Getting Started
===============

.. _installation:

Installation
------------

To install MOSNA for use with GPU compatible libraries:

.. code-block:: console

  conda create --solver=libmamba -n mosna-gpu -c rapidsai -c conda-forge -c nvidia -c pytorch rapids=23.04.01 python=3.10 cuda-version=11.2 pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 scanpy
  conda activate mosna-gpu

Alternatively without GPU:

.. code-block:: console

  conda create --solver=libmamba -n mosna -c conda-forge python=3.10 scanpy
  conda activate mosna

Then, install some essential dependencies:

.. code-block:: console

  pip install ipykernel ipywidgets
  pip install tysserand
  pip install -e .
  pip install scipy==1.13


Alternatively, you can create a new Conda environment that has tysserand, mosna and all their dependencies installed:

.. code-block:: bash
  
  conda env create -f mosna.yml

or copy the YAML content directly:

.. literalinclude:: mosna.yml
  :language: yaml
  :linenos:

or, if you prefer, you can download the Conda environment file here:

* :download:`mosna.yml <mosna.yml>`