Reproducible environments

Being able to create a reproducible environment is probably one of the biggest challenges when it comes to reproducibility.

When reproducing the results of a research paper you would like to use the same environment as was used when writing the paper. This can be achieved by publishing a Docker image.

We recommend that you publish a docker image every time you create a new version of your code (see Versioning for more info about how to create a version).

You can read more about how to publish a docker image here and you can see an example Dockerfile in the example-paper repo.

Additional resources on reproducible environments can be found at Simula Tools meetup: Reproducible Environments/

Language specific dependencies

You should also list the language specific packages you used to generate the results for your paper. In Python these are typically listed in a requirements.txt file.

To export the exact dependencies in Python you use the following command

pip freeze > requirements.txt

conda

Many people use conda for their applications. In this section, we assume that you are familiar with how to set up a conda environment file. We will use a simple environment.yml file, whose environment only needs DOLFIN

name: test-env
channels:
  - conda-forge
dependencies:
  - fenics-dolfin

We create the following Dockerfile to install the conda environment

FROM condaforge/mambaforge

ENV DEBIAN_FRONTEND=noninteractive

# Install ssh (missing dependency to run conda envs)
RUN apt-get update && \
    apt-get install -y ssh build-essential

# Upgrade mamba
RUN mamba upgrade -y mamba

# Copy environment and requirements files into docker env
COPY environment.yml .

# Update environment file with new environment name
RUN mamba env update --file environment.yml --name dockerenv
SHELL ["mamba", "run", "-n", "dockerenv", "/bin/bash", "-c"]