FAIR-Cells 1.0.13

FAIR-Cells allows the user to interactively create a Docker image from a Jupyter Notebook.

FAIR-Cells

FAIR-Cells is a Jupyter Notebook extension that allows the user to interactively create a Docker image from a Jupyter Notebook. Our tool can be used to generate Docker images from single cells of a Jupyter Notebook. The generated image will run a web service that will output the specified cell. This includes image outputs like plots. Code introspection for Python enables the services to change cell output at service run-time.

Among other things, FAIR-Cells is useful for reusing notebook components in workflows that support web services.

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Installation

FAIR-Cells can be downloaded using pip. It then needs to be enabled using three Jupyter commands. Docker is required for the extension to have any effect.

$ [sudo] pip install jupyter --user
$ [sudo] pip install fair-cells --user
$ jupyter serverextension enable --py fair-cells --user
$ jupyter nbextension install --py fair-cells --user
$ jupyter nbextension enable fair-cells --user --py

Run with Docker

docker run -it -p 8888:8888  -e GEN_CERT=yes -v /var/run/docker.sock:/var/run/docker.sock qcdis/fair-cells 

Development

To keep your system clean it is recommended to develop using Docker. The following command will run a Jupyter Notebook server with FAIR-Cells enabled at http://localhost:8888. Autoreload is enabled for Python files, you will need to reload your browser to see changes in the front-end.

$ docker-compose up --build main

To test the helper server that runs inside of the container run the following command. This uses a dummy notebook that can be found in docker/helper_dummy. The notebook will be available at http://localhost:10000

$ docker-compose up --build helper