Installation 
============

First, create and activate a virtual environment named STAIR-test:

.. code-block:: bash

   conda create -n STAIR-test python=3.9.13
   conda activate STAIR-test

Then, install the appropriate versions of PyTorch and PyG for your device. We will follow https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html and use CUDA 11.3 as an example:

.. code-block:: bash

   pip install torch==1.12.1+cu113 torchvision==0.13.1+cu113 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu113

Confirm that the installed PyTorch version is correct:

.. code-block:: bash

   (STAIR-test)[yuyuanyuan@mu03 ~]$ python -c "import torch; print(torch.version)"
   1.12.1+cu113
   (STAIR-test)[yuyuanyuan@mu03 ~]$ python -c "import torch; print(torch.version.cuda)"
   11.3

Next, install the corresponding PyG and its related packages:

.. code-block:: bash

   pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-1.12.1+cu113.html

Finally, install the latest version of STAIR-tools via pip:

.. code-block:: bash

   pip install STAIR-tools

To perform a complete STAIR analysis, in addition to the installation steps, you need to install the following software packages:

.. code-block:: bash
   
   pip install anndata
   pip install scanpy
   pip install --user scikit-misc
   conda install rpy2
   conda install r-base=4.1.3
   conda install conda-forge::r-mclust
   pip install plotly
   conda install bioconda::r-lisi

Then STAIR can be used in python:

.. code-block:: python

   import STAIR

Downloading STAIR code from https://github.com/yuyuanyuana/STAIR