FlowKit tutorials

This is a Binder repository of tutorials for learning how to use FlowKit for CDR analysis. The tutorials are Jupyter notebooks which use the FlowClient python client to interact with FlowKit. These tutorials are designed to be used with the Ghana FlowCloud deployment.

Running the tutorials

Locally (using conda)

To run the tutorials on your local machine, you will need to do the following (these instructions assume that you have conda installed):

1. Clone this repository
2. Create a conda environment for the tutorials, using environment.yml
3. Activate the flowkit-tutorials environment you just created
4. Install the jupyter-widgets lab extension (so that FlowKit progress bars will appear in the notebooks)
5. Start a Jupyter Lab session (or Jupyter Notebook, if you prefer), and open index.ipynb

You can run the following in a bash shell (or a git-bash terminal on Windows) to set everything up:

git clone https://github.com/Flowminder/FlowKit-tutorials-Ghana
cd FlowKit-tutorials-Ghana
conda env create -f environment.yml
conda activate flowkit-tutorials
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter lab index.ipynb

Binder

To run the tutorials online, click the Binder badge at the top of this README. This will start a Jupyter server in the cloud with all dependencies installed, which you can use to run the tutorial notebooks.

Note: The Binder session will shut down after a period of inactivity, and any changes you make to the tutorial notebooks will be lost. To download a copy of a tutorial notebook with any changes you made, use File→Download.