Installation Guide
==================

Welcome to the installation guide for wepy. Follow the steps below to
set up the environment and install wepy.

Prerequisites
-------------

Ensure that you are using **Python 3.10**. It is recommended to set up a
conda environment for managing dependencies and ensuring compatibility.

.. code:: bash

   conda create -n wepy-env python=3.10
   conda activate wepy-env

Installing wepy
---------------

You can install wepy from the latest git repository.

Installing from Git (for the latest version):

.. code:: bash

   pip install git+https://github.com/ADicksonLab/wepy.git

Installing OpenMM and mdtraj
----------------------------

To install OpenMM, which is highly recommended for running molecular
dynamics simulations:

.. code:: bash

   conda install -c conda-forge openmm=8.0.0

If the conda version of openmm doesn't work for your compute
environment, consult the `OpenMM
documentation <http://docs.openmm.org/latest/userguide/application.html#installing-openmm>`__.

The mdtraj library is used by wepy to create and manipulate system
topologies. It can also be installed via conda:

.. code:: bash

   conda install -c conda-forge mdtraj=1.9.9

These version numbers work correctly at the time of this writing and
avoid some incompatibility issues with numpy and pandas dependencies.

Verifying Installation
----------------------

After installation, you should be able to import wepy in python. Verify
it by running:

.. code:: bash

   python -c "import wepy"

If the installation was successful, you should not see any errors.