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

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

* Python ≥ 3.10
* The four upstream PEN-STACK packages (pinned versions):

  * ``genome-atlas>=0.7.2,<0.8.0``
  * ``mech-class>=0.5.4,<0.6.0``
  * ``pen-score>=0.1.3,<0.2.0``
  * ``pen-assemble>=0.5.2,<0.6.0``

From source
-----------

.. code-block:: bash

   git clone https://github.com/ahmedanees-m/pen-compare.git
   cd pen-compare
   pip install -e ".[webserver,rag]"

Docker (recommended for full pipeline)
---------------------------------------

.. code-block:: bash

   docker run --rm \
     -v ~/pen-assemble:/workspace/pen-assemble \
     -p 8501:8501 \
     pen-stack/compare:0.1.0

Streamlit Community Cloud
--------------------------

The Streamlit app is deployed at the repository's GitHub URL. It uses pre-computed
JSON caches in ``data/cache/`` and requires only the packages listed in
``requirements.txt``.