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· 8 min read
Chris Ottinger

Container images provide an ideal software packaging solution for DataOps and python based data pipeline workloads. Containers enable Data Scientists and Data Engineers to incorporate the latest packages and libraries without the issues associated with introducing breaking changes into shared environments. A Data Engineer or Data Scienctist can quickly release new functionality with the best tools available.

Container images provide safer developer environments but as the number of container images used for production workloads grow, a maintenance challenge can emerge. Whether using pip or poetry to manage python packages and dependencies, updating a container definition requires edits to the explicit package versions as well as to the pinned or locked versions of the package dependencies. This process can be error prone without automation and a repeatable CICD workflow.

A workflow pattern based on docker buildkit / moby buildkit multi-stage builds provides an approach that maintains all the build specifications in a single Dockerfile, while build tools like make provide a simple and consistent interface into the container build stages. The data pipeline challenges addresses with a multi-stage build pattern include:

  • automating lifecycle management of the Python packages used by data pipelines
  • integrating smoke testing of container images to weed out compatibility issues early
  • simplifying the developer experience with tools like make that can be used both locally and in CI/CD pipelines

The Dockerfile contains the definitions of the different target build stages and order of execution from one stage to the next. The Makefile wraps the Dockerfile build targets into a standard set of workflow activities, following a similar to $ config && make && make install

The DataOps Container Lifecycle Workflow

A typical dataops/gitops style workflow for maintaining container images includes actions in the local environment to define the required packages and produce the pinned dependency poetry.lock file or requirements.txt packages list containing the full set of pinned dependent packages.

Given and existing project in a remote git repository with a CI/CD pipeline defined, the following workflow would be used to update package versions and dependencies:

Multi-stage build workflow

The image maintainer selects the packages to update or refresh using a local development environment, working from a feature branch. This includes performing an image smoke-test to validate the changes within the container image.

Once refreshed image has been validated, the lock file or full pinned package list is commited back to the repository and pushed to the remote repository. The CI/CD pipeline performs a trial build and conducts smoke testing. On merge into the main branch, the target image is built, re-validated, and pushed to the container image registry.

The multi-stage build pattern can support both defining both the declared packages for an environment as well as the dependent packages, but poetry splits the two into distinct files, a pyproject.toml file containing the declated packages and a poetry.lock file that contains the full set of declared and dependent packages, including pinned versions. pip supports loading packages from different files, but requires a convention for which requirements file contains the declared packages and while contains the full set of pinned package versions produced by pip freeze. The example code repo contains examples using both pip and poetry.

The following example uses poetry in a python:3.8 base image to illustrate managing the dependencies and version pinning of python packages.

Multi-stage Dockerfile

The Dockerfile defines the build stages used for both local refresh and by the CICD pipelines to build the target image.

Dockerfile Stages

The Dockerfile makes use of the docker build arguments feature to pass in whether the build should refresh package versions or build the image from pinned packages.

Build Stage: base-pre-pkg

Any image setup and pre-python package installation steps. For poetry, this includes setting the config option to skip the creation of a virtual environment as the container already provides the required isolation.

FROM python:3.8 as base-pre-pkg

RUN install -d /src && \
pip install --no-cache-dir poetry==1.1.13 && \
poetry config virtualenvs.create false

Build Stage: python-pkg-refresh

The steps to generate a poetry.lock file containing the pinned package versions.

FROM base-pre-pkg as python-pkg-refresh
COPY pyproject.toml poetry.lock /src/
RUN poetry update && \
poetry install

Build Stage: python-pkg-pinned

The steps to install packages using the pinned package versions.

FROM base-pre-pkg as python-pkg-pinned
COPY pyproject.toml poetry.lock /src/
RUN poetry install

Build Stage: base-post-pkg

A consolidation build target that can refer to either the python-pkg-refresh or the python-pkg-pinned stages, depending on the docker build argument and includes any post-package installation steps.

FROM python-pkg-${PYTHON_PKG_VERSIONS} as base-post-pkg

Build Stage: smoke-test

Simple smoke tests and validation commands to validate the built image.

FROM base-post-pkg as smoke-test
COPY tests/ ./tests
RUN poetry --version && \
python ./tests/

Build Stage: target-image

The final build target container image. Listing the target-image as the last stage in the Dockerfile has the effect of also making this the default build target.

FROM base-post-pkg as target-image

Multi-stage Makefile

The Makefile provides a workflow oriented wrapper over the Dockerfile build stage targets. The Makefile targets can be executed both in a local development environment as well as via a CICD pipeline. The Makefile includes several variables that can either be run using default values, or overridden by the CI/CD pipeline.

Makefile targets

Make Target: style-check

Linting and style checking of source code. Can include both application code as well as the Dockerfile itself using tools such as hadolint.

hadolint ./Dockerfile

Make Target: python-pkg-refresh

The python-pkg-refresh target builds a version of the target image with refreshed package versions. A temporary container instance is created from the target image and the poetry.lock file is copied into the local file system. The smoke-test docker build target is used to ensure image validation is also performed. The temporary container as well as the package refresh image are removed after the build.

@echo ">> Update python packages in container image"
docker build ${DOCKER_BUILD_ARGS} \
--target smoke-test \
--build-arg PYTHON_PKG_VERSIONS=refresh \
--tag ${TARGET_IMAGE_NAME}:$@ .
@echo ">> Copy the new poetry.lock file with updated package versions"
docker create --name ${TARGET_IMAGE_NAME}-$@ ${TARGET_IMAGE_NAME}:$@
docker cp ${TARGET_IMAGE_NAME}-$@:/src/poetry.lock .
@echo ">> Clean working container and refresh image"
docker rm ${TARGET_IMAGE_NAME}-$@
docker rmi ${TARGET_IMAGE_NAME}:$@

Make Target: build

The standard build target using pinned python package versions.

docker build ${DOCKER_BUILD_ARGS} \
--target target-image \

Make Target: smoke-test

Builds an image and peforms smoke testing. The smoke-testing image is removed after the build.

docker build ${DOCKER_BUILD_ARGS} \
--target smoke-test \
--tag ${TARGET_IMAGE_NAME}:$@ .
docker rmi ${TARGET_IMAGE_NAME}:$@


The toolchain combination of multi-stage container image builds with make provides a codified method for the lifecycle management of the containers used in data science and data engineering workloads.

The maintainer:

git checkout -b my-refresh-feature
make python-pkg-refresh
make smoke-test
git add pyproject.toml poetry.lock
git commit -m "python package versions updated"
git push

The CICD pipeline:

make build
make smoke-test
docker push <target-image>:<build-tag>

You can find the complete source code for this article at

· 7 min read
Chris Ottinger is a python based Data Engineering toolbox for building and operating Data Pipelines. Out of the box, Prefect provides an initial workflow for managing data pipelines that results in a container image per data pipeline job.

The one-to-one relationship between data pipeline jobs and container images enables data engineers to craft pipelines that are loosely coupled and don't require a shared runtime environment configuration. However, as the number of data pipeline jobs grow the default container per job approach starts to introduce workflow bottlenecks and lifecycle management overheads. For example, in order to update software components used by flows, such as upgrading the version of Prefect, all the data pipeline job images have to be rebuilt and redeployed. Additionally the container image per job workflow introduces a wait time for data engineers to re-build data pipeline container images and test flows centrally on Prefect Server or Prefect Cloud environment.

Fortunately, Prefect comes to its own rescue with the ability to open up the box, exposing the flexibility in the underlying framework.

Out of the box - Prefect DockerStorage

Out of the box, Prefect provides a simple workflow for defining and deploying data pipelines as container images. After getting a first data pipeline running in a local environment, the attention turns to scaling up development and deploying flows into a managed environment, using either the Prefect Cloud service or a Prefect Server.

Combining Prefect Cloud or Prefect Server with Kubernetes provides a flexible and scalable platform solution for moving data pipelines into production. There are a number of options for packaging data pipeline flow code for execution on kubernetes clusters. The Docker Storage option provides the workflow for bundling the data pipeline job code into container images, enabling a common controlled execution environment and well understood distribution mechanism. The data pipeline runs as a pod using the flow container image.

Prefect Docker Storage workflow steps for building and deploying data pipeline flows include:

Workflow Steps

  • packaging a flow (python code) as a serialised/pickled object into a container image
  • registering the flow using the container image name
  • pushing the container image to a container repository accessible from the kubernetes cluster
  • running the flow by running an instance of the named container image as a kubernetes pod

This is relatively simple immutable workflow. Each data pipeline flow version is effectively a unique and self contained 'point-in-time' container image. This initial workflow can also be extended to package multiple related flows into a single container image, reducing the number of resulting container images. But, as the number of data pipeline jobs grow, there issues of container image explosion and data engineering productivity remain.

Using Prefect GitStorage for flows addresses both container image proliferation as well as development bottlenecks.

Prefect Git Storage

Prefect Git Storage provides a workflow for developing and deploying data pipelines directly from git repositories, such as Gitlab or Github. The data pipeline code (python) is pulled from the git repository on each invocation with the ability to reference git branches and git tags. This approach enables:

  • reducing the number of container images to the number of different runtime configurations to be supported.
  • improving the data engineering development cycle time by removing the need to build and push container images on each code change.
  • when combined with kubernetes Prefect Run Configs and Job templates, enables selection of specific runtime environment images

Note that the GitStorage option does required access from the runtime kubernetes cluster to the central git storage service, e.g. gitlab, github, etc.

Prefect Git Storage workflow steps for 'building' and deploying data pipeline flows include:

Workflow Steps

  • pushing the committed code to the central git service
  • registering the flow using the git repository url and branch or tag reference
  • running the flow by pulling the reference code from the git service in a kubernetes pod

The container image build and push steps are removed from the developer feedback cycle time. Depending on network bandwidth and image build times, this can save remove 5 to 10 minutes from each deployment iteration.

Pushing the flow code

Once a set of changes to the data pipeline code has been committed, push to the central git service.

$ git commit
$ git push

Registering the flow

The flow can be registered with Prefect using either a branch (HEAD or latest) or tag reference. Assuming a workflow with feature branches:

  • feature branches: register the flow code using the feature branch. This enables the latest version (HEAD) of the pushed flow code to be used for execution. It also enables skipping re-registration of the flow on new changes as the HEAD of the branch is pulled on each flow run
  • main line branches: register pinned versions of the flow using git tags. This enables the use of a specific version of the flow code to be pulled on each flow run, regardless of future changes.

Determining the which reference to use:

# using gitpython module to work with repo info
from git import Repo

# presidence for identifing where to find the flow code
# BUILD_TAG => GIT_BRANCH => active_branch
build_tag = branch_name = None
build_tag = os.getenv("BUILD_TAG", "")
if build_tag == "":
branch_name = os.getenv("GIT_BRANCH", "")
if branch_name == "":
branch_name = str(Repo(os.getcwd()).active_branch)

Configuring Prefect Git storage:

from import Git
import my_flows.hello_flow as flow # assuming flow is defined in ./my_flows/

# example using Gitlab
# either branch_name or tag must be empty string "" or None
storage = Git(

storage.add_flow(flow.flow) = storage


Once registered, the flow storage details can be viewed in the Prefect Server or Prefect Cloud UI. In this example, Prefect will use the HEAD version of the main branch on each flow run.

hello flow storage details

Next Steps - Run Config

With Prefect Git Storage the runtime configuration and environment management is decoupled from the data pipeline development workflow. Unlike with Docker Storage, with Git Storage, the runtime execution environment and data pipeline development workflows are defined and managed separately. As an added benefit, the developer feedback loop cycle time is also reduced.

With the data engineering workflow addressed, the next step in scaling out the Prefect solution turns to configuration and lifecycle management of the runtime environment for data pipelines. Prefect Run Configs and Job templates provide the tools retaining the flexibility on container image based runtime environments with improved manageability.