Software Installation and Requirements
======================================

This section outlines the requirements and steps required to install the software.
Multiple method of instilation, including `pip`, `conda`, `Docker` and manual instillation
are available, and should be selected according to the users requirements (pip and conda installs are recommended
for development and Docker is recomended for using the tool).
Below are the software dependencies and corresponding installation instructions for different environments.


.. note::

   We are developing a desktop application for BRAD that can be installed without requiring the
   any environment or package management by the user.

Software Requirements
----------------------

The software relies on the following packages and libraries:

- Python 3.11 or higher
- Various Python libraries (listed below)
- `pip` or `conda` for package management
- `Docker` (optional, for containerized deployment)

Dependencies
~~~~~~~~~~~~

The following libraries are required and can be installed using `pip` or `conda`. These are listed in the `requirements.txt` and `environment.yml` files.

**Key Libraries:**

- `transformers`
- `torch>=2.0.1`
- `sentence-transformers`
- `scikit-learn`
- `matplotlib`
- `seaborn`
- `gget`
- `biopython`
- `requests`
- `beautifulsoup4`
- `semantic-router`
- `langchain`

Refer to the full list of dependencies in the `requirements.txt` and `environment.yml` files for exact versions.

Pip Installation
----------------

To install the required dependencies using `pip`, follow these steps:

1. **Ensure Python 3.11 or higher is installed.**
   - You can download Python from `python.org <https://www.python.org/downloads/>`_.

2. **Install dependencies from `requirements.txt`:**

   First, clone the repository and navigate to the root directory:

>>> git clone <repo_url>
>>> cd BRAD                                               
>>> pip install -r requirements.txt


This will install all necessary Python packages, including torch, transformers, langchain, and more.

Conda Instillation
------------------

Alternatively, you can install the dependencies using `conda`. A `conda` environment file is provided to easily set up the project environment:

Install Conda: If Conda is not already installed, download and install it from `here <https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_.

In the root directory of the project, run the following command to create an environment named `BRAD-1`


>>> conda env create -f environment.yml
>>> conda list                                               
>>> conda activate BRAD-1

Docker Instillation
-------------------


>>> docker build -t brad:local .
>>> docker run -it brad:local