walice / reproducibility-demo

[Minimal] repository for a reproducible Binder-compatible project structure

Reproducibility Demo

Binder

Creating Binder Badge

Created on Binder:

• GitHub: https://github.com/dddlab/reproducibility-demo
• Git branch, tag, or commit: prep-for-binder
• (Optional) Path to a notebook file: work/nonneg_matrix_fact.ipynb

Pushing back to GitHub

• The cloned repository on Binder will say master branch
• In order to push back to prep-for-binder branch, checkout the branch first:
  git checkout prep-for-binder

Starting Jupyter Notebook on VM

• Jupyter Notebook environment is started with docker-compose.yml
• Docker image will be created from Dockerfile if necessary
• setup.sh will download a utility to create a password an encryption keys for your Jupyter notebook
• Install docker and other utilities:

  # install necessary packages on debian or ubuntu
  sudo apt-get update && \
    sudo apt-get install -y wget git docker.io docker-compose && \
    sudo usermod -aG docker $USER
  
  # re-login to to apply docker group setting

• Build docker image and start Jupyter notebook server

  git clone https://github.com/dddlab/reproducibility-demo.git
  cd reproducibility-demo/
  git checkout prep-for-binder
  chmod u+x setup.sh
  ./setup.sh 
  docker-compose up --build -d

• Open https://[VM ip address]:8889 to reach your server (note the default port 8889 in docker-compose.yml).