Jupyter interface#

The CADET-RDM Jupyter interface only works with Jupyter Lab, and not with the old Jupyter Notebook interface at the moment.

General concepts#

Jupytext#

Jupyter Notebooks are not well suited for version control with git, as the metadata and cell outputs are stored besides the input code. This overwhelms the inspection of differences within commits and the comparisons between branches.

Therefore, the jupytext extension is used by default to convert .ipynb files into a .py files, with the markdown cells included as block comments. All .ipynb files are removed from git’s version control through the .gitignore file and only changes in the .py files are tracked. The .py files are automatically created and updated whenever a .ipynb file is saved.

Please ensure, that juyptext is working for you and that a .py file is created after saving your notebook, otherwise your code will not be version-controlled.

Reproducibility#

To ensure results from .ipynb files are perfectly reproducible, CADET-RDM does not allow for the tracking of results generated during live-coding usage. Therefore, before committing results, all previous outputs are cleared and all cells are executed sequentially from top to bottom and then committed to the output repository.

To maintain the link between Markdown annotation, code, and inline graphs, the final notebook is also saved as a .html webpage into the output folder for future inspection.

Tracking Results#

To use CADET-RDM from within an .ipynb file, please include this at the top of your file.

from cadetrdm.repositories import JupyterInterfaceRepo

repo = JupyterInterfaceRepo()

Then, at the end of your file, run:

repo.commit_nb_output(
    "path-to-the-current-notebook.ipynb",
    results_commit_message="Results commit message"
)

This will re-run the .ipynb file from the start, save a html version of the completed notebook into the output repo and commit all changes to the output repo.

Committing changes to your code#

You can commit all current changes to your code directly from Jupyter by running

from cadetrdm.repositories import JupyterInterfaceRepo

repo = JupyterInterfaceRepo()

repo.commit("Commit message")

Other workflows#

All other workflows function identically as described in the Python interface section.

Jupyter interface

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