Added installation and contributing instructions for Apple Silicon us…

…ers.
scverse · Oct 4, 2023 · c55102b · c55102b
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diff --git a/docs/contributing.md b/docs/contributing.md
@@ -13,9 +13,11 @@ 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 Installation guide](installation.md#apple-silicon) and replace the last two steps described there with the code above.
 
 ## Code-style
 

diff --git a/docs/installation.md b/docs/installation.md
@@ -40,8 +40,43 @@ 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 (``ìmport 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/