Tracking Changes

Last updated on 2024-11-19 | Edit this page

Estimated time: 20 minutes

Overview

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.

First let’s make sure we’re still in the right directory. You should be in the data-dictionary directory.

BASH

$ cd ~/Desktop/data-dictionary

Let’s create a file called amr-data-dictionary.txt that will contain the description of the variables in our AMR data. We’ll use RStudio to edit the file; but you can use whatever editor you like. In particular, this does not have to be the core.editor you set globally earlier.

First create the file from the command line:

BASH

$ touch amr-data-dictionary.txt

Now open the file in RStudio (or your preferred editor).

Type the text below into the amr-data-dictionary.txt file:

OUTPUT

AMR data
100,000 rows of 12 variables

These data represent the sort of data that might be obtained from the Second Generation Surveillance System (SGSS)

and save the file.

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

BASH

$ ls

OUTPUT

amr-data-dictionary.txt

amr-data-dictionary.txt should contain 4 lines, which we can see by running:

BASH

$ cat amr-data-dictionary.txt

OUTPUT

AMR data
100,000 rows of 12 variables

These data represent the sort of data that might be obtained from the Second Generation Surveillance System (SGSS)

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

BASH

$ git status

OUTPUT

On branch main

No commits yet

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

	amr-data-dictionary.txt

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:

BASH

$ git add amr-data-dictionary.txt

and then check that the right thing happened:

BASH

$ git status

OUTPUT

On branch main

No commits yet

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

	new file:   amr-data-dictionary.txt

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

BASH

$ git commit -m "Start data dictionary for AMR data"

OUTPUT

[main (root-commit) f22b25e] Start notes on Mars as a base
 1 file changed, 1 insertion(+)
 create mode 100644 amr-data-dictionary.txt

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 f22b25e. 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:

BASH

$ git status

OUTPUT

On branch main
nothing to commit, working tree 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:

BASH

$ git log

OUTPUT

commit f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: <John Doe> <john.doe@unkown.com>
Date:   Thu Aug 22 09:51:46 2013 -0400

    Start data dictionary for AMR data

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 amr-data-dictionary.txt. 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 suppose we add more information to the file. (Again, we’ll edit with RStudio and then cat the file to show its contents; you may use a different editor, and don’t need to cat.)

BASH

$ cat amr-data-dictionary.txt

OUTPUT

AMR data
100,000 rows of 12 variables

These data represent the sort of data that might be obtained from the Second Generation Surveillance System (SGSS)

* id Integer - A unique identifier for each person

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

BASH

$ git status

OUTPUT

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:   amr-data-dictionary.txt

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:

BASH

$ git diff

OUTPUT

diff --git a/amr-data-dictionary.txt b/amr-data-dictionary.txt
index df0654a..315bf3a 100644
--- a/amr-data-dictionary.txt
+++ b/amr-data-dictionary.txt
@@ -2,3 +2,5 @@ AMR data
 100,000 rows of 12 variables

 These data represent the sort of data that might be obtained from the Second Generation Surveillance System (SGSS)
+
+* id Integer - A unique identifier for each person

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:

BASH

$ git commit -m "Add entry for the id column"

OUTPUT

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:   amr-data-dictionary.txt

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:

BASH

$ git add amr-data-dictionary.txt
$ git commit -m "Add entry for the id column"

OUTPUT

[main 7464434] Add entry for the id column
 1 file changed, 2 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!

A diagram showing how "git add" registers changes in the staging area, while "git commit" moves changes from the staging area to the repository

Let’s watch as our changes to a file move from our editor to the staging area and into long-term storage. First, we’ll add a few more lines to the file and complete our dictionary:

BASH

$ cat amr-data-dictionary.txt

OUTPUT

AMR data

100,000 rows of 12 variables

These data represent the sort of data that might be obtained from the Second Generation Surveillance System (SGSS)

 * id Integer - A unique identifier for each person
 * dob Character - a string giving the date of birth
 * spec_date Character - a string giving the date a specimen was taken
 * sex_male Binary - indicates whether the person from whom the specimen was taken was male or not. 1 (male) 0 (not male)
 * region Character - a string indicating the England region of laboratory testing the specimen
 * had_surgery_past_yr Binary - indicates whether person from whom sample was taken had undergone surgery in hospital in the past year before specimen taken. 1 (surgery within last year) 0 (No surgery within last year)
 * ethnicity Character - indicates self-reported ethnicity group according to Office for National Statistics groupings
 * imd Integer - indicates the Index of Multiple Deprivation for residence for person from whom specimen was taken. Range: 1 (least deprived) - 5 (most deprived)
 * organism Character - indicates the species name for the organism detected
 * coamox Binary - indicates specimen was resistant to Coamoxiclav
 * gentam Binary - indicates specimen was resistant to Gentamicin
 * ciprof Binary - indicates specimen was resistant to Ciprofloxacin

BASH

$ git diff

OUTPUT

diff --git a/amr-data-dictionary.txt b/amr-data-dictionary.txt
index f2c537e..c9a8214 100644
--- a/amr-data-dictionary.txt
+++ b/amr-data-dictionary.txt
@@ -4,3 +4,14 @@ AMR data
 These data represent the sort of data that might be obtained from the Second Generation Surveillance System (SGSS)

 * id Integer - A unique identifier for each person
+* dob Character - a string giving the date of birth
+* spec_date Character - a string giving the date a specimen was taken
+* sex_male Binary - indicates whether the person from whom the specimen was taken was male or not. 1 (male) 0 (not male)
+* region Character - a string indicating the England region of laboratory testing the specimen
+* had_surgery_past_yr Binary - indicates whether person from whom sample was taken had undergone surgery in hospital in the past year before specimen taken. 1 (surgery within last year) 0 (No surgery within last year)
+* ethnicity Character - indicates self-reported ethnicity group according to Office for National Statistics groupings
+* imd Integer - indicates the Index of Multiple Deprivation for residence for person from whom specimen was taken. Range: 1 (least deprived) - 5 (most deprived)
+* organism Character - indicates the species name for the organism detected
+* coamox Binary - indicates specimen was resistant to Coamoxiclav
+* gentam Binary - indicates specimen was resistant to Gentamicin
+* ciprof Binary - indicates specimen was resistant to Ciprofloxacin

So far, so good: we’ve added the necessary lines to the end of the file (shown with a + in the first column). Now let’s put that change in the staging area and see what git diff reports:

BASH

$ git add amr-data-dictionary.txt
$ 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:

BASH

$ git diff --staged

OUTPUT

diff --git a/amr-data-dictionary.txt b/amr-data-dictionary.txt
index f2c537e..c9a8214 100644
--- a/amr-data-dictionary.txt
+++ b/amr-data-dictionary.txt
@@ -4,3 +4,14 @@ AMR data
 These data represent the sort of data that might be obtained from the Second Generation Surveillance System (SGSS)

 * id Integer - A unique identifier for each person
+* dob Character - a string giving the date of birth
+* spec_date Character - a string giving the date a specimen was taken
+* sex_male Binary - indicates whether the person from whom the specimen was taken was male or not. 1 (male) 0 (not male)
+* region Character - a string indicating the England region of laboratory testing the specimen
+* had_surgery_past_yr Binary - indicates whether person from whom sample was taken had undergone surgery in hospital in the past year before specimen taken. 1 (surgery within last year) 0 (No surgery within last year)
+* ethnicity Character - indicates self-reported ethnicity group according to Office for National Statistics groupings
+* imd Integer - indicates the Index of Multiple Deprivation for residence for person from whom specimen was taken. Range: 1 (least deprived) - 5 (most deprived)
+* organism Character - indicates the species name for the organism detected
+* coamox Binary - indicates specimen was resistant to Coamoxiclav
+* gentam Binary - indicates specimen was resistant to Gentamicin
+* ciprof Binary - indicates specimen was resistant to Ciprofloxacin

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

BASH

$ git commit -m "Complete the data dictionary"

OUTPUT

[main 1c642ba] Complete the data dictionary
 1 file changed, 11 insertions(+)

check our status:

BASH

$ git status

OUTPUT

On branch main
nothing to commit, working tree clean

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

BASH

$ git log

OUTPUT

commit 1c642ba5c32a722081ea9e3c80ef0634b4e071f3 (HEAD -> main)
Author: John Doe <john.doe@unkown.com>
Date:   Wed Aug 14 15:01:56 2024 +0100

    Complete the data dictionary

commit 746443401e4f3e41a4bb67844dfb03e0241a1721
Author: John Doe <john.doe@unkown.com>
Date:   Wed Aug 14 14:57:35 2024 +0100

    Add entry for the id column

commit 0f988204ddcf33c060ecb849d640b3bd7aec71cc
Author: John Doe <john.doe@unkown.com>
Date:   Wed Aug 14 14:54:11 2024 +0100

    Start data dictionary

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:

BASH

$ git log -1

OUTPUT

commit 1c642ba5c32a722081ea9e3c80ef0634b4e071f3 (HEAD -> main)
Author: John Doe <john.doe@unkown.com>
Date:   Wed Aug 14 15:01:56 2024 +0100

    Complete the data dictionary

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

BASH

$ git log --oneline

OUTPUT

1c642ba (HEAD -> main) Complete the data dictionary
7464434 Add entry for the id column
0f98820 Start data dictionary

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:

BASH

$ git log --oneline --graph

OUTPUT

* 1c642ba (HEAD -> main) Complete the data dictionary
* 7464434 Add entry for the id column
* 0f98820 Start data dictionary

Directories

Two important facts you should know about directories in Git.

  1. Git does not track directories on their own, only files within them. Try it for yourself:

BASH

$ mkdir notes
$ git status
$ git add notes
$ git status

Note, our newly created empty directory notes 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.

  1. 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:

BASH

git add <directory-with-files>

Try it for yourself:

BASH

$ touch notes/2024-08-14.txt spaceships/2024-08-13.txt
$ git status
$ git add notes
$ git status

Before moving on, we will commit these changes.

BASH

$ git commit -m "Add meeting notes"

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):

A diagram showing two documents being separately staged using git add, before being combined into one commit using git commit

Choosing a Commit Message

Which of the following commit messages would be most appropriate for the last commit made to amr-data-dictionary.txt?

  1. “Changes”
  2. “Added lines 7-17 to amr-data-dictionary.txt”
  3. “Add description for each data variable”

Answer 1 is not descriptive enough, and the purpose of the commit is unclear; and answer 2 is redundant to using “git diff” to see what changed in this commit; but answer 3 is good: short, descriptive, and imperative.

Committing Changes to Git

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

  1. BASH

       $ git commit -m "my recent changes"
  2. BASH

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

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

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

  1. Add some text to amr-data-dictionary.txt to mention that more detailed information on each variable can be found in a separate file with the same name as the variable.
  2. Create a new file ciprof.txt with a short description of what Ciproflaxacin is (feel free to make something up).
  3. Add changes from both files to the staging area, and commit those changes.

The output below from cat amr-data-dictionary.txt reflects only content added during this exercise. Your output may vary.

First we make our changes to the amr-data-dictionary.txt and ciprof.txt files:

BASH

$ cat amr-data-dictionary.txt

OUTPUT

More information on each variable can be found in the corresponding file.

BASH

$ cat ciprof.txt

OUTPUT

Ciprofloxacin is a fluoroquinolone antibiotic used to treat a number of bacterial infections.

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

BASH

$ git add amr-data-dictionary.txt ciprof.txt

Or with multiple commands:

BASH

$ git add amr-data-dictionary.txt
$ git add ciprof.txt

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

BASH

$ git commit -m "Add more detailed information about ciprofloxacin"

```output
[main cc127c2]
 Add more detailed information about ciprofloxacin
 2 files changed, 2 insertions(+)
 create mode 100644 ciprof.txt

bio Repository

  • Create a new Git repository on your computer called bio.
  • Write a three-line biography for yourself in a file called me.txt, commit your changes
  • Modify one line, add a fourth line
  • Display the differences between its updated state and its original state.

If needed, move out of the data-dictionary folder:

BASH

$ cd ..

Create a new folder called bio and ‘move’ into it:

BASH

$ mkdir bio
$ cd bio

Initialise git:

BASH

$ git init

Create your biography file me.txt using nano or another text editor. Once in place, add and commit it to the repository:

BASH

$ git add me.txt
$ git commit -m "Add biography file" 

Modify the file as described (modify one line, add a fourth line). To display the differences between its updated state and its original state, use git diff:

BASH

$ git diff me.txt

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.