acksmaggart / rpy2

Interface to use R from Python

Installation

pip should work out of the box:

pip install rpy2

The package is known to compile on Linux, MacOSX, and Windows (provided that developper tools are installed, and you are ready figure out how by yourself).

In case you find yourself with this source without any idea of what it takes to compile anything on your platform, try first

python setup.py install

Non-system R installations

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}

Docker

Note: the automated build of Docker image is currently broken.

Alternatively, there is a Docker image available to try rpy2 out without concerns about the installation process.

To run the ipython console:

docker run -it --rm -p 8888:8888 rpy2/jupyter-ubuntu ipython

To run jupypter notebook on port 8888:

docker run --rm -p 8888:8888 rpy2/jupyter-ubuntu

More information about Docker images can be found in the docker image repository.

Images with jupyter are can be used with mybinder.

Documentation

Documentation is available either in the source tree (to be built), or online (on readthedocs).

Testing

rpy2 is now relying on 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 tests/

For code coverage, do:

pytest --cov=rpy2.rinterface_lib

--cov=rpy2.rinterface --cov=rpy2.ipython --cov=rpy2.robject tests

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.