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

Requirements
------------

AMBER requires Python 3.9 or higher and the following dependencies:

* **polars** >= 0.20.0 - High-performance DataFrame library
* **numpy** >= 1.20.0 - Numerical computing
* **networkx** >= 2.5 - Graph and network analysis
* **matplotlib** >= 3.3.0 - Plotting and visualization
* **seaborn** >= 0.11.0 - Statistical data visualization

Install from PyPI
------------------

The easiest way to install AMBER is using pip:

.. code-block:: bash

   pip install ambr

This will install AMBER and all required dependencies.

Install from Source
-------------------

To install the latest development version from GitHub:

.. code-block:: bash

   git clone https://github.com/a11to1n3/AMBER.git
   cd AMBER
   pip install -e .

Development Installation
------------------------

For development, install with additional dependencies:

.. code-block:: bash

   git clone https://github.com/a11to1n3/AMBER.git
   cd AMBER
   pip install -e ".[dev]"

This includes testing, documentation, and code quality tools.

Verify Installation
-------------------

To verify that AMBER is installed correctly, run:

.. code-block:: python

   import ambr as am
   print(am.__version__)

You should see the version number printed without any errors.

Optional Dependencies
---------------------

For enhanced functionality, you may want to install:

* **jupyter** - For interactive development and analysis
* **plotly** - For interactive visualizations
* **tqdm** - For progress bars in long simulations

.. code-block:: bash

   pip install jupyter plotly tqdm

Troubleshooting
---------------

Common Issues
~~~~~~~~~~~~~

**Import Error**: If you get import errors, make sure all dependencies are installed:

.. code-block:: bash

   pip install --upgrade polars numpy networkx matplotlib seaborn

**Performance Issues**: For large simulations, consider:

* Using the latest version of Polars
* Installing numpy with accelerated BLAS libraries
* Running on systems with sufficient RAM

**Jupyter Setup**: For interactive development with Jupyter:

.. code-block:: bash

   pip install ipykernel
   python -m ipykernel install --user

Getting Help
~~~~~~~~~~~~

If you encounter issues:

1. Check the `GitHub Issues <https://github.com/a11to1n3/AMBER/issues>`_
2. Read the documentation thoroughly
3. Ask questions in the community forums
4. Report bugs with minimal reproducible examples