Ansible role: mambaorg.micromamba

Install micromamba, and optionally create a root/base conda environment.

Links

• GitHub
• Galaxy
• Advanced usage example for bootstrapping and setting up a system conda environment in a Docker image

Motivation

Conda is a very powerful Python-centric dependency management tool. Unfortunately, for environments with large numbers of dependencies, its slow dependency solver can take hours to complete.

The new Mamba project addresses this issue by reimplementing the dependency solver in C++, and is lightning-fast. Apart from the solver, mamba delegates most tasks to the otherwise dependable conda tool.

Micromamba is a highly experimental pure C++ package manager for conda environments. Because it has no Python dependencies, it can efficiently create environments for any version of Python from a single micromamba binary. If none of your conda packages has a Python dependency, then Micromamba will even create a conda environment without Python!

Micromamba eliminates the need for "distributions" such as Anaconda or Miniconda. You can set up your desired environment directly.

Role Variables

arch: linux-64
version: latest

For the latest architectures and version numbers, check distributions[#].basename, which has the format {arch}/micromamba-{version}.tar.bz2. Current possible values for arch are linux-64, linux-aarch64, osx-64, osx-arm64, win-64. The format of version is either latest or something like 0.15.2-0, where -0 denotes the build number.

---

dest: /usr/local/bin/micromamba

Location of the micromamba executable.

---

root_prefix: /opt/conda

When the root prefix is defined and does not already exist, a new root prefix will be created in this location.

---

packages:
  - mamba
  - python=3.9

A list of initial conda packages to be installed when a new root prefix is created.

---

file: /tmp/environment.yaml

As an alternative to the list of packages, an environment file or lock file can be provided.

---

root_prefix_condarc:
  channels:
    - conda-forge

Contents to write to .condarc in the new root prefix. If not defined, then no .condarc file is created.

Example Playbooks

- hosts: servers
  become: yes
  roles:
      - mambaorg.micromamba

This downloads the micromamba executable to the default location of /usr/local/bin/micromamba.

---

- hosts: servers
  become: yes
  roles:
      - mambaorg.micromamba
  vars:
    dest: /tmp/micromamba
    root_prefix: /opt/conda
    packages:
      - mamba
      - python=3.9

This downloads micromamba into /tmp/micromamba and creates a new root prefix in /opt/conda/ with Python 3.9 and Mamba.

---

- hosts: servers
  become: yes
  become_user: condauser
  roles:
      - mambaorg.micromamba
  vars:
    root_prefix: ~/micromamba
    root_prefix_condarc:
      channels:
        - conda-forge
    packages:
      - s3fs-fuse

This creates a new root prefix in /home/conda-user/micromamba and creates a conda environment without Python. It also places a .condarc file in the root prefix to configure packages to be installed by default from the conda-forge channel.

Subsequent Usage

In order run any commands from a conda environment, it must first be activated. Activation involves altering the PATH and other environment variables in the active shell (usually Bash). This can be accomplished in various ways.

Directly

eval "$(micromamba shell hook --shell=bash)"
micromamba activate --prefix=/opt/conda

The first command executes a sequence of commands which define a Bash function, also named micromamba. (Otherwise, the micromamba executable would run as a subprocess which is unable to modify the environment of the shell.) The second command runs the newly-defined Bash function to activate the environment located at /opt/conda.

With an initialization script

micromamba shell init --shell=bash --prefix=/opt/conda

This modifies ~/.bashrc so that in subsequent interactive Bash sessions, the command micromamba activate suffices to activate the environment. (The command micromamba activate can be added to ~/.bashrc if desired.)

With mamba or conda

Since micromamba is experimental, instead of relying on the above possibilities which use micromamba for activation, it is advisable to install mamba into the environment and run

/opt/conda/bin/conda init bash
/opt/conda/bin/mamba init bash

These commands modify ~/.bashrc so that the environment will be fully activated in subsequent interactive Bash sessions.

Troubleshooting

If Bash is not being run interactively, then the .bashrc will not be sourced, so running micromamba activate will fail. In this case, you can either use the direct activation procedure or force an interactive shell by passing the -i flag to the bash command.

License

MIT

Author Information

Currently maintained by Ben Mares (@maresb) and Andreas Trawoeger (@atrawog). Initial version by @maresb. Contributions are welcome!