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 planets directory.

$ cd ~/example_git

Let’s create a file called steps.txt that contains some notes about how to create a git repo. We’ll use nano to edit the file; 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 steps.txt

Type the text below into the steps.txt file:

to initialise a repo: git init

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

$ ls

steps.txt

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

$ cat steps.txt

to initialise a repo: git init

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

$ git status

On branch master

No commits yet

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

	steps.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 steps.txt

and then check that the right thing happened:

$ git status

On branch master

No commits yet

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

	new file:   steps.txt

Git now knows that it’s supposed to keep track of steps.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 "First step for using git"

[master (root-commit) f22b25e] First step for using git
 1 file changed, 1 insertion(+)
 create mode 100644 steps.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:

$ git status

On branch master
nothing to commit, working directory 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 f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: DC User <dcuser@obss.2020>
Date:   Thu Aug 22 09:51:46 2013 -0400

    First step for using git

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 steps.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 we want to add 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 steps.txt
$ cat steps.txt

to initialise a repo: git init
to check status: git status

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

$ git status

On branch master
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:   steps.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/steps.txt b/steps.txt
index df0654a..315bf3a 100644
--- a/steps.txt
+++ b/steps.txt
@@ -1 +1,2 @@
 to initialise a repo: git init
+to check status: git status

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:

$ git commit -m "notes on how to check status"
$ git status

On branch master
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:   steps.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 steps.txt
$ git commit -m "notes on how to check status"

[master 34961b1] notes on how to check status
 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!

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 steps.txt
$ cat steps.txt

to initialise a repo: git init
to check status: git status
to add a file: git add

$ git diff

diff --git a/steps.txt b/steps.txt
index 315bf3a..b36abfd 100644
--- a/steps.txt
+++ b/steps.txt
@@ -1,2 +1,3 @@
 to initialise a repo: git init
 to check status: git status
+to add a file: git add

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 steps.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/steps.txt b/steps.txt
index 315bf3a..b36abfd 100644
--- a/steps.txt
+++ b/steps.txt
@@ -1,2 +1,3 @@
 to initialise a repo: git init
 to check status: git status
+to add a file: git add

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 "notes on how to add"

[master 005937f] note on how to add
 1 file changed, 1 insertion(+)

check our status:

$ git status

On branch master
nothing to commit, working directory clean

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

$ git log

commit 005937fbe2a98fb83f0ade869025dc2636b4dad5
Author: DC User <dcuser@obss.2020>
Date:   Thu Aug 22 10:14:07 2013 -0400

    notes on how to add

commit 34961b159c27df3b475cfe4415d94a6d1fcd064d
Author: DC User <dcuser@obss.2020>
Date:   Thu Aug 22 10:07:21 2013 -0400

    notes on how to check status

commit f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: DC User <dcuser@obss.2020>
Date:   Thu Aug 22 09:51:46 2013 -0400

   First step for using git

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:

$ git log -1

commit 005937fbe2a98fb83f0ade869025dc2636b4dad5
Author: DC User <dcuser@obss.2020>
Date:   Thu Aug 22 10:14:07 2013 -0400

   notes on how to add

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

$ git log --oneline

005937f notes on how to add 
34961b1 notes on how to check status
f22b25e First step for using git

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 master, or other Git references:

$ git log --oneline --graph

* 005937f (HEAD -> master) notes on how to add 
* 34961b1 notes on how to check status
* f22b25e First sep for using git

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 example_scripts
   $ git status
   $ git add example_scripts
   $ git status
   

   Note, our newly created empty directory example_scripts 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>
   

   Try it for yourself:

   $ touch example_scripts/qc.sh example_scripts/analysis.sh
   $ git status
   $ git add example_scripts
   $ git status
   

   Before moving on, we will commit these changes.

   $ git commit -m "Some example scripts"
   

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):

This lesson was derived from https://swcarpentry.github.io/git-novice/04-changes/index.html

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.