Python environment in a container

Objectives

• Learn how to create a Python environment in an apptainer image

Background

Python environments are nowadays very popular due to the popularity of Python as a scientific programming language. These environments can sometimes be problematic for the filesystem as they require thousands of files.

Exercise 1: Creating Python image with image’s pip

Install Python environment to base python image

Use the base python image and install following packages to the image:

• python

• numpy

• pandas

Solution

Create the following definition file python_definition.def:

Bootstrap: docker
From: python:latest

%post
    # Python is already installed in the image
    pip install numpy pandas

You can then create the container with:

$ apptainer build python_environment.sif python_definition.def

You can test out the python with:

$ apptainer run python_environment.sif python

Exercise 2: Creating conda/mamba environment in an image

Install an environment to an apptainer image using an optimized definition file

Create an environment with this definition file customized for environment creation:

https://github.com/simo-tuomisto/micromamba-apptainer

Install the following packages to the environment:

• python

• numpy

• pandas

Solution

Write the following environment.yml:

name: base
channels:
  - conda-forge
dependencies:
  - python
  - numpy
  - pandas

Obtain the micromamba_apptainer.def bootstrap definition file from the repository:

Bootstrap: docker
From: mambaorg/micromamba:latest

%files
environment.yml /opt

%post
    micromamba install -q -y -n base -f /opt/environment.yml

    micromamba clean --all --yes

%labels
    EnvironmentFile: /opt/environment.yml

%help
    This container containes a Python environment created
    from an environment file.

    To run Python from the environment:

        apptainer run my_environment.sif python

    To see the environment file used to create the environment:

        apptainer run my_environment.sif cat /opt/environment.yml

    To see what packags are in the environment:

        apptainer run micromamba list

You can then create the container with:

$ apptainer build my_environment.sif micromamba_apptainer.def

You can test out the python with:

$ apptainer run my_environment.sif python