Documentation for the DataJoint’s Miniconda3 Image

A minimal base docker image with conda.
For more details, have a look at prebuilt images, source, and documentation.

Image Hierarchy

_images/image_hierarchy.png

Launch Locally

Debian

docker-compose -f dist/debian/docker-compose.yaml --env-file config/.env up --build

Alpine

docker-compose -f dist/alpine/docker-compose.yaml --env-file config/.env up --build

Features

  • Provides a minimal docker image with conda, python, and pip.

  • Adds conda-forge channel as default.

  • Disables conda auto-update functionality. This prevents the image from growing large between builds. To update, invoke conda update explicitly.

  • Includes en_US.UTF-8 locale.

  • Creates an internal system user anaconda. By default, utilizes anaconda:anaconda when creating containers.

  • Image avoids using root to preserve possible privilege escalation vulnerabilities on docker host. As a means to perform installs while under anaconda:anaconda, you may utilize any combination of the following and trigger it via /entrypoint.sh [command to run once completed] e.g. /entrypoint.sh echo done.

    • Debian dependencies: Create a \n delimited file containing the system dependencies at /tmp/apt_requirements.txt. This can be created manually within container/image or mounted in.

    • Alpine dependencies: Create a \n delimited file containing the system dependencies at /tmp/apk_requirements.txt. This can be created manually within container/image or mounted in.

    • Conda dependencies: Create a \n delimited file containing the conda dependencies at /tmp/conda_requirements.txt. This can be created manually within container/image or mounted in.

    • Pip dependencies: Create a \n delimited file containing the pip dependencies at /tmp/pip_requirements.txt. This can be created manually within container/image or mounted in.

  • When mounting volumes (avoid mounting files with root permissions only!), accessing files within image via anaconda:anaconda can result in permission denied errors. To avoid this, simply add a user spec in docker-compose.yaml with the appropriate HOST_UID e.g. user: 1000:anaconda. Running /entrypoint.sh will then trigger a reassociation of anaconda’s UID to allow permissions to access mounted files. Note that entrypoint.sh is automatically invoked when starting containers. If you are utilizing the included reference docker-compose.yaml files, you may simply set the HOST_UID environment value when building or starting the container.

  • Allows user anaconda to be renamed by setting environment variable NEW_USER before launching container.

  • Allows user’s HOME directory to be moved to a new directory based on setting environment variable NEW_HOME before launching container. Behavior is that it will move the directory but also create a symbolic link from /home/${USER} to the new HOME for convenience.

  • Applies image compresssion.

Usage Notes

  • As long as a container user is a member of anaconda group, they should have acccess to perform conda and pip operations within the default environment i.e. base.

  • To properly shell into the container and activate the default environment, see the CMD specification in the Dockerfile. For example:

    docker exec -it debian_app_1 bash || docker exec -it alpine_app_1 sh

  • When installing a conda package, make sure to pin the python version to prevent upgrade within the base environment or perform the conda install in a new conda environment.

Testing

To rebuild and run tests locally, execute the following statements:

set -a  # automatically export sourced variables
. config/.env  # source config for build and tests
docker buildx bake -f dist/${DISTRO}/docker-compose.yaml --set *.platform=${PLATFORM} --set *.context=. --load # build image
tests/main.sh  # run tests
set +a  # disable auto-export behavior for sourced variables

Miniconda3 Release Archive

Acknowledgements

Development for this image was heavily borrowed from https://github.com/ContinuumIO/docker-images.