Installation Apple Silicon

docs/contributing.md

@@ -13,10 +13,16 @@ In addition to the packages needed to _use_ this package, you need additional py
 the documentation_. It's easy to install them using `pip`:
 
 ```bash
+git clone https://github.com/theislab/pertpy.git
 cd pertpy
 pip install -e ".[dev,test,doc]"
 ```
 
+```{note}
+If you're working on an Apple Silicon machine, the installation is slightly more complex. In that case, follow
+the steps described in the Apple Silicon section of the installation guide and replace the last two steps described there with the code above.
+```
+
 ## Code-style
 
 This project uses [pre-commit][] to enforce consistent code-styles. On every commit, pre-commit checks will either

docs/installation.md

@@ -40,8 +40,50 @@ Once you have a copy of the source, you can install it with:
 $ make install
 ```
 
+## 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)
+
+    ```console
+    $ brew install --cask mambaforge
+    ```
+
+3. Create a new environment using mamba (here with python 3.10) and activate it
+
+    ```console
+    $ mamba create -n pertpy-env python=3.10
+    $ mamba activate pertpy-env
+    ```
+
+4. Clone the GitHub Repository
+
+    ```console
+    $ git clone https://github.com/theislab/pertpy.git
+    ```
+
+5. Go inside the pertpy folder and install pertpy
+    ```console
+    $ cd pertpy
+    $ pip install .
+    ```
+    Now you're ready to use pertpy as usual within the environment (`import pertpy`).
+    ```
+
+    ```
+
 [github repo]: https://github.com/theislab/pertpy
 [pip]: https://pip.pypa.io
 [poetry]: https://python-poetry.org/
 [python installation guide]: http://docs.python-guide.org/en/latest/starting/installation/
 [tarball]: https://github.com/theislab/pertpy/tarball/master
+[scvi-tools]: https://docs.scvi-tools.org/en/latest/installation.html
+[Homebrew]: https://brew.sh/