DVC - Data Versioning

This article also lives on GitHub

About DVC (Data Version Control)

What's DVC?

version control system for data science and machine learning
compatible with git (it's based on git)

What can DVC do?

track
- data
- model
- pipeline
- metrics
use storage directly
no external services needed

Who are the targeted users of DVC?

ML research / engineer
DevOps & Engineers

Why DVC?

It links your data, model, and pipelines with your metrics.
- reproducibility
- trackable

Read DVC - Versioning Data and Models for more use cases

How to use DVC?

Install DVC globally

I suggest using pipx if you're to install DVC globally. However, an even better way is to install it inside the virtual environment within your project.

$ pip install pipx
$ pipx install dvc
$ dvc --version

2.3.0

DVC also provides Shell Completion and Syntax Highlighting Plugins for popular editors.

Take a look at the example project

I'll use dvc_example to demonstrate how I applied DVC to an existing machine learning project. The example is based on Recognizing hand-written digits from scikit-learn documentation. All the DVC parts start from v1-base. You can git checkout to the tag to follow along.

$ git clone https://github.com/Lee-W/dvc_example/ --branch v1-base
$ cd dvc_example
$ tree
.
├── LICENSE
├── Pipfile
├── Pipfile.lock
├── digit_recognizer
│   ├── __init__.py
│   └── digit_recognizer.py
├── docs
│   └── README.md
├── mkdocs.yml
├── output
└── tasks.py

To set up the development environment, you'll need pipenv and invoke. If you run into an error when running pipenv install, you can run export SYSTEM_VERSION_COMPAT=1 before it. It's an open issue (Issue with NumPy, macOS 11 Big Sur, Python 3.9.1 Does pipenv not use the latest pip? #4564) of pipenv as of now. Or, you can just run the following commands.

# install needed tools
pipx install pipenv invoke

# set up environments
invoke init-dev

We'll use digit_recognizer/digit_recognizer.py for training a model that can recognize handwritten digits.

def main():
    X, y = load_data()
    X_train, X_test, y_train, y_test = process_data(X, y)
    model = train_model(X_train, y_train)
    predicted_y = model.predict(X_test)
    output_results(y_test, predicted_y)
    output_metrics(y_test, predicted_y)

Install DVC into the virtual environment

pipenv install dvc

If you're to save data to remote storage, you might need to install extra dependencies.
(e.g., pipenv install dvc[s3])

Supported types

[s3]
[azure]
[gdrive]
[gs]
[oss]
[ssh]

Or, use pipenv install dvc[all] to install them all

Read dvc remote for more information

Initialize DVC

# initialize DVC configurations
$ pipenv run dvc init

# see what's created by DVC
$ tree .dvc

.dvc
├── config
└── plots
    ├── confusion.json
    ├── confusion_normalized.json
    ├── default.json
    ├── linear.json
    ├── scatter.json
    └── smooth.json

# track DVC configuration through git
$ git add .dvc

# git commit
$ pipenv run cz commit

Add DVC remote

I'll use another local directory ../dvc_remote as our remote storage. You can change it to s3 or other remote storage.

mkdir ../dvc_remote
dvc remote add --default local ../dvc_remote

Through --default flag, we can push/pull from local remote without specifying remote name.

Let see what's changed in .dvc/config.

$ cat .dvc/config

[core]
remote = local
['remote "local"']
url = ../../dvc_remote

The url is ../../dvc_remote instead of ../dvc_remote because it's the relative path to .dvc. As we've not yet push anything to our pseudo remote, ../dvc_remote is still empty.

Track data through DVC

By this time, the data is loaded through sklearn.datasets.load_digits. We're going to change it to read from static file in data/.

def load_data():
    # Load data
    digits = datasets.load_digits()
    ...

We can use the following script to output the digit data into data/. Note that it's a one-time use script. We won't add it into git.

import os

import pandas as pd
from sklearn import datasets

os.mkdir("data")

digits = datasets.load_digits()

df = pd.DataFrame(digits.data)
df.to_csv("data/digit_data.csv", header=False, index=False)

df = pd.DataFrame(digits.target)
df.to_csv("data/digit_target.csv", header=False, index=False)

We'll need to make changes to load_data and main functions to read data from these files.

def load_data(X_path, y_path):
    with open(X_path) as input_file:
        csv_reader = csv.reader(input_file, quoting=csv.QUOTE_NONNUMERIC)
        X = list(csv_reader)

    with open(y_path) as input_file:
        csv_reader = csv.reader(input_file, quoting=csv.QUOTE_NONNUMERIC)
        y = [row[0] for row in csv_reader]

    return X, y

......

def main():
    X, y = load_data("data/digit_data.csv", "data/digit_target.csv")
    ......

Run pipenv run python digit_recognizer/digit_recognizer.py to check whether everything works as we expected. If so, add these code changes into git.

Next, add data/ to DVC.

$ pipenv run dvc add data

100% Add|████████████████|1/1 [00:00,  2.14file/s]

To track the changes with git, run:

git add data.dvc .gitignore

dvc add creates a data.dvc file to track data/ and add it into .gitignore so that data/ will only be tracked through DVC but not git.

# Add DVC files into git track
git add .gitignore data.dvc

# git commit
pipenv run cz commit

In data.dvc, we can see 2 files (digit_data.csv and digit_target.csv) are tracked.

$ cat data.dvc

outs:
- md5: b8d81f4964ecb86739c79c833fb491f3.dir
  size: 494728
  nfiles: 2
  path: data

Push these tracked data into DVC remote

dvc push

See what's changed in our repo storage ../dvc_remote

$ tree ../dvc_remote

../dvc_remote
├── 02
│   └── b861b6dc8e08da6d66547860f69277
├── 8c
│   └── ba569595920d230ade453b150f372b
└── b8
    └── d81f4964ecb86739c79c833fb491f3.dir

3 directories, 3 files

The md5 value of our tracked data is b8d81f4964ecb86739c79c833fb491f3.dir. There's also a corresponding file in ../dvc_remote/b8/d81f4964ecb86739c79c833fb491f3.dir.

$ cat ../dvc_remote/b8/d81f4964ecb86739c79c833fb491f3.dir

[{"md5": "02b861b6dc8e08da6d66547860f69277", "relpath": "digit_data.csv"}, {"md5": "8cba569595920d230ade453b150f372b", "relpath": "digit_target.csv"}]%

This file indicates where the actual data sources are stored in ../dvc_remote.

In conclusion, if we want to know how data is stored through DVC,

find the md5 value in *.dvc in our project

find the path that matches this md5 value in our remote storage

use the md5 value specified in the previous step to find the data sources in our remote storage

But most of the time, we don't need to do so. We can leave the tracking work to DVC.

Fetch data from DVC remote storage

# temporary delete our data locally
$ rm -rf data

# check whether DVC actually tracks our data
$ dvc status

data.dvc:
changed outs:
    deleted:            data

# bring our data back from remote storage
$ dvc checkout data

data
├── digit_data.csv
└── digit_target.csv

Add data changes into DVC

To demonstrate how DVC track data changes, let's remove the last 2 rows from data/digit_data.csv and data/digit_target.csv.

# check what's changed
$ dvc status

data.dvc:
changed outs:
    modified:           data

# Add these changes to DVC and git
$ dvc add
$ git add data.dvc
# git commit
$ pipenv run cz commit

# Push these changes to our remote storage
$ dvc push

The md5 value has been changed, and the size of our data is smaller than our previous record, 494728.

$ cat data.dvc

outs:
- md5: a333e114a49194e823ab9a4fa9e33ee9.dir
  size: 494172
  nfiles: 2
  path: data

More files are added to ../dvc_remote due to the data changes. You can follow the steps in the previous section to see what're actually store.

$ tree ../dvc_remote

../dvc_remote
├── 02
│   └── b861b6dc8e08da6d66547860f69277
├── 2a
│   └── 6cfa13365ac9b3af5146133aca6789
├── 8c
│   └── ba569595920d230ade453b150f372b
├── 94
│   └── 2481fce846fb9750b7b8023c80a5ef
├── a3
│   └── 33e114a49194e823ab9a4fa9e33ee9.dir
└── b8
    └── d81f4964ecb86739c79c833fb491f3.dir

6 directories, 6 files

Let's git checkout to the previous git commit to see what happens if we only revert the changes in data.dvc.

# or "git checkout v2-track-data"
git checkout HEAD~1

After running wc -l data/digit_data.csv, we'll still find 1795 rows instead of 1797 rows in the previous stage. That's because we need to run dvc checkout as well.

We might easily forget this step. Thus, DVC implements a git-hook that can trigger dvc checkout right after git checkout. You can install these git-hooks through dvc install. These hooks are added into .git/hooks. If you want to know the detail of what's added, read dvc install.

Test these steps again. There should be an additional line after running git checkout. This is the output message of dvc checkout.

M       data/

Push our code to a remote git repository

git remote add origin <REMOTE GIT REPO>
git push origin main

Fetch code and data changes from remote

We've already pushed all the code and data changes to remote. Let's see how we could reproduce in another environment.

# check what's in our repo
$ dvc list <REMOTE GIT REPO>

.dvcignore
.github
.gitignore
LICENSE
Pipfile
Pipfile.lock
data
data.dvc
digit_recognizer
docs
mkdocs.yml
output
tasks.py

Although git does not track data/, we can still list it through DVC.

Because we use relative path ../dvc_remote as DVC remote storage, we need to create the new project in the same layer as dvc_example. We'll clone the project into ../dvc_example_on_another_machine.

# Clone repo git repo
$ git clone <YOUR REMOTE GIT REPO> ../dvc_example_on_another_machine
$ cd ../dvc_example_on_another_machine
$ tree .

.
├── LICENSE
├── Pipfile
├── Pipfile.lock
├── data.dvc
├── digit_recognizer
│   ├── __init__.py
│   └── digit_recognizer.py
├── docs
│   └── README.md
├── mkdocs.yml
├── output
└── tasks.py

3 directories, 9 files

As you can see, data/ has not yet been added to the project. We can now pull data from our DVC remote storage.

# pull data from default DVC remote storage
$ dvc pull

A   data/
1 file added and 2 files fetched

# `data` has now been added to the project
$ tree .

.
├── LICENSE
├── Pipfile
├── Pipfile.lock
├── data
│   ├── digit_data.csv
│   └── digit_target.csv
├── data.dvc
├── digit_recognizer
│   ├── __init__.py
│   └── digit_recognizer.py
├── docs
│   └── README.md
├── mkdocs.yml
├── output
└── tasks.py

4 directories, 11 files

That's all for data versioning in DVC. In the next post, We'll continue on versioning a data pipeline, tracking parameters and metrics. We won't need dvc_example_on_another_machine for the following steps. Feel free to remove it and change directory back to dvc_example.

Reference

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