Jupyter Chaste

Source code for the jupyter-chaste Service on o²S²PARC.

Kernels

C++

Xeus-cling provides C++ 11, 14 and 17 kernels

Python

Basic Python kernel included

Chaste

Chaste is installed and built into /home/jovyan/chaste directory Simlink is established between Chaste projects directory /home/jovyan/chaste/src/projects and the /home/jovyan/work/workspace/projects directory so that it would be saved into study data.

Information for developers

Building the docker image:

make build

Test the built image locally:

make run-local

Note that the validation directory will be mounted inside the service.

Raising the version can be achieved via one for three methods. The major,minor or patch can be bumped, for example:

make version-patch

If you already have a local copy of o²S²PARC running and wish to push data to the local registry:

make publish-local

Testing manually

Once you have a running version of the Service, you can test chaste and the C++ kernels, as shown in this webinar.

Test chaste

In a new terminal, run the following to create a new project from a template

cd work/workspace/projects
new_project.sh
cd template_project
build_project.sh test

Run one of the existing tutorials:

cd ~/chaste/src/
build_project.sh lung

Test the JupyterLab C++ kernels

Open a new notebook with any of the existing C++ kernels and run one of the existing notebooks in the xeus-cling repository, for example xcpp.ipynb.