How to automatically create a environment.yml that works with repo2docker

This how-to explains how to create a environment.yml that specifies all installed packages and their precise versions from your environment.

The challenge

conda env export -f environment.yml creates a strict export of all packages. This is the most robust for reproducibility, but it does bake in potential platform-specific packages, so you can only use an exported environment on the same platform.

repo2docker uses a linux based image as the starting point for every docker image it creates. However a lot of people use OSX or Windows as their day to day operating system. This means that the environment.yml created by a strict export will not work with error messages saying that certain packages can not be resolved (ResolvePackageNotFound).

The solution

Follow this procedure to create a strict export of your environment that will work with repo2docker and sites like mybinder.org.

We will launch a terminal inside a basic docker image, install the packages you need and then perform a strict export of the environment.

1. install repo2docker on your computer by following Installing repo2docker
2. in a terminal launch a basic repository repo2docker https://github.com/binder-examples/conda-freeze inside repo2docker
3. open the URL printed at the end in a browser, the URL should look like http://127.0.0.1:61037/?token=30e61ec80bda6dd0d14805ea76bb59e7b0cd78b5d6b436f0
4. open a terminal by clicking “New -> Terminal” next to the “Upload” button on the right hand side of the webpage
5. install the packages your project requires with conda install <yourpackages>
6. use conda env export -n root to print the environment
7. copy and paste the environment you just printed into a environment.yml in your projects repository
8. close your browser tabs and exit the repo2docker session by pressing Ctrl-C.

This will give you a strict export of your environment that precisely pins the versions of packages in your environment based on a linux environment.