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Get Started: Data Pipelines

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Versioning large data files and directories for data science is powerful, but often not enough. Data needs to be filtered, cleaned, and transformed before training ML models - for that purpose DVC introduces a build system to define, execute and track data pipelines — a series of data processing stages, that produce a final result.

💫 DVC is a "Makefile" system for machine learning projects!

DVC pipelines are versioned using Git, and allow you to better organize projects and reproduce complete workflows and results at will. You could capture a simple ETL workflow, organize your project, or build a complex DAG (Directed Acyclic Graph) pipeline.

Later, we will find DVC allows you to manage machine learning experiments on top of these pipelines - controlling their execution, injecting parameters, etc.

Setup

Working inside an initialized DVC project, let's get some sample code for the next steps:

$ wget https://code.dvc.org/get-started/code.zip
$ unzip code.zip && rm -f code.zip

Get the sample code like this:

$ tree
.
├── params.yaml
└── src
    ├── evaluate.py
    ├── featurization.py
    ├── prepare.py
    ├── requirements.txt
    └── train.py

The DVC tracked data needed to run this example can be downloaded using dvc get:

$ dvc get https://github.com/iterative/dataset-registry \
          get-started/data.xml -o data/data.xml

Now, let's go through some usual project setup steps (virtualenv, requirements, Git).

First, create and use a virtual environment (it's not a must, but we strongly recommend it):

$ virtualenv venv && echo "venv" > .gitignore
$ source venv/bin/activate

Next, install the Python requirements:

$ pip install -r src/requirements.txt

Finally, this is a good time to commit our code to Git:

$ git add .github/ data/ params.yaml src .gitignore
$ git commit -m "Initial commit"

Pipeline stages

Use dvc stage add to create stages. These represent processing steps (usually scripts/code tracked with Git) and combine to form the pipeline. Stages allow connecting code to its corresponding data input and output. Let's transform a Python script into a stage:

$ 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 the pipeline definition to automatically track the data used and produced by any stage, so there's no need to manually run dvc add for data/prepared!

Details on the command options used above:

  • -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. Any stage can depend on parameter values from a parameters file (params.yaml by default). We'll discuss those more in the Metrics, Parameters, and Plots page.

prepare:
  split: 0.20
  seed: 20170428
  • -d src/prepare.py and -d data/data.xml mean that the stage depends on these files (dependencies) to work. Notice that the source code itself is marked as a dependency as well. If any of these files change, DVC will know that this stage needs to be reproduced when the pipeline is executed.

  • -o data/prepared specifies an output directory for this script, which writes two files in it.

    This is how the workspace looks 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've added a stage, you can run the pipeline with dvc repro.

Dependency graphs

By using dvc stage add multiple times, defining outputs of a stage as dependencies of another, we can describe a sequence of dependent commands which gets to some desired result. This is what we call a dependency graph which forms a full cohesive pipeline.

Let's create a 2nd 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 will now be updated to include the two stages.

And finally, let's add a 3rd train stage:

$ 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

Finally, our dvc.yaml should have all 3 stages.

This would be a good time to commit the changes with Git. These include .gitignore(s) and dvc.yaml — which describes our pipeline.

$ git add .gitignore data/.gitignore dvc.yaml
$ git commit -m "pipeline defined"

Great! Now we're ready to run the pipeline.

Reproducing

The pipeline definition in dvc.yaml allow us to easily reproduce the pipeline:

$ dvc repro

You'll notice a dvc.lock (a "state file") was created to capture the reproduction's results.

dvc repro relies on the dependency graph of stages defined in 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: 22a1a2931c8370d3aeedd7183606fd7f
        size: 14445097
      - path: src/prepare.py
        md5: f09ea0c15980b43010257ccb9f0055e2
        size: 1576
    params:
      params.yaml:
        prepare.seed: 20170428
        prepare.split: 0.2
    outs:
      - path: data/prepared
        md5: 153aad06d376b6595932470e459ef42a.dir
        size: 8437363
        nfiles: 2

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

It's good practice to immediately commit dvc.lock to Git after its creation or modification, to record the current state & results:

$ git add dvc.lock && git commit -m "first pipeline repro"

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

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

You will 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 was reused.

Visualizing

Having built our pipeline, we need a good way to understand its structure. Visualizing it as a graph of connected stages helps with that. 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.

Summary

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 a way that can be built and reproduced is the first necessary step before introducing CI/CD systems. See our sister project CML for some examples.
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