This tutorial shows how to use
gittargets with the Git-based data versioning backend. Before proceeding, please read the README file or documentation website front page for an overview of the package.
Please begin with the installation instructions on the documentation website. In addition, if your
targets pipeline generates large data files, consider installing Git LFS. The Git data backend in
gittargets automatically opts into Git LFS, so you should not need to do any manual configuration to reap the performance benefits.
This backend is uses local Git only. It is possible to push the snapshotted data store to a cloud service like GitHub, GitLab, or Bitbucket, but this is the user’s responsibility. Pipelines usually generate large data files, and GitHub and its peers have file size limitations. Also,
gittargets automatically opts into Git LFS locally (unless
tar_git_init()), and Git LFS on the cloud is a paid service.
The most important steps of the Git data backend are as follows. The rest of this vignette walks through these steps in greater depth.
tar_git_init(): initialize a Git/Git-LFS repository for the data store.
tar_make()) and commit any changes to the source code.
tar_git_snapshot(): create a data snapshot for the current code commit.
tar_git_checkout(): revert the data to the appropriate prior snapshot.
To begin development, we write
_targets.R file for a
targets can handle large complex pipelines for machine learning, Bayesian data analysis, and much more. However, this tutorial focuses on a much simpler pipeline for the sake of pedagogical simplicity.
With our target script in hand, we run the pipeline.1
We inspect the output with
We usually iterate between writing code and running the pipeline until we have a decent set of results. After that, we commit the code to a Git repository, which may or may not live on GitHub.2 Happy Git with R is a great way to learn Git, and the
gert package is a convenient way to interact with Git from R.
Before we snapshot the data, we should check that the code is up to date in the Git repository and the targets are up to date in the pipeline. The
tar_git_status() function is an easy way to do this.3
Our code and pipeline look ready for a data snapshot. First, we initialize the data repository with
tar_git_init() writes a
.gitattributes file in the data store that automatically opts into Git LFS. If you have Git LFS but do not wish to use it, please remove the
.gitattributes after calling
Then, we create our first data commit with
In the Git data backend, a data snapshot is a special kind of Git commit (gray boxes above). Each data commit is part of a data branch (vertical dashed lines above), and each data branch is specific to the current code commit (green and brown boxes above). In fact, each data branch name is of the form
<SHA1> is the Git SHA1 hash of the corresponding code commit. You can always create a data snapshot, but it will supersede any prior data snapshot you already have for the current code commit. To revert to a previous data snapshots for a given code snapshot, you will need to manually enter the repository and check out the relevant data commit.
Development typically happens in cycles: develop the code, run the pipeline, commit the code, snapshot the data, and repeat. Not all code commits need a data snapshot, especially if the
targets pipeline generates a lot of data. But even then, it is helpful to snapshot the data at key milestones, e.g. if an alternative research question comes up and it is desirable to create a new Git branch for the code. For example, suppose we wish to apply the same pipeline to a different dataset. The code changes:
We run the pipeline and inspect the new output.
We put the code in a new Git branch.
Finally, we create a data snapshot for the new code commit.
Now, suppose we want to switch the project back to the original dataset (
airquality). To transition completely, we need to revert both the code and the data. If we only revert the code, then the data store will sill reflect the
UKgas dataset, and none of our targets will be up to date. At this point, it is a good time to pause and check the
gittargets log to see which code commits have available data snapshots.5
To check out the old
airquality code, we use
But because we did not revert the data, our results still reflect the
Thus, all our targets are out of date.
To bring our targets back up to date with the
airquality data, instead of beginning a potentially long computation with
tar_make(), we can check out the data snapshot that matches our current code commit.
Now, our results reflect the
airquality dataset we previously analyzed.
And all our targets are up to date.
It is common to merge code branches into one another. When this happens, a new merge commit is created in the code repository, and the data repository remains unchanged. In fact, the only change is that the code repository is now at a new commit that has no data snapshot yet. If you wish, simply create a new data snapshot with
tar_git_snapshot(). If the code commit immediately prior had an up-to-date data snapshot of its own, then the new snapshot for the merge commit should cost little storage or runtime.
Only files inside the
targets data store are tracked in a
gittargets data snapshot. If your pipeline requires custom external files, you may put them in a folder called
_targets/user/. That way,
gittargets will automatically put them under data version control in the next snapshot.
targets pipeline generates large data files, consider installing Git LFS. Once you install Git LFS, it should just work on your project right out of the box because
tar_git_init() writes the following to
In addition, every data snapshot with
tar_git_snapshot() creates a new Git branch. With thousands of commits and thus thousands of branches, performance may suffer unless you ensure
TRUE in the function call (default).6(https://git-scm.com/docs/git-pack-refs) in the command line with your working directory inside
Alternatives to GitHub include GitLab and Bitbucket.↩︎
tar_git_status_data() each generate a piece of the
tar_git_snapshot() shows runs
tar_git_status() and prompts the user to confirm the snapshot. But in this example, we skip this step.↩︎
If you chose not to call
tar_git_snapshot() for some code commits, then not all your code commits will have available data snapshots.↩︎
Alternatively, you can call
tar_git_snapshot(pack_refs = FALSE) and then afterwards run
git pack-refs --all↩︎