Installation instructions
***************************

qdiv can be installed with pip.

.. code-block:: console

   pip install qdiv

Some functions in the ``sequence_comparisons`` module support compilation via Numba. Installing qdiv with the optional ``accelerate`` extra 
enables faster sequence distance computations. 

.. code-block:: console

   pip install qdiv[accelerate]

The recommended method is to download `Anaconda <https://www.anaconda.com/products/individual>`_ or `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_

Open the Anaconda or Miniconda prompt (a terminal window).

Create a new environment. You can, for example, call it qdiv_env. Then, activate the environment and install qdiv.

.. code-block:: console

   conda create -n qdiv_env python=3.11
   conda activate qdiv_env
   pip install qdiv[accelerate]

To start using qdiv, you need some way of writing and executing Python code. One way is to use a Jupyter noteboook.

You can install Jupyter like this:

.. code-block:: console

   conda install jupyter

To start a Jupyter notebook, simply type:

.. code-block:: console

   jupyter notebook

To check if qdiv works, you can run the following code:

.. code-block:: python

   import qdiv
   obj = qdiv.MicrobiomeData.load_example("Saheb-Alam2019_DADA2")
   obj.info()

Hopefully, this will run without errors and print some information about the loaded example data.