[FIXED] Is there an equivalent to magic `%run` with R kernel in Jupyter?

Issue

This question is somewhat related to Is there a way to do Jupyter cell magic with R.

When you use JupyterLab with a Python kernel, you can split your analysis into several notebooks, like this:

.
├── 01-preprocessing.ipynb
└── 02-analysis.ipynb

and you can start your notebook 02-analysis.ipynb by the magic instruction:

%run 01-preprocessing.ipynb

so that the previous work can be retrieved and continued.

I noticed that this simple solution does not work if those notebooks are R notebooks. Instead, you get an error:

Error in parse(text = x, srcfile = src): <text>:1:1: unexpected input
1: %run 01-preprocessing.ipynb
    ^
Traceback:

As I understand it, the magic commands are not a feature of the Jupyter environment itself: it's a feature of the Python kernel only. But is there any equivalent of that for an R kernel? Or, as an R-user, have you any way to split your analysis between several 'dependent' notebooks like this?

Thanks!

Solution

Indeed magics are not implemented in IRkernel. As noted by the maintainer here you can use nbconvert.

run_notebook = function(path) {
    if (!file.exists(path)) {
        stop(paste('No such a file:', path))
    }
    eval(
        parse(
            text = system2(
                'jupyter',
                c('nbconvert', path, '--to=script', '--stdout'),
                stdout = TRUE
            )
        )
    )
}
run_notebook('01-preprocessing.ipynb')

This may become easier in the future. There are alternative R kernels that plan to implement magics.

Answered By - krassowski