Tracking Changes

Last updated on 2024-03-12 | Edit this page

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.

Let’s start to tell the story of your project while you are working on it!

The Console and the Terminal

In this episode, we are going to use both, the Console and the Terminal.

So look at the upper right corner of the code chunks in this episode:

R < > belongs to the Console.
BASH < > belongs to the Terminal.

Add changes

First, in the Rstudio Console, let’s make sure we’re still in the right R project. You should be in the cases directory.

R

usethis::proj_path()

OUTPUT

C:/~/cases

Let’s create a file called sitrep.Rmd that contains the situation report (Sitrep) describing the data in terms of person, time, and place.

We can do this from the Console. Run:

R

usethis::edit_file("sitrep.Rmd")

• Modify 'sitrep.Rmd'

This opens the file in the Source pane to edit it.

Type the text below into the sitrep.Rmd file:

OUTPUT

Comparison of attack rates in different age groups

Save the file.

Checklist

Remember always to Save the file. Only saved files are recognized by Git.

Now, in the Terminal, 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)

	sitrep.Rmd

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 sitrep.Rmd

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:   sitrep.Rmd

Commit changes

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

BASH

$ git commit -m "Start Sitrep with attack rate analysis"

OUTPUT

[main (root-commit) f22b25e] Start Sitrep with attack rate analysis
 1 file changed, 1 insertion(+)
 create mode 100644 sitrep.Rmd

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 VIM (or whatever other editor we configured as core.editor) so that we can write a longer message.

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 Enter or ↵ or on Macs, Return. If you want to save your changes and quit, press Esc then type :wq and hit Enter or ↵ or on Macs, Return.

Do we need to change git core editor?

With Rstudio you don’t need to do change any editor. You can open all your files in the Source pane.

Also, to write commit messages you can use the Rstudio IDE. We invite you to read the supplemental episode.

However, if needed, Dracula can set his favorite text editor following this table:

Editor	Configuration command
Atom	`$ git config --global core.editor "atom --wait"`
nano	`$ git config --global core.editor "nano -w"`
BBEdit (Mac, with command line tools)	`$ git config --global core.editor "bbedit -w"`
Sublime Text (Mac)	`$ git config --global core.editor "/Applications/Sublime\ Text.app/Contents/SharedSupport/bin/subl -n -w"`
Sublime Text (Win, 32-bit install)	`$ git config --global core.editor "'c:/program files (x86)/sublime text 3/sublime_text.exe' -w"`
Sublime Text (Win, 64-bit install)	`$ git config --global core.editor "'c:/program files/sublime text 3/sublime_text.exe' -w"`
Notepad (Win)	`$ git config --global core.editor "c:/Windows/System32/notepad.exe"`
Notepad++ (Win, 32-bit install)	`$ git config --global core.editor "'c:/program files (x86)/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"`
Notepad++ (Win, 64-bit install)	`$ git config --global core.editor "'c:/program files/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"`
Kate (Linux)	`$ git config --global core.editor "kate"`
Gedit (Linux)	`$ git config --global core.editor "gedit --wait --new-window"`
Scratch (Linux)	`$ git config --global core.editor "scratch-text-editor"`
Emacs	`$ git config --global core.editor "emacs"`
Vim	`$ git config --global core.editor "vim"`
VS Code	`$ git config --global core.editor "code --wait"`

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

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.

Good practice

A good commit:

Contains less than 50 characters in first line.
Start with an infinitive verb.
Recalls an specific action.

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.

Show the history

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

BASH

$ git log

OUTPUT

commit f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 09:51:46 2013 -0400

    Start Sitrep with attack rate analysis

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.

These commands are so similar!

The git status command displays the state of the working directory and the staging area. It lets you see which changes have been staged, which haven’t, and which files aren’t being tracked by Git. Status output does not show you any information regarding the committed project history (the local repository). For this, you need to use git log. (Atlassian, 2023)

Where Are My Changes?

If, in the Terminal, we run ls at this point, we will still see just one file called sitrep.Rmd. 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).

Compare changes

Now suppose Dracula adds more information to the file. For this, let’s return to the sitrep.Rmd file:

R

usethis::edit_file("sitrep.Rmd")

OUTPUT

Comparison of attack rates in different age groups
This can identify priority groups for interventions

Save the file.

In the Terminal, 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:   sitrep.Rmd

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. In the Terminal, 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/sitrep.Rmd b/sitrep.Rmd
index df0654a..315bf3a 100644
--- a/sitrep.Rmd
+++ b/sitrep.Rmd
@@ -1 +1,2 @@
 Comparison of attack rates in different age groups
+This can identify priority groups for interventions

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; df0654a and 315bf3a 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 a line.

Staging area

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

BASH

$ git commit -m "Add purpose of attack rate analysis"

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:   sitrep.Rmd

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 sitrep.Rmd
$ git commit -m "Add purpose of attack rate analysis"

OUTPUT

[main 34961b1] Add purpose of attack rate analysis
 1 file changed, 1 insertion(+)

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!

Checklist

Use git status to display the state of the working directory and the staging area. git add your changes before you git commit them to the Local repository. Use the git log to get the history of changes in it. Use git diff to compare these changes.

Group Challenges

Choosing a Commit Message

Which of the following commit messages would be most appropriate for the last commit made to sitrep.Rmd?

“Changes”
“Added line ‘Maps illustrate the spread and impact of outbreak’ to sitrep.Rmd”
“Discuss effects of Sitrep’ climate on the Mummy”

Show me the solution

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?

BASH
```
  $ git commit -m "my recent changes"
```

BASH

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

BASH

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

BASH

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

Show me the solution

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

Your turn!

Take 10 minutes to the following two sections:

Practice the workflow
Relevant callouts

If you want to keep practicing, move to the last one:

Individual Challenges

Practice the workflow

Let’s watch as our changes to a file move from our editor to the staging area and into long-term storage. First, in the Console, we’ll add another line to the file:

R

usethis::edit_file("sitrep.Rmd")

OUTPUT

Comparison of attack rates in different age groups
This can identify priority groups for interventions
Maps illustrate the spread and impact of outbreak

Save the file.

In the Terminal, check the difference:

BASH

$ git diff

OUTPUT

diff --git a/sitrep.Rmd b/sitrep.Rmd
index 315bf3a..b36abfd 100644
--- a/sitrep.Rmd
+++ b/sitrep.Rmd
@@ -1,2 +1,3 @@
 Comparison of attack rates in different age groups
 This can identify priority groups for interventions
+Maps illustrate the spread and impact of outbreak

So far, so good: we’ve added one line 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 sitrep.Rmd
$ 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/sitrep.Rmd b/sitrep.Rmd
index 315bf3a..b36abfd 100644
--- a/sitrep.Rmd
+++ b/sitrep.Rmd
@@ -1,2 +1,3 @@
 Comparison of attack rates in different age groups
 This can identify priority groups for interventions
+Maps illustrate the spread and impact of outbreak

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 "Add geospatial visualization objective"

OUTPUT

[main 005937f] Add geospatial visualization objective
 1 file changed, 1 insertion(+)

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 005937fbe2a98fb83f0ade869025dc2636b4dad5 (HEAD -> main)
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 10:14:07 2013 -0400

    Add geospatial visualization objective

commit 34961b159c27df3b475cfe4415d94a6d1fcd064d
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 10:07:21 2013 -0400

    Add purpose of attack rate analysis

commit f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 09:51:46 2013 -0400

    Start Sitrep with attack rate analysis

Relevant callouts

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 005937fbe2a98fb83f0ade869025dc2636b4dad5 (HEAD -> main)
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 10:14:07 2013 -0400

   Add geospatial visualization objective

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

BASH

$ git log --oneline

OUTPUT

005937f (HEAD -> main) Add geospatial visualization objective
34961b1 Add purpose of attack rate analysis
f22b25e Start Sitrep with attack rate analysis

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

* 005937f (HEAD -> main) Add geospatial visualization objective
* 34961b1 Add purpose of attack rate analysis
* f22b25e Start Sitrep with attack rate analysis

Directories

Two important facts you should know about directories in Git.

Git track files, not empty directories

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

BASH

$ mkdir analyses
$ git status
$ git add analyses
$ git status

Note, our newly created empty directory analyses 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.

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 analyses/attack-rate.R analyses/geospatial.R
$ git status
$ git add analyses
$ git status

Before moving on, we will commit these changes.

BASH

$ git commit -m "Add analysis scripts on attack rate and geospatial"

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):

Individual Challenges

Committing Multiple Files

The staging area can hold changes from any number of files that you want to commit as a single snapshot.

Add some text to sitrep.Rmd noting your decision to consider a data cleaning preliminary step.
Create a new file clean.Rmd with your initial thoughts about Data as an step for you and your friends.
Add changes from both files to the staging area, and commit those changes.

Show me the solution

The output below from sitrep.Rmd reflects only content added during this exercise. Your output may vary.

First we make our changes to the sitrep.Rmd and clean.Rmd files:

R

usethis::edit_file("sitrep.Rmd")

OUTPUT

Maybe I should start with a data cleaning step.

R

usethis::edit_file("clean.Rmd")

OUTPUT

Data is a messy file and I definitely should consider a data cleaning step.

Save both files.

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

BASH

$ git add sitrep.Rmd clean.Rmd

Or with multiple commands:

BASH

$ git add sitrep.Rmd
$ git add clean.Rmd

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 "Write plans to start a data cleaning step"

OUTPUT

[main cc127c2]
 Write plans to start a data cleaning step
 2 files changed, 2 insertions(+)
 create mode 100644 clean.Rmd

`bio` Repository

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

Show me the solution

If needed, create a project out of the cases folder:

R

usethis::create_project(path = "bio")

Initialise git:

R

usethis::use_git()

Create your biography file me.md using the Rstudio editor.

R

usethis::edit_file("me.md")

Save the file.

Once in place, in the Terminal add and commit it to the repository:

BASH

$ git add me.md
$ 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.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.