******************
Installation Guide
******************

Welcome to the installation guide for `QuantumDNA`. Follow the steps below to install the package, set up a virtual environment, and start using `qDNA` either through a Graphical User Interface or a Jupyter Notebook.

Prerequisites
=============

Before proceeding, make sure the following prerequisites are met:

1. **Python Installation**:

   - Verify that Python is installed by running:

     .. code-block:: bash

        python --version

   - If Python is not installed, download and install it from `python.org <https://www.python.org/downloads/>`_.

2. **Linux/macOS Users**:

   - Ensure `pip` and `tkinter` are installed:

     .. code-block:: bash

        python3 -m pip --version
        python3 -m tkinter

   - If they are not installed, install them using your package manager:

3. **Windows Users**:

   - Ensure Git is installed by running:

     .. code-block:: bash

        git --version

   - If Git is not installed, download and install it from `Git for Windows <https://gitforwindows.org/>`_.


Installation via PyPI
=====================

The easiest way to install `qDNA` is through PyPI. We recommend creating a new virtual environment to avoid package conflicts.

Steps
-----

1. **Create a New Virtual Environment**:

   Open your terminal and navigate to your project folder. Run:

   .. code-block:: bash

      python -m venv .venv

2. **Activate the Virtual Environment**:

   - **Windows**:

     .. code-block:: bash

        .venv\Scripts\activate

   - **macOS/Linux**:

     .. code-block:: bash

        source .venv/bin/activate

3. **Install the `qDNA` Package**:

   .. code-block:: bash

      pip install qDNA

4. **Optional: Use `qDNA` Inside a Jupyter Notebook**:

   Install Jupyter and launch the notebook:

   .. code-block:: bash

      pip install ipykernel notebook
      jupyter notebook


Installation via Cloning the GitHub Repository
==============================================

If you plan to contribute to the development or make changes to the source code, install `qDNA` in editable mode by cloning its GitHub repository.

Steps
-----

1. **Clone the GitHub Repository**:

   .. code-block:: bash

      git clone https://github.com/dehe1011/QuantumDNA.git

2. **Navigate to the Cloned Repository**:

   .. code-block:: bash

      cd QuantumDNA

3. **Run the Activation Script**:

   Use the provided activation script to complete the installation. Instructions vary by platform (see below).


Platform-Specific Instructions for Activation
=============================================

**Windows**
-----------

1. Navigate to the project directory:

   .. code-block:: powershell

      Set-Location -Path "C:\Users\<YourUsername>\QuantumDNA"

2. Run the activation script:

   .. code-block:: powershell

      powershell -ExecutionPolicy Bypass -File scripts\Activate.ps1

**macOS**
---------

1. Navigate to the project directory:

   .. code-block:: bash

      cd /Users/<YourUsername>/QuantumDNA

2. Run the activation script:

   .. code-block:: bash

      source scripts/activate

**Linux**
---------

1. Navigate to the project directory:

   .. code-block:: bash

      cd /home/<YourUsername>/QuantumDNA

2. Run the activation script:

   .. code-block:: bash

      source scripts/activate


Post-Installation and Usage
===========================

If all tests pass, the package has been successfully installed! You can now:

- Launch the **Graphical User Interface** or
- Start using `qDNA` inside a **Jupyter Notebook**.

Run the activation script as mentioned in the platform-specific instructions to start the **Graphical User Interface** or a **Jupyter Notebook**. It is recommended to always run the activation script.


Uninstallation
==============

To remove the package:

.. code-block:: bash

   pip uninstall qDNA

If you cloned the GitHub repository, manually delete the `QuantumDNA` folder from your computer.


**Congratulations!** You've successfully installed and set up `QuantumDNA`.