Get Started: Data Pipelines

Versioning large data files and directories for data science is great, but not enough. How is data filtered, transformed, or used to train ML models? DVC introduces a mechanism to capture data pipelines — series of data processes that produce a final result.

DVC pipelines and their data can also be easily versioned (using Git). This allows you to better organize projects, and reproduce your workflow and results later — exactly as they were built originally! For example, you could capture a simple ETL workflow, organize a data science project, or build a detailed machine learning pipeline.

Watch and learn, or follow along with the code example below!

Pipeline stages

Use dvc stage add to create stages. These represent processes (source code tracked with Git) which form the steps of a pipeline. Stages also connect code to its corresponding data input and output. Let's transform a Python script into a stage:

⚙️ Expand to download example code.

Get the sample code like this:

$ wget https://code.dvc.org/get-started/code.zip
$ unzip code.zip
$ rm -f code.zip
$ tree
.
├── params.yaml
└── src
    ├── evaluate.py
    ├── featurization.py
    ├── prepare.py
    ├── requirements.txt
    └── train.py

Now let's install the requirements:

We strongly recommend creating a virtual environment first.

$ pip install -r src/requirements.txt

Please also add or commit the source code directory with Git at this point.

$ dvc stage add -n prepare \
                -p prepare.seed,prepare.split \
                -d src/prepare.py -d data/data.xml \
                -o data/prepared \
                python src/prepare.py data/data.xml

A dvc.yaml file is generated. It includes information about the command we want to run (python src/prepare.py data/data.xml), its dependencies, and outputs.

DVC uses these metafiles to track the data used and produced by the stage, so there's no need to use dvc add on data/prepared manually.

💡 Expand to see what happens under the hood.

The command options used above mean the following:

-n prepare specifies a name for the stage. If you open the dvc.yaml file you will see a section named prepare.
-p prepare.seed,prepare.split defines special types of dependencies — parameters. We'll get to them later in the Metrics, Parameters, and Plots page, but the idea is that the stage can depend on field values from a parameters file (params.yaml by default):

prepare:
  split: 0.20
  seed: 20170428

-d src/prepare.py and -d data/data.xml mean that the stage depends on these files to work. Notice that the source code itself is marked as a dependency. If any of these files change later, DVC will know that this stage needs to be reproduced.

-o data/prepared specifies an output directory for this script, which writes two files in it. This is how the workspace should look like after the run:

 .
 ├── data
 │   ├── data.xml
 │   ├── data.xml.dvc
+│   └── prepared
+│       ├── test.tsv
+│       └── train.tsv
+├── dvc.yaml
+├── dvc.lock
 ├── params.yaml
 └── src
     ├── ...

The last line, python src/prepare.py data/data.xml is the command to run in this stage, and it's saved to dvc.yaml, as shown below.

The resulting prepare stage contains all of the information above:

stages:
  prepare:
    cmd: python src/prepare.py data/data.xml
    deps:
      - src/prepare.py
      - data/data.xml
    params:
      - prepare.seed
      - prepare.split
    outs:
      - data/prepared

Once you added a stage, you can run the pipeline with dvc repro. Next, you can use dvc push if you wish to save all the data to remote storage (usually along with git commit to version DVC metafiles).

Dependency graphs (DAGs)

By using dvc stage add multiple times, and specifying outputs of a stage as dependencies of another one, we can describe a sequence of commands which gets to a desired result. This is what we call a data pipeline or dependency graph.

Let's create a second stage chained to the outputs of prepare, to perform feature extraction:

$ dvc stage add -n featurize \
                -p featurize.max_features,featurize.ngrams \
                -d src/featurization.py -d data/prepared \
                -o data/features \
                python src/featurization.py data/prepared data/features

The dvc.yaml file is updated automatically and should include two stages now.

💡 Expand to see what happens under the hood.

The changes to the dvc.yaml should look like this:

 stages:
   prepare:
     cmd: python src/prepare.py data/data.xml
     deps:
     - data/data.xml
     - src/prepare.py
     params:
     - prepare.seed
     - prepare.split
     outs:
     - data/prepared
+  featurize:
+    cmd: python src/featurization.py data/prepared data/features
+    deps:
+    - data/prepared
+    - src/featurization.py
+    params:
+    - featurize.max_features
+    - featurize.ngrams
+    outs:
+    - data/features

⚙️ Expand to add more stages.

Let's add the training itself. Nothing new this time; just the same dvc run command with the same set of options:

$ dvc stage add -n train \
                -p train.seed,train.n_est,train.min_split \
                -d src/train.py -d data/features \
                -o model.pkl \
                python src/train.py data/features model.pkl

Please check the dvc.yaml again, it should have one more stage now.

This should be a good time to commit the changes with Git. These include .gitignore, dvc.lock, and dvc.yaml — which describe our pipeline.

Reproduce

The whole point of creating this dvc.yaml file is the ability to easily reproduce a pipeline:

$ dvc repro

⚙️ Expand to have some fun with it.

Let's try to play a little bit with it. First, let's try to change one of the parameters for the training stage:

Open params.yaml and change n_est to 100, and
(re)run dvc repro.

You should see:

$ dvc repro
Stage 'prepare' didn't change, skipping
Stage 'featurize' didn't change, skipping
Running stage 'train' with command: ...

DVC detected that only train should be run, and skipped everything else! All the intermediate results are being reused.

Now, let's change it back to 50 and run dvc repro again:

$ dvc repro
Stage 'prepare' didn't change, skipping
Stage 'featurize' didn't change, skipping

As before, there was no need to rerun prepare, featurize, etc. But this time it also doesn't rerun train! The previous run with the same set of inputs (parameters & data) was saved in DVC's run-cache, and reused here.

💡 Expand to see what happens under the hood.

dvc repro relies on the DAG definition from dvc.yaml, and uses dvc.lock to determine what exactly needs to be run.

The dvc.lock file is similar to a .dvc file — it captures hashes (in most cases md5s) of the dependencies and values of the parameters that were used. It can be considered a state of the pipeline:

schema: '2.0'
stages:
  prepare:
    cmd: python src/prepare.py data/data.xml
    deps:
      - path: data/data.xml
        md5: a304afb96060aad90176268345e10355
      - path: src/prepare.py
        md5: 285af85d794bb57e5d09ace7209f3519
    params:
      params.yaml:
        prepare.seed: 20170428
        prepare.split: 0.2
    outs:
      - path: data/prepared
        md5: 20b786b6e6f80e2b3fcf17827ad18597.dir

dvc status command can be used to compare this state with an actual state of the workspace.

DVC pipelines (dvc.yaml file, dvc stage add, and dvc repro commands) solve a few important problems:

Automation: run a sequence of steps in a "smart" way which makes iterating on your project faster. DVC automatically determines which parts of a project need to be run, and it caches "runs" and their results to avoid unnecessary reruns.
Reproducibility: dvc.yaml and dvc.lock files describe what data to use and which commands will generate the pipeline results (such as an ML model). Storing these files in Git makes it easy to version and share.
Continuous Delivery and Continuous Integration (CI/CD) for ML: describing projects in way that can be reproduced (built) is the first necessary step before introducing CI/CD systems. See our sister project CML for some examples.

Visualize

Having built our pipeline, we need a good way to understand its structure. Seeing a graph of connected stages would help. DVC lets you do so without leaving the terminal!

$ dvc dag
         +---------+
         | prepare |
         +---------+
              *
              *
              *
        +-----------+
        | featurize |
        +-----------+
              *
              *
              *
          +-------+
          | train |
          +-------+

Refer to dvc dag to explore other ways this command can visualize a pipeline.

Get Started: Data Pipelines

Pipeline stages

Dependency graphs (DAGs)

Reproduce

Visualize

Content