revbayes_kernel

A Jupyter kernel for RevBayes

Installing revbayes_kernel

sudo python3 setup.py install
python3 -m revbayes_kernel.install
pip3 install metakernel

Note that Linux users may have to subsitute

python3 -m revbayes_kernel.install install

for the middle line.

The current version of revbayes_kernel calls the RevBayes executable named rb-jupyter. Support to compile rb-jupyter with the command ./build.sh -jupyter true was added to the development branch of the main RevBayes repository in commit 6028eb2. To find build.sh, first change your working directory cd <revbayes_path>/projects/cmake/.

The rb-jupyter binary must be found using the which command or be located using the environment variable, REVBAYES_JUPYTER_EXECUTABLE. For instance, you can set the environment variable using

export REVBAYES_JUPYTER_EXECUTABLE=<revbayes_path>/revbayes/projects/cmake/rb-jupyter

Example notebooks

Run these notebook examples from within the revbayes_kernel folder to correctly access the example data.

Notebook demo for simple MCMC analysis [preview]

jupyter notebook revbayes_mcmc_demo.ipynb

Notebook demo for jupyter magics (some RevBayes-python-R interoperability) [preview]

jupyter notebook revbayes_magic_demo.ipynb