Recording Changes Locally

Overview

Questions

• How do I create a new Git repository for my project?
• How do I check which files have been modified?
• How do I record a snapshot of my work?
• How can I review what has changed between versions?

Objectives

• Initialise a repository with git init.
• Explain the roles of the working directory, staging area, and repository.
• Track new or modified files with git add and record them with git commit.
• Use git status to see the state of the working directory and staging area.
• Compare changes with git diff and inspect history with git log.
• Restore a file to an earlier state with git restore (or git checkout -- for older Git versions).

Introduction

---

With Git configured, we can start tracking changes. Think of Git as a camera: every time you take a commit you capture a snapshot of the files that are staged. Much like arranging subjects before pressing the shutter, you choose what to record with git add.

Three locations matter (see diagram below):

1. Working directory – files you edit in your editor/IDE.
2. Staging area – a holding zone for the next snapshot.
3. Repository – the permanent, time‑stamped history.

1. Create a repository

A repository, or repo, is a fundamental element of Git. It’s a space where project files live, allowing for version control and collaboration.

You can think of a repository as a project folder that tracks changes, stores history, and lets multiple people work together seamlessly.

We are going to create a folder for our project MyProject which will turn into a git repository.

BASH

mkdir MyProject 

You can go into MyProject by running

BASH

$ mkdir MyProject
$ cd `MyProject` 

In its current state the directory, MyProject is not a Git repository.

If you want this folder to be a Git repository so that you can track all changes you make, type git init command.

BASH

$ git init            # creates .git directory

When you run the git init command in an ordinary folder, it allows you to transform that folder into a trackable git repository where you can use Git commands.

git init creates a hidden .git folder that stores all future history.

Challenge 1: First contact

Run git status immediately after git init. What output do you see and why?

Show me the solution

Git reports

On branch main (or master)

No commits yet
nothing to commit (create/copy files and use "git add" to track)

because we have not created any files or commits; the repository is empty.

2. Add a README file

A README file in a Git repository provides essential information about the project, including its purpose, usage instructions, how to get started, where to find help, and details on contributors. It serves as an introductory guide for visitors, helping them understand and utilize the project effectively

Callout

Markdown Files

README files are typically named README.md. The .md extension indicates that the file is written in Markdown, a lightweight markup language that allows you to add formatting (like headings, bold text, lists, and code blocks) using plain text.

When you view a repository on platforms like GitHub, GitLab, or Bitbucket, they automatically detect README.md (or similar filenames like README.txt, README) in the root directory. These platforms then render the Markdown content into beautifully formatted HTML, making the project’s introduction easily readable directly in your web browser without needing to open the file in a text editor. This automatic rendering is a key reason Markdown is so popular for repository documentation.

Let’s create a new file by running touch README.md then run git status again. Now you should see that you have an untracked file README.md.

BASH

$ echo "# My eddie Python project" > README.md
$ git status          # untracked file appears in red

OUTPUT

On branch main

No commits yet

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

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

An untracked file is one that has not been added to the staging area. To add files to the staging area, you can use the git add command.

Git add

There are quite a few ways to use this command. For example, you can use git add . to add all files to the staging area from the working directory or use git add filename to add a specific file to the staging area.

BASH

$ git add README.md   # stage the file

If you run git status again, this will show you that README.md is in the staging area

BASH

$ git status          # file appears in green (staged)

OUTPUT

On branch main

No commits yet

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

When files are added to the staging area, that means they are in safe keeping before you commit them. Think of using the Git add command as telling Git, “Please keep track of this file in its current state.”

Staging tells Git which changes, Changes to be committed, belong to the next snapshot.

If you make additional changes to the tracked files, you’ll need to use the git add command again for Git to keep track of them.

3. Commit the snapshot

To add snapshot to repository use the git commit command. For each commit you will need to add a message using the -m option.

Git messages

1. Limit the Subject Line: Keep the subject or summary line to 50 characters or fewer. This ensures it’s easily readable in various Git tools.​
2. Use the Imperative Mood: Frame your commit message as a command or action, e.g., “Fix” rather than “Fixed” or “Fixes.”​
3. Avoid Vague Messages: Instead of writing “Update code” or “Fix bug”, specify what you did, such as “Add error handling for login process.”

Let’s run git commit -m “initial commit” to see what happens.

BASH

$ git commit -m "initial commit"

OUTPUT

[main (root-commit) 72041c0] Add README with project title
 1 file changed, 1 insertion(+)
 create mode 100644 README.md

Every commit receives a unique 40‑character hash (displayed here as 72041c0 for brevity).

You’ll see that you have “1 file changed, 1 insertion(+)” because you just added one new files, and the files has one line of code.

Now that your changes are committed, your working directory should be clean. You can verify this by running git status again:

BASH

git status

This output means there are no new changes to track or commit since your last snapshot. Your project’s state is now safely recorded in your Git history!

OUTPUT

On branch main
nothing to commit, working tree clean

That’s how you use the git add and git commit commands together! Well done tracking changes and storing your new work.

Git Log: Tracing Your Project’s History

The git log command is your window into the history of your Git repository. After you’ve made and committed changes (like we did with the README.md file), your git status shows a clean working tree because those changes are now safely recorded. git log then lets you see a chronological list of all those recorded commits, starting from the most recent one and working backward. Each commit represents a snapshot of your project at a specific point in time, along with who made the change and why.

BASH

git log

OUTPUT

commit f00b5b49b39884a9bf978bc272c82d862976abcb (HEAD -> main)​

Author: firstname surname <emailaddress@ed.ac.uk>​

Date:   Tue Sep 24 10:06:58 2024 +0100​

initial commit

Challenge 2: Where is my commit?

Use git log --oneline to view the history. How many commits appear and what information is shown?

Show me the solution

One commit appears:

72041c0 (HEAD -> main) initial commit

We see the abbreviated hash, the branch name, and the commit message.

4. Modifying a file

Edit README.md

BASH

nano README.md

add a Run Script section

# My eddie Python project​

To run Python on eddie need to run:​
    module load igmm/apps/python/3.7

git status

BASH

$ git status          # modified file in red

OUTPUT

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:   README.md

Viewing changes

---

We can you the command git diff to view our change.

BASH

$ git diff README.md  # view changes

OUTPUT

diff --git a/README.md b/README.md
index a4c6c69..603f621 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,4 @@
 # My eddie Python project
+
+To run Python on eddie need to run:
+    module load igmm/apps/python/3.7

---

What Each Part Means

---

diff --git a/README.md b/README.md

• This is the file being changed: README.md
• a/README.md = the old version
• b/README.md = the new version
• This line starts the diff block for that file.

---

index a4c6c69..603f621 100644

• a4c6c69 = commit hash of the file before the change
• 603f621 = commit hash of the file after the change
• 100644 = file mode (normal non-executable file)

---

➖ --- a/README.md

➕ +++ b/README.md

• Shows what version is being removed (---) and added (+++)
• Still refers to the same file (README.md), before and after

---

@@ -1 +1,4 @@

• This is a “hunk header” showing line number context
• -1 = from line 1 of the old file
• +1,4 = starting at line 1 of the new file, and it now spans 4 lines

---

Content Change Section

DIFF

 # My eddie Python project
+
+To run Python on eddie need to run:
+    module load igmm/apps/python/3.7

Symbol	Meaning	Explanation
	(no symbol)	This line was already there
+	Line was added	These 3 new lines were inserted below the original first line

---

---

Stage and commit the update:

Once we are happy with the changes we can stage the changes and then commit into the git repository.

BASH

$ git add README.md
$ git commit -m "Describe how to run analysis script"

OUTPUT

[main 370eb9d] Describe how to run analysis script
  1 file changed, 3 insertions(+)

5. Inspecting differences between commits

BASH

$ git diff HEAD~1 README.md   # compare current commit to one before

HEAD is a symbolic name for the current commit; HEAD~1 means one commit ago.

OUTPUT

diff --git a/README.md b/README.md
index a4c6c69..603f621 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,4 @@
 # My eddie Python project
+
+To run Python on eddie need to run:
+    module load igmm/apps/python/3.7

Challenge 3: Predict the diff

Suppose the original README contained only a title. After adding a section called Data, what colour will the new lines appear in the diff output and why?

Show me the solution

They will be green with a + prefix because new lines are additions relative to the previous snapshot.

6. Undoing a change in the working directory

If you accidently stage a file you can discard unstaged edits using git restore:

BASH

$ git restore README.md   # newer Git (>=2.23)
# or
$ git checkout -- README.md  # older Git versions

Be cautious: this removes changes permanently unless they were staged or committed.

7. Adding directories and data

Git tracks files, not empty directories. To include a folder you must add at least one file inside it (often an empty .gitkeep):

BASH

$ mkdir Src
$ touch Src/.gitkeep
$ git add Src/.gitkeep

Let download a file into a Data directory

BASH

$ mkdir Data
$ curl -L -o Data/data.csv https://figshare.com/ndownloader/files/14632895

We can now add ito staging area and commit to repository.

BASH

$ git add Data/data.csv # Comment on when to commit data​
$ git commit -m "Add example dataset"

Challenge 4: Multiple file workflow

Create a simple Python script Src/hello.py that prints “Hello World!”. Add and commit it. Then modify the script to read the CSV file added above and print the number of rows. Use git diff before committing to verify the change.

PYTHON

        #!/usr/bin/env python
        print("Hello World!")

Show me the solution

1. Create the file:

   PYTHON

       #!/usr/bin/env python
       print("Hello World!")

   BASH

   $ git add Src/hello.py
   $ git commit -m "Add hello world script"

Challenge 4: Multiple file workflow (continued)

2. Edit the script, stage, inspect, commit:

   PYTHON

   #!/usr/bin/env python​
   ​
   # load pandas library​
   import pandas as pd​
   ​
   # Read the data​
   variants =  pd.read_csv("Data/data.csv")​
   ​
   # Check we have the data​
   print(variants)

Show me the solution

SH

``` python
#!/usr/bin/env python​
​
# load pandas library​
import pandas as pd​
​
# Read the data​
variants =  pd.read_csv("Data/data.csv")​
​
# Check we have the data​
print(variants)
```

``` bash
$ git diff Src/hello.py   # shows additions
$ git add Src/hello.py
$ git commit -m "Read CSV and report row count"
```

8. Viewing the complete history

BASH

$ git log

Key Points

• git init turns a directory into a repository by creating .git.
• git status gives you a report on your git repository.
• Stage files with git add; record them permanently with git commit -m.
• Use git diff to inspect unstaged or staged changes.
• git log reveals the history; hashes uniquely identify commits.
• Empty directories are not tracked—add a file such as .gitkeep.
• git restore returns a file to a known state.