cmdstanjupyter

This extension provides syntax highlighting for Stan code in JupyterLab, as well as a %%stan magic command to define Stan models in Jupyter notebooks and build them with CmdStanPy.

Requirements

• JupyterLab >= 4.0.0

Install

To install the extension, execute:

pip install cmdstanjupyter

Note: this does not install CmdStanPy for you, in case you are only interested in Stan syntax highlighting and not the %%stan magic!

Install it separately using pip or conda!

Usage

To use the magic in your notebook, you need to lead the extension:

%load_ext cmdstanjupyter

To define a stan model inside a jupyter notebook, start a cell with the %%stan magic. You can also provide a variable name, which is the variable name that the cmdstanpy.CmdStanModel object will be assigned to. For example:

%%stan paris_female_births
data {
    int male;
    int female;
}

parameters {
    real<lower=0, upper=1> p;
}

model {
    female ~ binomial(male + female, p);
}

When you run this cell, cmdstanjupyter will create a cmdstanpy CmdStanModel object, which will compile your model and allow you to sample from it.

If the above code was stored in a file births.stan, the following is equivalent:

%stanf births.stan paris_female_births

To use your compiled model:

fit = paris_female_births.sample(
    data={'male': 251527, 'female': 241945},
)

Credits

The %magic is heavily based on the previous jupyterstan package. The highlighting code is inspired by jupyterlab-stata-highlight.