Code outside of Dockerfile

[minump]

Code (the ipynb files) should be outside of Dockerfile. The code will be in github and participants will clone the repo. This would reduce the number of deployements needed when the code is changed.

The repo should be structured properly. The data will live in the github repo.
SAM checkpoints will be in Docker container.

[minump]

In hold for now. Still deciding if this is a good idea.