Installation

Stable release

To install ehrapy, run this command in your terminal:

pip install ehrapy

This is the preferred method to install ehrapy, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

If you run into “RuntimeError: CMake must be installed to build qdldl” ensure that you have CMake installed to build lightgbm. Run conda install -c anaconda cmake and conda install -c conda-forge lightgbm to do so.

Optional dependencies

leiden clustering

To use ehrapy.tools.leiden, install the leiden extra (which pulls in igraph):

pip install ehrapy[leiden]

From sources

The sources for ehrapy can be downloaded from the Github repo.

You can either clone the public repository:

git clone git://github.com/theislab/ehrapy

Or download the tarball:

curl -OJL https://github.com/theislab/ehrapy/tarball/master