Installation

Stable release

To install pertpy, run this command in your terminal:

$ pip install pertpy

This is the preferred method to install pertpy, 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.

Google Colab and TascCODA support

TascCODA requires an additional set of dependencies (ete3 and pyqt5) that can be installed using

$ pip install pertpy[coda]

this also solves any “AttributeError: module ‘pertpy.plot’ has no attribute ‘coda’” issues.

From sources

The sources for pertpy can be downloaded from the Github repo. Please note that you require poetry to be installed.

You can either clone the public repository:

$ git clone git://github.com/theislab/pertpy

Or download the tarball:

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

Apple Silicon

If you want to install and use pertpy on a machine with macOS and M-Chip, the installation is slightly more complex. This is because pertpy depends on scvi-tools, which can currently only run on Apple Silicon machines when installed using a native python version (due to a dependency on jax, which cannot be run via Rosetta).

Follow these steps to install pertpy on an Apple Silicon machine (tested on a MacBook Pro with M1 chip and macOS 14.0):

1. Install Homebrew

2. Install Apple Silicon version of Mambaforge (If you already have Anaconda/Miniconda installed, make sure having both mamba and conda won’t cause conflicts)

   $ brew install --cask mambaforge
   

3. Create a new environment using mamba (here with python 3.10) and activate it

   $ mamba create -n pertpy-env python=3.11
   $ mamba activate pertpy-env
   

4. Clone the GitHub Repository

   $ git clone https://github.com/theislab/pertpy.git
   

5. Go inside the pertpy folder and install pertpy

   $ cd pertpy
   $ pip install .
   

Now you’re ready to use pertpy as usual within the environment (import pertpy).