How to include R dependency in a python package

31 Views Asked by mbeyss At 14 March 2024 at 16:46

I have a python project, that has an R dependency. The R package is available through Biocunductor. It can be installed with the following code

import rpy2.robjects as robjects
import rpy2.robjects.packages as rpackages


utils = rpackages.importr("utils")
if not rpackages.isinstalled("BiocManager"):
    utils.install_packages("BiocManager")
robjects.r('BiocManager::install(pkgs="IsoCorrectoR", ask=FALSE)')

My project is set up with a pyproject.toml file, and a pip install works fine, but the R dependency is not installed.

With the pyproject.toml I see no place to execute the above code snippet. Executing it on runtime would be a possibility, but feels inelegant.

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