rpy2

Python -> R bridge

The project's webpage is here: https://rpy2.github.io/

Installation

Released versions can be installed from a package repository (default being pypi) using pip:

pip install rpy2

The package has optional depencies providing specific functionalities not otherwise required to use the rest of rpy2.

For example, to be able to run the unit tests:

pip install 'rpy2[test]'

To install all optional dependencies (numpy, pandas, ipython), use:

pip install 'rpy2[all]'

Installation for rpy2 developers

If a developer, the package can be installed from its source tree. rpy2 is a namespace package with its consituting parts in different "sub-packages".

To install from the source tree, just enter:

pip install ./rpy2-rinterface/ ./rpy2-robjects/ .

Various optional dependencies can be specified through dependency groups. For example:

pip install ./rpy2-rinterface'[all]' ./rpy2-robjects'[all]' '.[all]'

rpy2-rinterface contains the binding to R's C API. Building from source require a compilation toolchain / developper tools installed, and you will have to figure out how to have them installed on your system by yourself. The CI pipeline builds binary wheels for Linux, MacOS, and Windows. Watching how things are set up there is pretty much all documentation from the package maintainers on the matter.

Issues loading shared C libraries

Whenever R is in not installed in a system location, the system might not know where to find the R shared library.

If R is in the PATH, that is entering R on the command line successfully starts an R terminal, but rpy2 does not work because of missing C libraries, try the following before starting Python:

export LD_LIBRARY_PATH="$(python -m rpy2.situation LD_LIBRARY_PATH)":${LD_LIBRARY_PATH}

Documentation

Documentation is available either in the source tree (doc/), or online.

Testing

rpy2 uses pytest, with the plugin pytest-cov for code coverage. To test the package from the source tree, either to check and installation on your system or before submitting a pull request, do:

pytest rpy2-rinterface/ rpy2-robjects/

For code coverage, do:

pytest --cov=rpy2.rinterface_lib \
       --cov=rpy2.rinterface \
       --cov=rpy2.ipython \
       --cov=rpy2.robject \
       rpy2-rinterface/ rpy2-robjects/

For more options, such as how to run specify tests, please refer to the pytest documentation.

License

RPy2 can be used under the terms of the GNU General Public License Version 2 or later (see the file gpl-2.0.txt). This is the very same license R itself is released under.