ignore rules.

Including Specific Files

How would you ignore all .dat files in your root directory except for final.dat? Hint: Find out what ! (the exclamation point operator) does

Solution

You would add the following two lines to your .gitignore:

*.dat           # ignore all data files
!final.dat      # except final.data

The exclamation point operator will include a previously excluded entry.

Note also that because you’ve previously committed .dat files in this lesson they will not be ignored with this new rule. Only future additions of .dat files added to the root directory will be ignored.

Ignoring Nested Files: Variation

Given a directory structure that looks similar to the earlier Nested Files exercise, but with a slightly different directory structure:

results/data
results/images
results/plots
results/analysis

How would you ignore all of the contents in the results folder, but not results/data?

Hint: think a bit about how you created an exception with the ! operator before.

Solution

If you want to ignore the contents of results/ but not those of results/data/, you can change your .gitignore to ignore the contents of results folder, but create an exception for the contents of the results/data subfolder. Your .gitignore would look like this:

results/*               # ignore everything in results folder
!results/data/          # do not ignore results/data/ contents

Ignoring all data Files in a Directory

Assuming you have an empty .gitignore file, and given a directory structure that looks like:

results/data/position/gps/a.dat
results/data/position/gps/b.dat
results/data/position/gps/c.dat
results/data/position/gps/info.txt
results/plots

What’s the shortest .gitignore rule you could write to ignore all .dat files in result/data/position/gps? Do not ignore the info.txt.

Solution

Appending results/data/position/gps/*.dat will match every file in results/data/position/gps that ends with .dat. The file results/data/position/gps/info.txt will not be ignored.

Ignoring all data Files in the repository

Let us assume you have many .dat files in different subdirectories of your repository. For example, you might have:

results/a.dat
data/experiment_1/b.dat
data/experiment_2/c.dat
data/experiment_2/variation_1/d.dat

How do you ignore all the .dat files, without explicitly listing the names of the corresponding folders?

Solution

In the .gitignore file, write:

**/*.dat               

This will ignore all the .dat files, regardless of their position in the directory tree. You can still include some specific exception with the exclamation point operator.

The Order of Rules

Given a .gitignore file with the following contents:

*.dat
!*.dat

What will be the result?

Solution

The ! modifier will negate an entry from a previously defined ignore pattern. Because the !*.dat entry negates all of the previous .dat files in the .gitignore, none of them will be ignored, and all .dat files will be tracked.

Log Files

You wrote a script that creates many intermediate log-files of the form log_01, log_02, log_03, etc. You want to keep them but you do not want to track them through git.

1. Write one .gitignore entry that excludes files of the form log_01, log_02, etc.

2. Test your “ignore pattern” by creating some dummy files of the form log_01, etc.

3. You find that the file log_01 is very important after all, add it to the tracked files without changing the .gitignore again.

4. Discuss with your neighbor what other types of files could reside in your directory that you do not want to track and thus would exclude via .gitignore.

Solution

1. append either log_* or log* as a new entry in your .gitignore
2. track log_01 using git add -f log_01

Key Points

• The .gitignore file tells Git what files to ignore.

Remotes in GitHub

Overview

Teaching: 30 min
Exercises: 0 min

Questions

• How do I share my changes with others on the web?

Objectives

• Explain what remote repositories are and why they are useful.

• Push to or pull from a remote repository.

Version control really comes into its own when we begin to collaborate with other people. We already have most of the machinery we need to do this; the only thing missing is to copy changes from one repository to another.

Systems like Git allow us to move work between any two repositories. In practice, though, it’s easiest to use one copy as a central hub, and to keep it on the web rather than on someone’s laptop. Most programmers use hosting services like GitHub, Bitbucket or GitLab to hold those main copies; we’ll explore the pros and cons of this in a later episode.

Let’s start by sharing the changes we’ve made to our current project with the world. Log in to GitHub, then click on the icon in the top right corner to create a new repository called simple-site:

Name your repository “simple-site” and then click “Create Repository”.

Note: Since this repository will be connected to a local repository, it needs to be empty. Leave “Initialize this repository with a README” unchecked, and keep “None” as options for both “Add .gitignore” and “Add a license.” See the “GitHub License and README files” exercise below for a full explanation of why the repository needs to be empty.

As soon as the repository is created, GitHub displays a page with a URL and some information on how to configure your local repository:

This effectively does the following on GitHub’s servers:

$ mkdir simple-site
$ cd simple-site
$ git init

If you remember back to the earlier episode where we added and committed our earlier work on index.md, we had a diagram of the local repository which looked like this:

Now that we have two repositories, we need a diagram like this:

Note that our local repository still contains our earlier work on index.md, but the remote repository on GitHub appears empty as it doesn’t contain any files yet.

The next step is to connect the two repositories. We do this by making the GitHub repository a remote for the local repository. The home page of the repository on GitHub includes the string we need to identify it:

Click on the ‘SSH’ link to change the protocol from HTTPS to SSH.

HTTPS vs. SSH

We use SSH here because, while it requires some additional configuration, it is a security protocol widely used by many applications. The steps below describe SSH at a minimum level for GitHub. A supplemental episode to this lesson discusses advanced setup and concepts of SSH and key pairs, and other material supplemental to git related SSH.

Copy that URL from the browser, go into the local simple-site repository, and run this command:

$ git remote add origin git@github.com:user.name/simple-site.git

Make sure to use the URL for your repository rather than user.name: the only difference should be your username instead of user.name.

origin is a local name used to refer to the remote repository. It could be called anything, but origin is a convention that is often used by default in git and GitHub, so it’s helpful to stick with this unless there’s a reason not to.

We can check that the command has worked by running git remote -v:

$ git remote -v

origin   git@github.com:user.name/simple-site.git (fetch)
origin   git@github.com:user.name/simple-site.git (push)

We’ll discuss remotes in more detail in the next episode, while talking about how they might be used for collaboration.

SSH Background and Setup

Before we can connect to a remote repository, we needs to set up a way for the computer to authenticate with GitHub so it knows it’s us trying to connect to the remote repository.

We are going to set up the method that is commonly used by many different services to authenticate access on the command line. This method is called Secure Shell Protocol (SSH). SSH is a cryptographic network protocol that allows secure communication between computers using an otherwise insecure network.

SSH uses what is called a key pair. This is two keys that work together to validate access. One key is publicly known and called the public key, and the other key called the private key is kept private. Very descriptive names.

You can think of the public key as a padlock, and only you have the key (the private key) to open it. You use the public key where you want a secure method of communication, such as your GitHub account. You give this padlock, or public key, to GitHub and say “lock the communications to my account with this so that only computers that have my private key can unlock communications and send git commands as my GitHub account.”

What we will do now is the minimum required to set up the SSH keys and add the public key to a GitHub account.

Advanced SSH

A supplemental episode in this lesson discusses SSH and key pairs in more depth and detail.

The first thing we are going to do is check if this has already been done on the computer you’re on. Because generally speaking, this setup only needs to happen once and then you can forget about it.

Keeping your keys secure

You shouldn’t really forget about your SSH keys, since they keep your account secure. It’s good practice to audit your secure shell keys every so often. Especially if you are using multiple computers to access your account.

We will run the list command to check what key pairs already exist on your computer.

ls -al ~/.ssh

Your output is going to look a little different depending on whether or not SSH has ever been set up on the computer you are using.

In this example, we have not set up SSH on this computer, so the output is

ls: cannot access '/c/Users/user.name/.ssh': No such file or directory

If SSH has been set up on the computer you’re using, the public and private key pairs will be listed. The file names are either id_ed25519/id_ed25519.pub or id_rsa/id_rsa.pub depending on how the key pairs were set up.

Since they don’t exist on this computer, we can use this command to create them:

$ ssh-keygen -t ed25519 -C "user@ucsb.edu"

If you are using a legacy system that doesn’t support the Ed25519 algorithm, use: $ ssh-keygen -t rsa -b 4096 -C "your_email@example.com"

Generating public/private ed25519 key pair.
Enter file in which to save the key (/c/Users/user.name/.ssh/id_ed25519):

We want to use the default file, so just press Enter.

Created directory '/c/Users/user.name We/.ssh'.
Enter passphrase (empty for no passphrase):

Now, it is prompting us for a passphrase. Since we is using this lab’s laptop that other people sometimes have access to, we want to create a passphrase. Be sure to use something memorable or save your passphrase somewhere, as there is no “reset my password” option.

Enter same passphrase again:

After entering the same passphrase a second time, we receive the confirmation

Your identification has been saved in /c/Users/user.name/.ssh/id_ed25519
Your public key has been saved in /c/Users/user.name/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:SMSPIStNyA00KPxuYu94KpZgRAYjgt9g4BA4kFy3g1o user@ucsb.edu
The key's randomart image is:
+--[ED25519 256]--+
|^B== o.          |
|%*=.*.+          |
|+=.E =.+         |
| .=.+.o..        |
|....  . S        |
|.+ o             |
|+ =              |
|.o.o             |
|oo+.             |
+----[SHA256]-----+

The “identification” is actually the private key. You should never share it. The public key is appropriately named. The “key fingerprint” is a shorter version of a public key.

Now that we have generated the SSH keys, we will find the SSH files when we check.

ls -al ~/.ssh

drwxr-xr-x 1 user.name 197121   0 Jul 16 14:48 ./
drwxr-xr-x 1 user.name 197121   0 Jul 16 14:48 ../
-rw-r--r-- 1 user.name 197121 419 Jul 16 14:48 id_ed25519
-rw-r--r-- 1 user.name 197121 106 Jul 16 14:48 id_ed25519.pub

Now we run the command to check if GitHub can read our authentication.

ssh -T git@github.com

The authenticity of host 'github.com (192.30.255.112)' can't be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
This key is not known by any other names
Are you sure you want to continue connecting (yes/no/[fingerprint])? y
Please type 'yes', 'no' or the fingerprint: yes
Warning: Permanently added 'github.com' (RSA) to the list of known hosts.
git@github.com: Permission denied (publickey).

Right, we forgot that we need to give GitHub our public key!

First, we need to copy the public key. Be sure to include the .pub at the end, otherwise you’re looking at the private key.

cat ~/.ssh/id_ed25519.pub

ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIDmRA3d51X0uu9wXek559gfn6UFNF69yZjChyBIU2qKI user@ucsb.edu

Now, going to GitHub.com, click on your profile icon in the top right corner to get the drop-down menu. Click “Settings,” then on the settings page, click “SSH and GPG keys,” on the left side “Account settings” menu. Click the “New SSH key” button on the right side. Now, you can add the title (here, we use the title “User’s Lab Laptop” so we can remember where the original key pair files are located), paste your SSH key into the field, and click the “Add SSH key” to complete the setup.

Now that we’ve set that up, let’s check our authentication again from the command line.

$ ssh -T git@github.com

Hi User.name! You've successfully authenticated, but GitHub does not provide shell access.

Push local changes to a remote

Now that authentication is setup, we can return to the remote. This command will push the changes from our local repository to the repository on GitHub:

$ git push origin main

Since we set up a passphrase, it will prompt us for it. If you completed advanced settings for your authentication, it will not prompt for a passphrase.

Enumerating objects: 16, done.
Counting objects: 100% (16/16), done.
Delta compression using up to 8 threads.
Compressing objects: 100% (11/11), done.
Writing objects: 100% (16/16), 1.45 KiB | 372.00 KiB/s, done.
Total 16 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), done.
To https://github.com/user.name/simple-site.git
 * [new branch]      main -> main

Proxy

If the network you are connected to uses a proxy, there is a chance that your last command failed with “Could not resolve hostname” as the error message. To solve this issue, you need to tell Git about the proxy:

$ git config --global http.proxy http://user:password@proxy.url
$ git config --global https.proxy https://user:password@proxy.url

When you connect to another network that doesn’t use a proxy, you will need to tell Git to disable the proxy using:

$ git config --global --unset http.proxy
$ git config --global --unset https.proxy

Password Managers

If your operating system has a password manager configured, git push will try to use it when it needs your username and password. For example, this is the default behavior for Git Bash on Windows. If you want to type your username and password at the terminal instead of using a password manager, type:

$ unset SSH_ASKPASS

in the terminal, before you run git push. Despite the name, Git uses SSH_ASKPASS for all credential entry, so you may want to unset SSH_ASKPASS whether you are using Git via SSH or https.

You may also want to add unset SSH_ASKPASS at the end of your ~/.bashrc to make Git default to using the terminal for usernames and passwords.

Our local and remote repositories are now in this state:

The ‘-u’ Flag

You may see a -u option used with git push in some documentation. This option is synonymous with the --set-upstream-to option for the git branch command, and is used to associate the current branch with a remote branch so that the git pull command can be used without any arguments. To do this, simply use git push -u origin main once the remote has been set up.

We can pull changes from the remote repository to the local one as well:

$ git pull origin main

From https://github.com/user.name/simple-site
 * branch            main     -> FETCH_HEAD
Already up-to-date.

Pulling has no effect in this case because the two repositories are already synchronized. If someone else had pushed some changes to the repository on GitHub, though, this command would download them to our local repository.

GitHub GUI

Browse to your simple-site repository on GitHub. Under the Code tab, find and click on the text that says “XX commits” (where “XX” is some number). Hover over, and click on, the three buttons to the right of each commit. What information can you gather/explore from these buttons? How would you get that same information in the shell?

Solution

The left-most button (with the picture of a clipboard) copies the full identifier of the commit to the clipboard. In the shell, git log will show you the full commit identifier for each commit.

When you click on the middle button, you’ll see all of the changes that were made in that particular commit. Green shaded lines indicate additions and red ones removals. In the shell we can do the same thing with git diff. In particular, git diff ID1..ID2 where ID1 and ID2 are commit identifiers (e.g. git diff a3bf1e5..041e637) will show the differences between those two commits.

The right-most button lets you view all of the files in the repository at the time of that commit. To do this in the shell, we’d need to checkout the repository at that particular time. We can do this with git checkout ID where ID is the identifier of the commit we want to look at. If we do this, we need to remember to put the repository back to the right state afterwards!

Uploading files directly in GitHub browser

Github also allows you to skip the command line and upload files directly to your repository without having to leave the browser. There are two options. First you can click the “Upload files” button in the toolbar at the top of the file tree. Or, you can drag and drop files from your desktop onto the file tree. You can read more about this on this GitHub page

GitHub Timestamp

Create a remote repository on GitHub. Push the contents of your local repository to the remote. Make changes to your local repository and push these changes. Go to the repo you just created on GitHub and check the timestamps of the files. How does GitHub record times, and why?

Solution

GitHub displays timestamps in a human readable relative format (i.e. “22 hours ago” or “three weeks ago”). However, if you hover over the timestamp, you can see the exact time at which the last change to the file occurred.

Push vs. Commit

In this episode, we introduced the “git push” command. How is “git push” different from “git commit”?

Solution

When we push changes, we’re interacting with a remote repository to update it with the changes we’ve made locally (often this corresponds to sharing the changes we’ve made with others). Commit only updates your local repository.

GitHub License and README files

In this episode we learned about creating a remote repository on GitHub, but when you initialized your GitHub repo, you didn’t add a README.md or a license file. If you had, what do you think would have happened when you tried to link your local and remote repositories?

Solution

In this case, we’d see a merge conflict due to unrelated histories. When GitHub creates a README.md file, it performs a commit in the remote repository. When you try to pull the remote repository to your local repository, Git detects that they have histories that do not share a common origin and refuses to merge.

$ git pull origin main

warning: no common commits
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/user.name/simple-site
 * branch            main     -> FETCH_HEAD
 * [new branch]      main     -> origin/main
fatal: refusing to merge unrelated histories

You can force git to merge the two repositories with the option --allow-unrelated-histories. Be careful when you use this option and carefully examine the contents of local and remote repositories before merging.

$ git pull --allow-unrelated-histories origin main

From https://github.com/user.name/simple-site
 * branch            main     -> FETCH_HEAD
Merge made by the 'recursive' strategy.
README.md | 1 +
1 file changed, 1 insertion(+)
create mode 100644 README.md

Key Points

• A local Git repository can be connected to one or more remote repositories.

• Use the SSH protocol to connect to remote repositories.

• git push copies changes from a local repository to a remote repository.

• git pull copies changes from a remote repository to a local repository.

Break

Overview

Teaching: min
Exercises: min

Questions

Objectives

Key Points

Collaborating

Overview

Teaching: 40 min
Exercises: 0 min

Questions

• How can I use version control to collaborate with other people?

Objectives

• Clone a remote repository.

• Collaborate by pushing to a common repository.

• Describe the basic collaborative workflow.

For the next step, get into pairs. One person will be the “Owner” and the other will be the “Collaborator”. The goal is that the Collaborator add changes into the Owner’s repository. We will switch roles at the end, so both persons will play Owner and Collaborator.

Practicing By Yourself

If you’re working through this lesson on your own, you can carry on by opening a second terminal window. This window will represent your partner, working on another computer. You won’t need to give anyone access on GitHub, because both ‘partners’ are you.

The Owner needs to give the Collaborator access. On GitHub, click the settings button on the right, select Manage access, click Invite a collaborator, and then enter your partner’s username.

To accept access to the Owner’s repo, the Collaborator needs to go to https://github.com/notifications. Once there she can accept access to the Owner’s repo.

Next, the Collaborator needs to download a copy of the Owner’s repository to her machine. This is called “cloning a repo”.

To clone the Owner’s repo into her Desktop folder, the Collaborator enters:

$ git clone https://github.com/User/simple-site.git ~/Desktop/user.name-simple-site

Replace ‘user name’ with the Owner’s username or name.

If you choose to clone without the clone path (~/Desktop/user.name-simple-site) specified at the end, you will clone inside your own simple-site folder! Make sure to navigate to the Desktop folder first.

The Collaborator can now make a change in her clone of the Owner’s repository, exactly the same way as we’ve been doing before. Let’s add ‘front matter’ used by github pages.

$ cd ~/Desktop/user.name-simple-site
$ nano index.md
$ cat index.md

---
title: Home
---
# Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

$ git add index.md
$ git commit -m "add frontmatter change"

 1 file changed, 1 insertions(+)

Then push the change to the Owner’s repository on GitHub:

$ git push origin main

Enumerating objects: 4, done.
Counting objects: 4, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (2/2), done.
Writing objects: 100% (3/3), 306 bytes, done.
Total 3 (delta 0), reused 0 (delta 0)
To https://github.com/user/simple-site.git
   9272da5..29aba7c  main -> main

Note that we didn’t have to create a remote called origin: Git uses this name by default when we clone a repository. (This is why origin was a sensible choice earlier when we were setting up remotes by hand.)

Take a look at the Owner’s repository on GitHub again, and you should be able to see the new commit made by the Collaborator. You may need to refresh your browser to see the new commit.

Some more about remotes

In this episode and the previous one, our local repository has had a single “remote”, called origin. A remote is a copy of the repository that is hosted somewhere else, that we can push to and pull from, and there’s no reason that you have to work with only one. For example, on some large projects you might have your own copy in your own GitHub account (you’d probably call this origin) and also the main “upstream” project repository (let’s call this upstream for the sake of examples). You would pull from upstream from time to time to get the latest updates that other people have committed.

Remember that the name you give to a remote only exists locally. It’s an alias that you choose - whether origin, or upstream, or fred - and not something intrinstic to the remote repository.

The git remote family of commands is used to set up and alter the remotes associated with a repository. Here are some of the most useful ones:

• git remote -v lists all the remotes that are configured (we already used this in the last episode)
• git remote add [name] [url] is used to add a new remote
• git remote remove [name] removes a remote. Note that it doesn’t affect the remote repository at all - it just removes the link to it from the local repo.
• git remote set-url [name] [newurl] changes the URL that is associated with the remote. This is useful if it has moved, e.g. to a different GitHub account, or from GitHub to a different hosting service. Or, if we made a typo when adding it!
• git remote rename [oldname] [newname] changes the local alias by which a remote is known - its name. For example, one could use this to change upstream to fred.

To download the Collaborator’s changes from GitHub, the Owner now enters:

$ git pull origin main

remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 3 (delta 0), reused 3 (delta 0), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/User/simple-site
 * branch            main     -> FETCH_HEAD
   9272da5..29aba7c  main     -> origin/main
Updating 9272da5..29aba7c
Fast-forward
 index.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 index.md

Now the three repositories (Owner’s local, Collaborator’s local, and Owner’s on GitHub) are back in sync.

A Basic Collaborative Workflow

In practice, it is good to be sure that you have an updated version of the repository you are collaborating on, so you should git pull before making our changes. The basic collaborative workflow would be:

• update your local repo with git pull origin main,
• make your changes and stage them with git add,
• commit your changes with git commit -m, and
• upload the changes to GitHub with git push origin main

It is better to make many commits with smaller changes rather than of one commit with massive changes: small commits are easier to read and review.

Switch Roles and Repeat

Switch roles and repeat the whole process.

Suggested changes to make on the script:

• expand the list of numbers
• add an informative comment
• reword the output of echo command

Review Changes

The Owner pushed commits to the repository without giving any information to the Collaborator. How can the Collaborator find out what has changed with command line? And on GitHub?

Solution

On the command line, the Collaborator can use git fetch origin main to get the remote changes into the local repository, but without merging them. Then by running git diff main origin/main the Collaborator will see the changes output in the terminal.

On GitHub, the Collaborator can go to the repository and click on “commits” to view the most recent commits pushed to the repository.

Comment Changes in GitHub

The Collaborator has some questions about one line change made by the Owner and has some suggestions to propose.

With GitHub, it is possible to comment the diff of a commit. Over the line of code to comment, a blue comment icon appears to open a comment window.

The Collaborator posts its comments and suggestions using GitHub interface.

Version History, Backup, and Version Control

Some backup software can keep a history of the versions of your files. They also allows you to recover specific versions. How is this functionality different from version control? What are some of the benefits of using version control, Git and GitHub?

Key Points

• git clone copies a remote repository to create a local repository with a remote called origin automatically set up.

Conflicts

Overview

Teaching: 45 min
Exercises: 0 min

Questions

• What do I do when my changes conflict with someone else’s?

Objectives

• Explain what conflicts are and when they can occur.

• Resolve conflicts resulting from a merge.

As soon as people can work in parallel, they’ll likely step on each other’s toes. This will even happen with a single person: if we are working on a piece of software on both our laptop and a server in the lab, we could make different changes to each copy. Version control helps us manage these conflicts by giving us tools to resolve overlapping changes.

To see how we can resolve conflicts, we must first create one. The file index.md currently looks something like this in both partners’ copies of our simple-site repository:

$ cat index.md

---
title: Home
---
# Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

What if the collaborator adds their own biographical details to the files:

$ nano index.md
$ cat index.md

---
title: Home
---

# Jon Jablonski

I am the Directory of the DREAM Lab.

# Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

and then push the change to GitHub:

$ git add index.md
$ git commit -m "Add Jon to index.md"

[main 5ae9631] Add Jon to index.md
 1 file changed, 1 insertion(+)

$ git push origin main

Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Delta compression using up to 8 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 331 bytes | 331.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To https://github.com/user/simple-site.git
   29aba7c..dabb4c8  main -> main

Now let’s have the owner make a different change to their copy without updating from GitHub:

$ nano index.md
$ cat index.md

Let’s use ## instead of # to use a smaller font size in the heading:

## Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

We can commit the change locally:

$ git add index.md
$ git commit -m "use smaller heading"

[main 07ebc69] use smaller heading
 1 file changed, 1 insertion(+)

but Git won’t let us push it to GitHub:

$ git push origin main

To https://github.com/user/simple-site.git
 ! [rejected]        main -> main (fetch first)
error: failed to push some refs to 'https://github.com/user/simple-site.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

Git rejects the push because it detects that the remote repository has new updates that have not been incorporated into the local branch. What we have to do is pull the changes from GitHub, merge them into the copy we’re currently working in, and then push that. Let’s start by pulling:

$ git pull origin main

remote: Enumerating objects: 5, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (1/1), done.
remote: Total 3 (delta 2), reused 3 (delta 2), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/user/simple-site
 * branch            main     -> FETCH_HEAD
    29aba7c..dabb4c8  main     -> origin/main
Auto-merging index.md
CONFLICT (content): Merge conflict in index.md
Automatic merge failed; fix conflicts and then commit the result.

The git pull command updates the local repository to include those changes already included in the remote repository. After the changes from remote branch have been fetched, Git detects that changes made to the local copy overlap with those made to the remote repository, and therefore refuses to merge the two versions to stop us from trampling on our previous work. The conflict is marked in in the affected file:

$ cat index.md

<<<<<<< HEAD
## Seth Erickson
=======
# Jon Jablonski

I am the Director of the DREAM Lab

# Seth Erickson
>>>>>>> 004b4d5f9a599a92d6a19c5c82a362d8126f4403

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

Our change is preceded by <<<<<<< HEAD. Git has then inserted ======= as a separator between the conflicting changes and marked the end of the content downloaded from GitHub with >>>>>>>. (The string of letters and digits after that marker identifies the commit we’ve just downloaded.)

It is now up to us to edit this file to remove these markers and reconcile the changes. We can do anything we want: keep the change made in the local repository, keep the change made in the remote repository, write something new to replace both, or get rid of the change entirely. Let’s replace both so that the file looks like this:

$ cat index.md

## Jon Jablonski

I am the Director of the DREAM Lab

## Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

To finish merging, we add index.md to the changes being made by the merge and then commit:

$ git add index.md
$ git status

On branch main
All conflicts fixed but you are still merging.
  (use "git commit" to conclude merge)

Changes to be committed:

	modified:   index.md

$ git commit -m "Merge changes from GitHub"

[main 2abf2b1] Merge changes from GitHub

Now we can push our changes to GitHub:

$ git push origin main

Enumerating objects: 10, done.
Counting objects: 100% (10/10), done.
Delta compression using up to 8 threads
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 645 bytes | 645.00 KiB/s, done.
Total 6 (delta 4), reused 0 (delta 0)
remote: Resolving deltas: 100% (4/4), completed with 2 local objects.
To https://github.com/user/simple-site.git
   dabb4c8..2abf2b1  main -> main

Git keeps track of what we’ve merged with what, so we don’t have to fix things by hand again when the collaborator who made the first change pulls again:

$ git pull origin main

remote: Enumerating objects: 10, done.
remote: Counting objects: 100% (10/10), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 6 (delta 4), reused 6 (delta 4), pack-reused 0
Unpacking objects: 100% (6/6), done.
From https://github.com/user/simple-site
 * branch            main     -> FETCH_HEAD
    dabb4c8..2abf2b1  main     -> origin/main
Updating dabb4c8..2abf2b1
Fast-forward
 index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

We get the merged file:

$ cat index.md

## Jon Jablonski

I am the Director of the DREAM Lab

## Seth Erickson

I am a data services librarian at UCSB.

My responsibilities include:

- Teaching Carpentry Workshops
- Helping students learn Git

See my [reading list](reading-list.html).

We don’t need to merge again because Git knows someone has already done that.

Git’s ability to resolve conflicts is very useful, but conflict resolution costs time and effort, and can introduce errors if conflicts are not resolved correctly. If you find yourself resolving a lot of conflicts in a project, consider these technical approaches to reducing them:

• Pull from upstream more frequently, especially before starting new work
• Use topic branches to segregate work, merging to main when complete
• Make smaller more atomic commits
• Where logically appropriate, break large files into smaller ones so that it is less likely that two authors will alter the same file simultaneously

Conflicts can also be minimized with project management strategies:

• Clarify who is responsible for what areas with your collaborators
• Discuss what order tasks should be carried out in with your collaborators so that tasks expected to change the same lines won’t be worked on simultaneously
• If the conflicts are stylistic churn (e.g. tabs vs. spaces), establish a project convention that is governing and use code style tools (e.g. htmltidy, perltidy, rubocop, etc.) to enforce, if necessary

Advanced Git: Resolving without a merge commit

Use git pull --rebase instead of git pull. If the remote has diverged from local and automerge doesn’t work, git rebase will ask you to resolve the conflict (same as git pull); you then git add the files with resolved conflict and git rebase --continue (instead of git commit). The end result is that your local changes are applied after the commits retrieved from the remote. A tidy sequence of commits, without a merge commit. After git rebase --continue , you push back to the remote.

Solving Conflicts that You Create

Clone the repository created by your instructor. Add a new file to it, and modify an existing file (your instructor will tell you which one). When asked by your instructor, pull her changes from the repository to create a conflict, then resolve it.

Conflicts on Non-textual files

What does Git do when there is a conflict in an image or some other non-textual file that is stored in version control?

Solution

Let’s try it. Suppose We takes a picture and calls it example files, ex-files.jpg.

If you do not have an image file of ex-files available, you can create a dummy binary file like this:

$ head -c 1024 /dev/urandom > ex-files.jpg
$ ls -lh ex-files.jpg

-rw-r--r-- 1 user 57095 1.0K Mar  8 20:24 ex-files.jpg

ls shows us that this created a 1-kilobyte file. It is full of random bytes read from the special file, /dev/urandom.

Now, suppose we add ex-files.jpg to our repository:

$ git add ex-files.jpg
$ git commit -m "Add picture of Martian surface"

[main 8e4115c] Add picture of Martian surface
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 ex-files.jpg

Suppose that our collaborator has added a similar picture in the meantime. Theirs is a picture of the Martian sky, but it is also called ex-files.jpg. When We tried to push, they gets a familiar message:

$ git push origin main

To https://github.com/user/simple-site.git
 ! [rejected]        main -> main (fetch first)
error: failed to push some refs to 'https://github.com/user/simple-site.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

We’ve learned that we must pull first and resolve any conflicts:

$ git pull origin main

When there is a conflict on an image or other binary file, git prints a message like this:

$ git pull origin main
remote: Counting objects: 3, done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 3 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (3/3), done.
From https://github.com/user/simple-site.git
 * branch            main     -> FETCH_HEAD
   6a67967..439dc8c  main     -> origin/main
warning: Cannot merge binary files: ex-files.jpg (HEAD vs. 439dc8c08869c342438f6dc4a2b615b05b93c76e)
Auto-merging ex-files.jpg
CONFLICT (add/add): Merge conflict in ex-files.jpg
Automatic merge failed; fix conflicts and then commit the result.

The conflict message here is mostly the same as it was for index.md, but there is one key additional line:

warning: Cannot merge binary files: ex-files.jpg (HEAD vs. 439dc8c08869c342438f6dc4a2b615b05b93c76e)

Git cannot automatically insert conflict markers into an image as it does for text files. So, instead of editing the image file, we must check out the version we want to keep. Then we can add and commit this version.

On the key line above, Git has conveniently given us commit identifiers for the two versions of ex-files.jpg. Our version is HEAD, and their version is 439dc8c0.... If we want to use our version, we can use git checkout:

$ git checkout HEAD ex-files.jpg
$ git add ex-files.jpg
$ git commit -m "Use image of surface instead of sky"

[main 21032c3] Use image of surface instead of sky

If instead we want to use their version, we can use git checkout with their commit identifier, 439dc8c0:

$ git checkout 439dc8c0 ex-files.jpg
$ git add ex-files.jpg
$ git commit -m "Use image of sky instead of surface"

[main da21b34] Use image of sky instead of surface

We can also keep both images. The catch is that we cannot keep them under the same name. But, we can check out each version in succession and rename it, then add the renamed versions. First, check out each image and rename it:

$ git checkout HEAD ex-files.jpg
$ git mv ex-files.jpg ex-files02.jpg
$ git checkout 439dc8c0 ex-files.jpg
$ mv ex-files.jpg ex-files01.jpg

Then, remove the old ex-files.jpg and add the two new files:

$ git rm ex-files.jpg
$ git add ex-files02.jpg
$ git add ex-files01.jpg
$ git commit -m "Use two images: surface and sky"

[main 94ae08c] Use two images: surface and sky
 2 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 ex-files01.jpg
 rename ex-files.jpg => ex-files02.jpg (100%)

Now both images of ex-files are checked into the repository, and ex-files.jpg no longer exists.

Key Points

• Conflicts occur when two or more people change the same lines of the same file.

• The version control system does not allow people to overwrite each other’s changes blindly, but highlights conflicts so that they can be resolved.