Tracking changes with a local repository

Overview

Teaching: 35 min
Exercises: 0 min

Questions

• How do I get started with Git?

• Where does Git store information?

Objectives

• Know how to set up a new Git repository.

• Understand how to start tracking files.

• Be able to commit changes to your repository.

Version control is centred round the notion of a repository which holds your directories and files. We’ll start by looking at a local repository. The local repository is set up in a directory in your local filesystem (local machine). For this we will use the command line interface.

Why use the command line?

There are lots of graphical user interfaces (GUIs) for using Git: both stand-alone and integrated into IDEs (e.g. MATLAB, Rstudio, PyCharm). We are deliberately not using a GUI for this course because:

• you will have a better understanding of how the git comands work (some functionality is often missing and/or unclear in GUIs)
• you will be able to use Git on any computer (e.g. remotely accessing HPC systems, which generally only have Linux command line access)
• you will be able to use any GUI, rather than just the one you have learned

By the end of the course, this should no longer be you:

Setting up Git

Instructions for setting up Git on your own machine are given under setup.

You can verify you have everything set up correctly like this:

$ ssh -T git@github.com

Hi <YOUR_GITHUB_USERNAME>! You've successfully authenticated, but GitHub does not provide shell access.

Tell Git who we are

As part of the information about changes made to files Git records who made those changes. In teamwork this information is often crucial (do you want to know who rewrote your ‘Conclusions’ section?). So, we need to tell Git about who we are (note that you need to enclose your name in quote marks):

$ git config --global user.name "Your Name" 			# Put your quote marks around your name
$ git config --global user.email yourname@yourplace.org

Set a default editor

When working with Git we will often need to provide some short but useful information. In order to enter this information we need an editor. We’ll now tell Git which editor we want to be the default one (i.e. Git will always bring it up whenever it wants us to provide some information).

You can choose any editor available on your system, but for this course we will use nano.

$ git config --global core.editor nano

Set remote merge strategy

Set the default behaviour for merging remote branches (this afternoon).

git config --global pull.rebase false

Git’s global configuration

We can now preview (and edit, if necessary) Git’s global configuration (such as our name and the default editor which we just set up). If we look in our home directory, we’ll see a .gitconfig file,

$ cat ~/.gitconfig

[user]
	name = Your Name
	email = yourname@yourplace.org
[core]
	editor = nano

These global configuration settings will apply to any new Git repository you create on your computer. i.e. the --global commands above are only required once per computer.

Create a new repository with Git

We will be working with a simple example in this tutorial. It will be a paper that we will first start writing as a single author and then work on it further with one of our colleagues.

First, let’s create a directory within your home directory:

$ cd								# Switch to your home directory.
$ pwd								# Print working directory (output should be /home/<username>)
$ mkdir paper
$ cd paper

Now, we need to set up this directory up to be a Git repository (or “initiate the repository”):

$ git init

Initialized empty Git repository in /home/user/paper/.git/

The directory “paper” is now our working directory.

If we look in this directory, we’ll find a .git directory:

$ ls .git

branches  config  description  HEAD  hooks  info  objects refs

The .git directory contains Git’s configuration files. Be careful not to accidentally delete this directory!

Tracking files with a git repository

Now, we’ll create a file. Let’s say we’re going to write a journal paper, so we will start by adding the author names and a title, then save the file.

$ nano paper.md
# Add author names and paper title

Text editors on your OS

nano should be available whatever OS you are using. If you prefer a different editor feel free to use that instead e.g. notepad on Windows:

notepad paper.md

Accessing files from the command line

In this lesson we create and modify text files using a command line interface (e.g. terminal, Git Bash etc), mainly for convenience. These are normal files which are also accessible from the file browser (e.g. Windows explorer), and by other programs.

Your typical workflow using version control might involve editing files using e.g. MATLAB, PyCharm, Rstudio etc and committing from a command line interface.

git status allows us to find out about the current status of files in the repository. So we can run,

$ git status

On branch master

Initial commit

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

paper.md

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

Information about what Git knows about the directory is displayed. We are on the master branch, which is the default branch in a Git respository (one way to think of branches is like parallel versions of the project - more on branches later).

For now, the important bit of information is that our file is listed as Untracked which means it is in our working directory but Git is not tracking it - that is, any changes made to this file will not be recorded by Git.

Default branch name

Some implementations of git (e.g. on newish Macs) have chosen to overwrite the default branch name, and use main instead of master. If this is the case, you can either mentally switch out master with main for the rest of the course, or if you prefer you can change the branch name to master using

git branch -m master

To make this a permanent change for new repos, you would need to run

git config --global init.defaultBranch master

Add files to a Git repository

To tell Git about the file, we will use the git add command:

$ git add paper.md
$ git status

On branch master

Initial commit

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

	new file:   paper.md

Now our file is listed underneath where it says Changes to be committed.

git add is used for two purposes. Firstly, to tell Git that a given file should be tracked. Secondly, to put the file into the Git staging area which is also known as the index or the cache.

The staging area can be viewed as a “loading dock”, a place to hold files we have added, or changed, until we are ready to tell Git to record those changes in the repository.

Commit changes

In order to tell Git to record our change, our new file, into the repository, we need to commit it:

$ git commit
# Type a commit message: "Add title and authors"
# Save the commit message and close your text editor (nano, notepad etc.)

Our default editor will now pop up. Why? Well, Git can automatically figure out that directories and files are committed, and by whom (thanks to the information we provided before) and even, what changes were made, but it cannot figure out why. So we need to provide this in a commit message.

If we save our commit message and exit the editor, Git will now commit our file.

[master (root-commit) 21cfbde]
1 file changed, 2 insertions(+) Add title and authors
create mode 100644 paper.md

This output shows the number of files changed and the number of lines inserted or deleted across all those files. Here, we have changed (by adding) 1 file and inserted 2 lines.

Now, if we look at its status,

$ git status

On branch master
nothing to commit, working directory clean

our file is now in the repository. The output from the git status command means that we have a clean directory i.e. no tracked but modified files.

Now we will work a bit further on our paper.md file by starting the introduction section.

$ nano paper.md
# Write introduction section

If we now run,

$ git status

we see changes not staged for commit section and our file is marked as modified:

On branch master
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:	 paper.md

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

This means that a file Git knows about has been modified by us but has not yet been committed. So we can add it to the staging area and then commit the changes:

$ git add paper.md
$ git commit				# "Write introduction"

Note that in this case we used git add to put paper.md to the staging area. Git already knows this file should be tracked but doesn’t know if we want to commit the changes we made to the file in the repository and hence we have to add the file to the staging area.

It can sometimes be quicker to provide our commit messages at the command-line by doing git commit -m "Write introduction section".

In our introduction, we should cite a paper describing the main instrument used.

$ nano paper.md 			# Cite instrument paper in introduction

Let’s also create a file refs.txt to hold our references:

$ nano refs.txt				# Add the reference

Now we need to record our work in the repository so we need to make a commit. First we tell Git to track the references.

$ git add refs.txt			# Track the refs.txt file
$ git status				# Verify that refs.txt is now tracked

The file refs.txt is now tracked. We also have to add paper.md to the staging area. But there is a shortcut. We can use commit -a. This option means “commit all files that are tracked and that have been modified”.

$ git commit -am "Reference J Bloggs and add references file"	# Add and commit all tracked files

and Git will add, then commit, both the directory and the file.

In order to add all tracked files to the staging area, use git commit -a (which may be very useful if you edit e.g. 10 files and now you want to commit all of them).

Key Points

• git init initializes a new repository

• 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

• Always write a log message when committing changes