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

The following instructions are for both MacOS and Linux systems. Windows users are encouraged to install the Windows Subsystem for Linux (WSL) and then install the software inside Ubuntu Linux.

1. Make a directory ``protocell/`` somewhere on your computer, and change to it: ::

	mkdir protocell
	cd protocell

2. Get the latest source code for **Araudia**: ::

	git clone https://bitbucket.org/ben_s_e/araudia.git

3. Make a Python3 virtual environment in the ``protocell/`` directory, activate it, and install the required libraries: ::

	python3 -m venv venv
	source venv/bin/activate
	pip install --upgrade pip
	pip install numpy
	pip install numba==0.60.0
	pip install matplotlib
	pip install networkx
	pip install scipy
	pip install pulp
	pip install colorama

.. note :: Ensure that ``numba`` version ``0.60.0`` (at least) is installed. This requires at least Python version ``3.10``.

4. The ``protocell/`` directory should now contain two sub-folders:
	
- ``araudia/``
- ``venv/``

Installation is complete.


HPC Cluster Installation
++++++++++++++++++++++++

The software can also be installed and used on an HPC computing cluster, following the same installation instructions above when logged in. The command ``module load Python`` may be necessary beforehand. It is advisable to install the same version of ``numpy`` on your local machine and on the HPC system (e.g. ``pip install numpy==2.0.2``), such that data files made on the HPC cluster (that contain pickled numpy objects) can later be opened on your local machine.

Simulations in :ref:`Our Paper` were run on a SLURM-based cluster, using the logic in the ``rstb/hpc.py`` script.