FAIR-Cells allows the user to interactively create a Docker image from a Jupyter Notebook.
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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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 pull qcdis/fair-cells docker run -it -p 8888:8888 -v /var/run/docker.sock:/var/run/docker.sock qcdis/fair-cells
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
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