wietsedv/micromamba repository overview

⁠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

⁠Typical 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

1. Create 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

1. Install from the spec file in your Dockerfile:

FROM mambaorg/micromamba:0.11.3
COPY env.yaml /root/env.yaml
RUN micromamba install -y -n base -f /root/env.yaml && \
    micromamba clean --all --yes

⁠Spec passed on command line

1. Pass package names in a RUN command in your Dockerfile:

FROM mambaorg/micromamba:0.11.3
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

FROM mambaorg/micromamba:0.11.3
COPY env1.yaml /root/env1.yaml
COPY env2.yaml /root/env2.yaml
RUN micromamba create -y -f /root/env1.yaml && \
    micromamba create -y -f /root/env2.yaml && \
    micromamba clean --all --yes

You will then need to use micromamba activate envX to activate env1 or env2. But don't put that micromamba activate envX in a Dockerfile RUN command, as it is only valid for the current invocation of your shell.

⁠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.

⁠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 i(or an equivalent) from a conda package or conda packages that are statically linked against glibc.

⁠Contributors and Acknowledgements

The following people have directly or indirectly contributed to this project:

• Will Holtz
• Wolf Vollprecht
• Thomas Buhrmann (via this github comment⁠)