Tracking Changes
Last updated on 2024-12-04 | 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.
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:
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):
OUTPUT
amr-data-dictionary.txtamr-data-dictionary.txt should contain 4 lines, which we
can see by running:
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:
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:
and then check that the right thing happened:
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:
OUTPUT
[main (root-commit) f22b25e] Start notes on Mars as a base
1 file changed, 1 insertion(+)
create mode 100644 amr-data-dictionary.txtWhen 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 we run git status now:
OUTPUT
On branch main
nothing to commit, working tree cleanit 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:
OUTPUT
commit f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: <John Doe> <john.doe@unkown.com>
Date: Thu Aug 22 09:51:46 2013 -0400
Start data dictionary for AMR datagit 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.)
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 personWhen we run git status now, it tells us that a file it
already knows about has been modified:
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:
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 personThe 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
diffcommand comparing the old and new versions of the file. - The second line tells exactly which versions of the file Git is
comparing;
df0654aand315bf3aare 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.
After reviewing our change, it’s time to commit it:
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:
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!
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:
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 CiprofloxacinOUTPUT
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 CiprofloxacinSo 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:
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:
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 Ciprofloxacinit shows us the difference between the last committed change and what’s in the staging area. Let’s save our changes:
OUTPUT
[main 1c642ba] Complete the data dictionary
1 file changed, 11 insertions(+)check our status:
OUTPUT
On branch main
nothing to commit, working tree cleanand look at the history of what we’ve done so far:
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 dictionaryWord-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_wordin all pages, press / and typesome_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:
OUTPUT
commit 1c642ba5c32a722081ea9e3c80ef0634b4e071f3 (HEAD -> main)
Author: John Doe <john.doe@unkown.com>
Date: Wed Aug 14 15:01:56 2024 +0100
Complete the data dictionaryYou can also reduce the quantity of information using the
--oneline option:
OUTPUT
1c642ba (HEAD -> main) Complete the data dictionary
7464434 Add entry for the id column
0f98820 Start data dictionaryYou 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:
OUTPUT
* 1c642ba (HEAD -> main) Complete the data dictionary
* 7464434 Add entry for the id column
* 0f98820 Start data dictionaryDirectories
Two important facts you should know about directories in Git.
- Git does not track directories on their own, only files within them. Try it for yourself:
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.
- 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:
Try it for yourself:
BASH
$ touch notes/2024-08-14.txt spaceships/2024-08-13.txt
$ git status
$ git add notes
$ git statusBefore moving on, we will commit these changes.
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 amr-data-dictionary.txt?
- “Changes”
- “Added lines 7-17 to amr-data-dictionary.txt”
- “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?
- 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.
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
amr-data-dictionary.txtto mention that more detailed information on each variable can be found in a separate file with the same name as the variable. - Create a new file
ciprof.txtwith a short description of what Ciproflaxacin is (feel free to make something up). - 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:
OUTPUT
More information on each variable can be found in the corresponding file.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:
Or with multiple commands:
Now the files are ready to commit. You can check that using
git status. If you are ready to commit use:
```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:
Create a new folder called bio and ‘move’ into it:
Initialise git:
Create your biography file me.txt using
nano or another text editor. Once in place, add and commit
it to the repository:
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:
Key Points
-
git statusshows 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 addputs files in the staging area. -
git commitsaves the staged content as a new commit in the local repository. - Write a commit message that accurately describes your changes.