Installation from source
========================

If you want to run PyGRA from source or contribute to the project,
install it in a Python environment. For pre-built installers see :doc:`download`.

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

- Python >= 3.11
- numpy >= 1.24
- scipy >= 1.10
- matplotlib >= 3.7
- PyQt5 >= 5.15

With conda (recommended)
------------------------

.. code-block:: bash

   conda env create -f environment.yml
   conda activate pygra

Or install into an existing environment (e.g. your oxDNA environment):

.. code-block:: bash

   conda activate oxdna
   pip install -e .

With pip
--------

.. code-block:: bash

   pip install -r requirements.txt
   pip install -e .

Linux: dock/launcher icon
--------------------------

Run the provided install script once after installation to register the icon
and add PyGRA to the application launcher:

.. code-block:: bash

   bash install_icon_linux.sh

This copies the icon to ``~/.local/share/icons`` and creates a ``.desktop``
file in ``~/.local/share/applications``. You may need to log out and back in
for the icon to appear in the dock.

Running the tests
-----------------

.. code-block:: bash

   python -m pytest tests/ -q

.. note::
   On Linux, always use ``python -m pytest`` rather than ``pytest`` directly,
   to ensure the correct Python environment is used.