Git allows us to tag commits, i.e. give names to specific points in the history of our project. This can be particularly important for reproducible research, but also for development projects that want to highlight specific versions of a software. A tag can be, for example, the version of the repository that was used for the manuscript submission, the version used during resubmission, and, most importantly, the version used for the final publication. The first two examples are mainly useful internally, but the latter is essential for other researchers to be able to rerun your published analysis.

Let’s assume that the status of the repository as it is now is ready for a submission to a journal. It may for example contain the scripts that were used to generate the manuscript figures. Let’s add a tag:

git tag "submission1"

We can now list all the tags available in the current repository:

git tag

Tip
You can use the flag -a or --annotate to give more detailed information about a specific tag, similar to a commit message. This can be quite useful when there are many changes that happened, in that it allows you to summarise them. You can, for example, do git tag -a submission1 -m "Annotation for tag submission1" to write the annotation along with the command (similar to the -m flag for committing) or just git tag -a submission1 to write the annotation with your default editor. To list all your tags along with their annotations you can use e.g. git tag -n10 (which will list the first 10 lines of each tag’s annotation).

Let’s assume we now got comments from the reviewers, and by fixing those we had to update our code. Open config.yml and change the line max_reads: 25000 to max_reads: 50000. Commit and tag the changes:

git add config.yml
git commit -m "Increase number of reads"
git tag "revision-1"

Now let’s say that the reviewers were happy and the manuscript was accepted for publication. Let’s immediately add a tag:

git tag "publication"

A good thing about using tags is that you can easily switch between versions of your code. Let’s move to the first submission version:

git checkout submission1

Open config.yml and note that the max_reads variable is 25000! To go back to the latest version, run:

git checkout main

Open config.yml and see that the value is now 50000.

Tip
You can also see the difference between tags in the same way as for branches and commits using e.g. git diff <tag1> <tag2>.

At this point could run git log --oneline --decorate to get a condensed commit history, where you should also be able to see the tagged commits.

Quick recap
We have now learned how to tag important commits:

git tag adds a tag to a commit.

git checkout moves between tags in a similar fashion as between branches.