Skip to main content

Python interface to the R language (embedded R)

Project description

Python -> R bridge

pypi Codecov GH Actions

PyPI - Downloads Conda Downloads

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.

Project details


Release history Release notifications | RSS feed

This version

3.6.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

rpy2-3.6.1.tar.gz (52.7 kB view details)

Uploaded Source

Built Distribution

rpy2-3.6.1-py3-none-any.whl (9.9 kB view details)

Uploaded Python 3

File details

Details for the file rpy2-3.6.1.tar.gz.

File metadata

  • Download URL: rpy2-3.6.1.tar.gz
  • Upload date:
  • Size: 52.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.10.12

File hashes

Hashes for rpy2-3.6.1.tar.gz
Algorithm Hash digest
SHA256 9f7409f254c359618839bc937859a5078d9d94ebceb48dfd1192d442aeffb350
MD5 f40b5b5cc419845cec1f616f405d5da7
BLAKE2b-256 6aca189761c689faf6f4168703f0d4cf340c09eeee4d70c07c4c493724236b7c

See more details on using hashes here.

File details

Details for the file rpy2-3.6.1-py3-none-any.whl.

File metadata

  • Download URL: rpy2-3.6.1-py3-none-any.whl
  • Upload date:
  • Size: 9.9 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.10.12

File hashes

Hashes for rpy2-3.6.1-py3-none-any.whl
Algorithm Hash digest
SHA256 f8f2a4979330c0daf6227f0c4de434234f13976f20dfa9e6f40020b98f4567a3
MD5 af45caf5a2c2a719d978b20bc9b2a2a8
BLAKE2b-256 e1be77c01409c3d4c275c283a69e64bca3ce8e2a7abcb6fa0edd41f991048034

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page