micromamba-docker

Micromamba for fast building of small conda-based containers.

Images available on Dockerhub at mambaorg/micromamba. Source code on GitHub at mamba-org/micromamba-docker.

"This is amazing. I switched CI for my projects to micromamba, and compared to using a miniconda docker image, this reduced build times more than 2x" -- A new micromamba-docker user

Usage

Single environment

Use the 'base' environment if you will only have a single environment in your container, as this environment already exists and is activated by default.

From a yaml spec file

Define your desired environment in a spec file:

name: base
channels:
  - conda-forge
dependencies:
  - pyopenssl=20.0.1
  - python=3.9.1
  - requests=2.25.1

Install from the spec file in your Dockerfile:

FROM mambaorg/micromamba:0.17.0
COPY --chown=micromamba:micromamba env.yaml /tmp/env.yaml
RUN micromamba install -y -n base -f /tmp/env.yaml && \
    micromamba clean --all --yes

Spec passed on command line

Pass package names in a RUN command in your Dockerfile:

FROM mambaorg/micromamba:0.17.0
RUN micromamba install -y -n base -c conda-forge \
       pyopenssl=20.0.1  \
       python=3.9.1 \
       requests=2.25.1 && \
    micromamba clean --all --yes

Multiple environments

This is not a common usage. Most use cases have a single environment per derived image.

FROM mambaorg/micromamba:0.17.0
COPY --chown=micromamba:micromamba env1.yaml /tmp/env1.yaml
COPY --chown=micromamba:micromamba env2.yaml /tmp/env2.yaml
RUN micromamba create -y -f /tmp/env1.yaml && \
    micromamba create -y -f /tmp/env2.yaml && \
    micromamba clean --all --yes

You can then set the active environment by passing the ENV_NAME environment variable like:

docker run -e ENV_NAME=env2 micromamba

Changing the user

Prior to June 30, 2021, the image defaulted to running as root. Now it defaults to running as the non-root user micromamba. Micromamba-docker can be run as any user by passing the docker run ... command the --user=UID:GID parameters. Running with --user=root is supported.

Minimizing final image size

Uwe Korn has a nice blog post on making small containers containing conda environments that is a good resource. He uses mamba instead of micromamba, but the general concepts still apply when using micromamba.

Support

Please open an issue if the micromamba docker image does not behave as you expect. For issues about the micromamba program, please use the mamba issue tracker.

Contributing

This project is a community effort and contributions are welcome. Best practice is to discuss proposed contributions on the issue tracker before you start writing code.

Development

Testing

The Bats testing framework is used to test the micromamba docker images and derived images. When cloning this repo you'll want to use git clone --recurse-submodules ..., which will bring in the git submodules for Bats. With the submodules present, ./test.sh will run the test suite. If GNU parallel is present, then the test suite will be run in parallel using all logical CPU cores available.

Parent container choice

As noted in the micromamba documentation, the official micromamba binaries require glibc. Therefore Alpine Linux does not work natively. To keep the image small, a Debian slim image is used as the parent. On going efforts to generate a fully statically linked micromamba binary are documented in mamba github issue #572, but most conda packages also depend on glibc. Therefore using a statically linked micromamba would require either a method to install glibc (or an equivalent) from a conda package or conda packages that are statically linked against glibc.

drelo/micromamba-docker