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Fibertree Notebooks

Fibertree Jupyter notebooks in a docker container

Start the container

  • Copy docker-compose.yaml.example from this repo to docker-compose.yaml in an otherwise empty directory
  • cd to the directory containing the docker-compose.yaml file
  • Edit docker-compose.yaml and follow instructions in the file to customize to your environment
  • Run the following command:
docker-compose up -d
  • Browse over to localhost:8888

⚠️ WARNING: This docker compose file disables Jupyter tokens, so do not use on a system exposed directly to the internet.

Refresh the container

To update the Docker container run:

     % docker-compose pull

Build the container

To build the container, first clone the repo (including the submodules) and build using the Makefile.

      % git clone --recurse-submodules https://github.com/Fibertree-Project/fibertree-docker
      % cd fibertree-docker
      % make build [ALTTAG=test] [BUILD_FLAGS="<Docker build flags, e.g., --no-cache>"]

Note: the Makefile also supports pushing the container to hub.docker.com.

      % make push

Work on the fibertree repo

It takes a little work, but you can work on a clone of the original fibertree git repo inside the docker container and then be able to push your changes. Assuming you have followed the conventions in the docker-compile.yaml.example file, you can do that as follows:

  • Clone the fibertree git repo into the local directory containing the docker-compose.yaml file
    git clone git@github.com:Fibertree-project/fibertree.git fibertree-repo
  • Mount the repo as a volume in your container by adding the following line to the volumes: section of your docker-compose.yaml file
 - ./fibertree-repo:/home/jovyan/fibertree-repo
  • Start the container and enter a shell either from the Jupyter notebook or running:
    docker-compose exec notebook /bin/bash
  • Then while in the container install the mounted version of the fibertree code:
    cd /home/jovyan/fibertree-repo
    pip install --user -e .
  • Edit the files in the fibertree repo (inside or outside the container) and those changes will be reflected in your Jupyter notebooks (after a kernel restart). You can then push those changes to the fibertree repo...

Note 1: The above procedure will override the use of the internal copy of the fibertree source code. You can restore that by getting into the container and running the following:

    cd /home/jovyan/src/fibertree
    pip install --user -e .

Note 2: If you already have cloned the fibertree-docker git repo and recursively cloned the submodules there is a copy of the fibertree repo in ./src/fibertree, so you can mount that as a volume in the container if you like.