Merge branch 'main' of github.com:bionetslab/netmap

Author: Anne Hartebrodt

README.md

@@ -1 +1,26 @@
+# NETMAP (single-cell gene regulatory networks using XAI)
 
+## Installation
+The repository is installable using pixi and pip. If you want to try out netmap, you can clone the repository, and install a kernel via pixi.
+Note: We do not include torch and cupy. These need to be installed separately when using pip, and will be installed automatically when using pixi installation
+
+### Pixi installation
+1. Download and setup [pixi.sh](https://pixi.prefix.dev/latest/).
+2. Install the jupyer kernel which includes torch and cupy and netmap. You can then set pixi_netmap as a kernel in your jupyterlab, or vscode environment
+3. You can add extra packages using ``` pixi add my-package ``` and reinstall the kernel to add extra packages.
+```{bash}
+git clone https://github.com/bionetslab/netmap
+cd netmap
+pixi run install-kernel
+```
+
+### pip install
+A local, editable install in a conda environment can be done as follows. You need to install extra denpendencies yourself e.g. torch, cupy depending on you system.
+
+```{bash}
+git clone https://github.com/bionetslab/netmap
+cd netmap
+conda create -n netmap_env
+conda activate netmap_env
+pip install -e .
+```