Version Control with Git

In this module, we will look at the version control system Git. Of the numerous version control systems available (Git, Subversion, CVS, Mercurial), Git seems to be the most popular, and we generally find that it is great for:

  • Collaborating with others on code

  • Supporting multiple concurrent versions (branches)

  • Tagging releases or snapshots in time

  • Restoring previous versions of files

  • What it lacks in user-friendliness it makes up for in good documentation

  • Intuitive web platforms available

After going through this module, students should be able to:

  • Create a new Git repository hosted on GitHub

  • Clone a repository, commit and push changes to the repository

  • Track the history of changes in files in a Git repository

  • Work collaboratively with others on the content in a Git repository

  • Demonstrate a basic understanding of forking, branching, and tags

GitHub is a web platform where you can host and share Git repositories (“repos”). Repositories can be public or private. Much of what we will do with this section requires you to have a GitHub account.

The Basics of Git

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.

../_images/play-changes.svg

Changes are saved sequentially.

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.

../_images/versions.svg

Different versions can be saved.

Unless there are conflicts, you can even incorporate two sets of changes into the same base document.

../_images/merge.svg

Multiple versions can be merged.

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.

Setting up Git

Log on to the class ISP server and check which version of Git is in your PATH.

[local]$ ssh username@isp02.tacc.utexas.edu   # use your account
(enter password)

[isp02]$ which git
/opt/apps/git/2.24.1/bin/git
$ git --version
git version 1.8.3.1

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,

  • 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, where verb is what we actually want to do. Here is how we set up our environment:

[isp02]$ git config --global user.name "Joe Allen"
[isp02]$ git config --global user.email "wallen@tacc.utexas.edu"

Please use your own name and email address. 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 in the future will include this information.

Tip

A key benefit of Git is that it is platform agnostic. You can use it equally to interact with the same files from your laptop, from a lab computer, or from a cluster.

Create a New Repository on the Command Line

First, let’s navigate back to our folder from the JSON module:

[isp02]$ cd ~/coe-332/week02-json

Then we will use a Git command to initialize this directory as a new Git repository - or a place where Git can start to organize versions of our files.

[isp02]$ git init
Initialized empty Git repository in /home/wallen/coe-332/week02-json/.git/

If we use ls -a, we can see that Git has created a hidden directory called .git:

[isp02]$ ls -a
./  ../  class.json  .git/  json_ex.py  json_write.py  states.json

Use the find command to get a overview of the contents of the .git/ directory:

[isp02]$ find .git/
.git
.git/refs
.git/refs/heads
.git/refs/tags
.git/branches
.git/description
.git/hooks
.git/hooks/applypatch-msg.sample
.git/hooks/commit-msg.sample
.git/hooks/post-update.sample
.git/hooks/pre-applypatch.sample
.git/hooks/pre-commit.sample
.git/hooks/pre-push.sample
.git/hooks/pre-rebase.sample
.git/hooks/prepare-commit-msg.sample
.git/hooks/update.sample
.git/info
.git/info/exclude
.git/HEAD
.git/config
.git/objects
.git/objects/pack
.git/objects/info

Git uses this special sub-directory 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 sub-directory, we will lose the project’s history. We can check that everything is set up correctly by asking Git to tell us the status of our project:

[isp02]$ git status
# On branch main
#
# Initial commit
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       class.json
#       json_ex.py
#       json_write.py
#       states.json
nothing added to commit but untracked files present (use "git add" to track)

Note

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

EXERCISE

  • Explore the files and folders in the .git/ directory

  • Can you find a file with your name and e-mail in it? How did it get there?

Tracking Changes

We will use this repository track some changes we are about to make to our example JSON parsing scripts. Above, Git mentioned that it found several “Untracked files”. This means there are files in this current directory that Git isn’t keeping track of. We can instruct Git to start tracking a file using git add:

[isp02]$ git add json_ex.py
[isp02]$ git status
# On branch main
#
# Initial commit
#
# Changes to be committed:
#   (use "git rm --cached <file>..." to unstage)
#
#       new file:   json_ex.py
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       class.json
#       json_write.py
#       states.json

Commit Changes to the Repo

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

[isp02]$ git commit -m "started tracking json example script"
[main (root-commit) 344ec9f] started tracking json example script
 1 file changed, 29 insertions(+)
 create mode 100644 json_ex.py

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 344ec9f. Your commit may have another identifier.

We use the -m flag (“m” for “message”) to record a short, descriptive, and specific comment that will help us remember later on what we did and why. 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” <commit message here>. 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:

[isp02]$ git status
# On branch main
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       class.json
#       json_write.py
#       states.json
nothing added to commit but untracked files present (use "git add" to track)

We find three remaining untracked files.

EXERCISE

Do a git add <file> followed by a git commit -m "descriptive message" for each file, one by one. Also do a git status in between each command.

Check the Project History

If we want to know what we’ve done recently, we can ask Git to show us the project’s history using git log:

[isp02]$ git log
commit 13e07d9dd6a6d3b47f4b7537035c9c532fb7cf4e
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:06:29 2021 -0600

    adding states.json

commit f20159ea98b276ff300b018fa420b514e53e2042
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:06:15 2021 -0600

    adding json_write.py

commit 3d5d6e2c6d23aa4fb3b800b535db6a228759866e
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:06:03 2021 -0600

    adding class.json

commit 344ec9fde550c6e009697b07298919946ff991f9
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:00:17 2021 -0600

    started tracking json example script

The command 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.

Making Further Changes

Now suppose we make a change to one of the files we are tracking. Edit the json_ex.py script your favorite text editor and add some random comments into the script:

[isp02]$ vim json_ex.py
# make some changes in the script
# save and quit

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

[isp02]$ 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:   json_ex.py
#
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:

[isp02]$ git diff json_ex.py
diff --git a/json_ex.py b/json_ex.py
index 5d986e9..21877cb 100644
--- a/json_ex.py
+++ b/json_ex.py
@@ -18,7 +18,7 @@ def check_char_match(str1, str2):
     else:
         return( f'{str1} match FAILS' )

-
+# open the json file and load into dict
 with open('states.json', 'r') as f:
     states = json.load(f)

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:

  • 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.

  • The second line tells exactly which versions of the file Git is comparing: 5d986e9 and 21877cb are unique computer-generated labels for those versions.

  • The third and fourth lines once again show the name of the file being changed.

  • 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 lines.

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

[isp02]$ git add json_ex.py
[isp02]$ git commit -m "added a descriptive comment"
[main 8d5f563] added a descriptive comment
 1 file changed, 1 insertion(+), 1 deletion(-)
[isp02]$ git status
# On branch main
nothing to commit, working directory clean

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).

Directories in Git

There are a couple important facts you should know about directories in Git. First, Git does not track directories on their own, only files within them. Try it for yourself:

[isp02]$ mkdir directory
[isp02]$ git status
[isp02]$ git add directory
[isp02]$ git status

Note, our newly created empty directory directory does not appear in the list of untracked files even if we explicitly add it (via git add) to our repository.

Second, if you create a directory in your Git repository and populate it with files, you can add all files in the directory at once by:

[isp02]$ git add <directory-with-files>

Tip

A trick for tracking an empty directory with Git is to add a hidden file to the directory. People sometimes will label this .gitcanary. Adding and committing that file to the repo’s history will cause the directory it is in to also be tracked.

Restoring Old Versions of Files

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 accidentally overwrite our file:

[isp02]$ echo "" > json_ex.py
[isp02]$ cat json_ex.py

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

[isp02]$ 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:   json_ex.py
#
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 and referring to the most recent commit of the working directory by using the identifier HEAD:

[isp02]$ git checkout HEAD json_ex.py
[isp02]$ cat json_ex.py
import json
...etc

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:

[isp02]$ git log
commit 8d5f563fa20060f4fbe2e10ec5cbc3c22fe92559
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:15:46 2021 -0600

 added a descriptive comment

commit 13e07d9dd6a6d3b47f4b7537035c9c532fb7cf4e
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:06:29 2021 -0600

 adding states.json

commit f20159ea98b276ff300b018fa420b514e53e2042
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:06:15 2021 -0600

 adding json_write.py

commit 3d5d6e2c6d23aa4fb3b800b535db6a228759866e
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:06:03 2021 -0600

 adding class.json

commit 344ec9fde550c6e009697b07298919946ff991f9
Author: Joe Allen <wallen@tacc.utexas.edu>
Date:   Wed Jan 27 23:00:17 2021 -0600

 started tracking json example script

[isp02]$ git checkout 344ec9f json_ex.py
# now you have a copy of json_ex.py without that comment we added

Again, we can put things back the way they were by using git checkout:

[isp02]$ git checkout HEAD json_ex.py
# back to the most recent version

Clone the Repository

Spend a few minutes browsing the web interface for GitHub. Now, anyone can make a full copy of my_first_repo including all the commit history by performing:

[isp02]$ git clone https://github.com/wjallen/json-parser
Cloning into 'json-parser'...
remote: Enumerating objects: 15, done.
remote: Counting objects: 100% (15/15), done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 15 (delta 4), reused 15 (delta 4), pack-reused 0
Unpacking objects: 100% (15/15), done.

Collaborating with Others

A public platform like GitHub makes it easier than ever to collaborate with others on the content of a repository. You can have as many local copies of a repository as you want, but there is only one “origin” repository - the repository hosted on GitHub. Other repositories may fall behind the origin, or have changes that are ahead of the origin. A common model for juggling multiple repositories where separate individuals are working on different features is the GitFlow model:

../_images/GitFlowMasterBranch.png

GitFlow model

Some important definitions (most can easily be managed right in the GitHub web interface):

FORK

A fork is a personal copy of another user’s repository that lives on your account. Forks allow you to freely make changes to a project without affecting the original. Forks remain attached to the original, allowing you to submit a pull request to the original’s author to update with your changes. You can also keep your fork up to date by pulling in updates from the original.

BRANCH

A branch is a parallel version of a repository. It is contained within the repository, but does not affect the primary or main branch allowing you to work freely without disrupting the “live” version. When you’ve made the changes you want to make, you can merge your branch back into the main branch to publish your changes. For more information, see About branches.

TAG

Git has the ability to tag specific points in history as being important. Typically people use this functionality to mark release points (v1.0, and so on).

PULL REQUEST / MERGE REQUEST

Pull requests are proposed changes to a repository submitted by a user and accepted or rejected by a repository’s collaborators. Like issues, pull requests ach have their own discussion forum. For more information, see About pull requests.

OTHER CONSIDERATIONS

Most repos will also contain a few standard files in the top directory, including:

README.md: The landing page of your repository on GitHub will display the contents of README.md, if it exists. This is a good place to describe your project and list the appropriate citations.

LICENSE.txt: See if your repository needs a license here.

Additional Resources