Tracking Changes

Overview

Teaching: 20 min
Exercises: 0 min

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 inflammation directory.

$ pwd

If you are still in infection navigate back up to inflammation

$ cd ..

Let’s create a file called project.txt that contains some notes about what we plan to do in this project. We’ll use nano 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. But remember, the bash command to create or edit a new file will depend on the editor you choose (it might not be nano). For a refresher on text editors, check out “Which Editor?” in The Unix Shell lesson.

$ nano project.txt

Type the text below into the project.txt file:

Some initial data analysis to identify how inflammation changes over time after surgery.

project.txt now contains a single line, which we can see by running:

$ ls

project.txt

$ cat project.txt

Some initial data analysis to identify how inflammation changes over time after surgery.

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

$ git status

On branch main

Initial commit

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

	project.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:

$ git add project.txt

and then check that the right thing happened:

$ git status

On branch main

Initial commit

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

	new file:   project.txt

Git now knows that it’s supposed to keep track of project.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:

$ git commit -m "Start notes on the patient inflammation project"

[[main (root-commit) 40b8a94] Start notes on the patient inflammation project
 1 file changed, 1 insertion(+)
 create mode 100644 project.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) summary of changes made in the commit. If you want to go into more detail, add a blank line between the summary line and your additional notes. They are usually written in the present tense.

If we run git status now:

$ git status

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:

$ git log

commit 40b8a9400329ed7324116cc9392dc8e4842d8501 (HEAD -> main)
Author: Jane Smith <jane.smith@university.ac.uk>
Date:   Wed Jan 3 10:34:07 2018 +0000

    Start notes on the patient inflammation project

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 project.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 Jane adds more information to the file. (Again, we’ll edit with nano and then cat the file to show its contents; you may use a different editor, and don’t need to cat.)

$ nano project.txt
$ cat project.txt

Some initial data analysis to identify how inflammation changes over time after surgery.
Jane is a Data Scientist and Samit is a statistician. We'll need to determine
who is responsible for what in this project.

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

$ 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:   project.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:

$ git diff

diff --git a/project.txt b/project.txt
index 17e2b79..2485f1d 100644
--- a/project.txt
+++ b/project.txt
@@ -1 +1,3 @@
 Some initial data analysis to identify how inflammation changes over time after surgery.
+Jane is a Data Scientist and Samit is a statistician. We'll need to determine
+who is responsible for what in this project.

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; 17e2b79 and 2485f1d 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 new lines.

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

$ git commit -m "Add note about project responsibilities"
$ 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:   project.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:

$ git add project.txt
$ git commit -m "Add note about project responsibilities"

[main 71ed26a] Add note about project responsibilities
 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 for the picture! 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 snapshots, you might get the extra with incomplete makeup walking on the stage for the snapshot because you used -a!) Try to stage things manually, or you might find yourself searching for “git undo commit” more than you would like.

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 another line to the file:

$ nano project.txt
$ cat project.txt

Some initial data analysis to identify how inflammation changes over time after surgery.
Jane is a Data Scientist and Samit is a statistician. We'll need to determine
who is responsible for what in this project.
We may need to bring a third person with Python programming skills into the project.

$ git diff

diff --git a/project.txt b/project.txt
index 2485f1d..3f80947 100644
--- a/project.txt
+++ b/project.txt
@@ -1,3 +1,4 @@
 Some initial data analysis to identify how inflammation changes over time after surgery.
 Jane is a Data Scientist and Samit is a statistician. We'll need to determine
 who is responsible for what in this project.
+We may need to bring a third person with Python programming skills into the project.

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:

$ git add project.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:

$ git diff --staged

diff --git a/project.txt b/project.txt
index 2485f1d..3f80947 100644
--- a/project.txt
+++ b/project.txt
@@ -1,3 +1,4 @@
 Some initial data analysis to identify how inflammation changes over time after surgery.
 Jane is a Data Scientist and Samit is a statistician. We'll need to determine
 who is responsible for what in this project.
+We may need to bring a third person with Python programming skills into the project.

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

$ git commit -m "Add note about extra team members"

[main 005937f] Add note about extra team members
 1 file changed, 1 insertion(+)

check our status:

$ git status

On branch main
nothing to commit, working directory clean

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

$ git log

commit 63f6bc6039c12ce897cf3f02bda1e95fd30fef58 (HEAD -> main)
Author: Jane Smith <jane.smith@university.ac.uk>
Date:   Wed Jan 3 10:42:09 2018 +0000

    Add note about extra team members

commit 71ed26a8f840d2929f5120327ea0accd55074070
Author: Jane Smith <jane.smith@university.ac.uk>
Date:   Wed Jan 3 10:39:19 2018 +0000

    Add note about project responsibilities

commit 40b8a9400329ed7324116cc9392dc8e4842d8501
Author: Jane Smith <jane.smith@university.ac.uk>
Date:   Wed Jan 3 10:34:07 2018 +0000

    Start notes on the patient inflammation project

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 the space bar.
• To search for some_word in all pages, type /some_word and 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:

$ git log -1

commit 63f6bc6039c12ce897cf3f02bda1e95fd30fef58 (HEAD -> main)
Author: Jane Smith <jane.smith@university.ac.uk>
Date:   Wed Jan 3 10:42:09 2018 +0000

   Add note about extra team members

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

$ git log --oneline

63f6bc6 (HEAD -> main) Add note about extra team members
71ed26a Add note about project responsibilities
40b8a94 Start notes on the patient inflammation project

You can also combine the --oneline options with others. One useful combination is:

$ git log --oneline --graph --all --decorate

* 63f6bc6 (HEAD -> main) Add note about extra team members
* 71ed26a Add note about project responsibilities
* 40b8a94 Start notes on the patient inflammation project

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:

$ mkdir directory
$ git status
$ git add directory
$ 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. 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.

2. 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:

git add <directory-with-files>

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):

Choosing a Commit Message

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

1. “Changes”
2. “Added line ‘We discussed who might be responsible for what’ to project.txt”
3. “Add note about project responsibilities”

Solution

Answer 1 is not descriptive enough, and answer 2 is too descriptive and redundant, but answer 3 is good: short but descriptive.

Committing Changes to Git

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

1. $ git commit -m "my recent changes"

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

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

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

Solution

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 project.txt noting your decision on what a third tem member might be resposnible for.
2. Create a new file analysis.txt with your initial thoughts about what data would be useful for your analysis project
3. Add changes from both files to the staging area, and commit those changes.

Solution

First we make our changes to the project.txt and analysis.txt files:

$ nano project.txt
$ cat project.txt

The third team member needs to be competent in both Python and R. They
also need to be familiar with matplotlib and ggplot

$ nano analysis.txt
$ cat analysis.txt

We need data about patients, wards, dates, temperatures and inflammation size

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

$ git add project.txt analysis.txt

Or with multiple commands:

$ git add project.txt
$ git add analysis.txt

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

$ git commit -m "Add note about what data would be useful"

[main a264d5c] Add note about what data would be useful
2 files changed, 3 insertions(+)
create mode 100644 analysis.txt

Author and Committer

For each of the commits you have done, Git stored your name twice. You are named as the author and as the committer. You can observe that by telling Git to show you more information about your last commits:

$ git log --format=full

When committing you can name someone else as the author:

$ git commit --author="Samit Patel <samit.patel@university.ac.uk>"

Create a new repository and create two commits: one without the --author option and one by naming a colleague of yours as the author. Run git log and git log --format=full. Think about ways how that can allow you to collaborate with your colleagues.

Solution

$ git add me.txt
$ git commit -m "Update Jane's bio." --author="Pete Jones <pete.jones@university.ac.uk>"

[main 4162a51] Update Jane's bio.
Author: Pete Jones <pete.jones@university.ac.uk>
1 file changed, 2 insertions(+), 2 deletions(-)

$ git log --format=full
commit 4162a51b273ba799a9d395dd70c45d96dba4e2ff
Author: Frank N. Stein <pete.jones@university.ac.uk>
Commit: Jane Smith <jane.smith@university.ac.uk>

Update Jane's bio.

commit aaa3271e5e26f75f11892718e83a3e2743fab8ea
Author: Jane Smith <jane.smith@university.ac.uk>
Commit: Jane Smith <jane.smith@university.ac.uk>

Jane's initial bio.

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.

• Always write a log message when committing changes.