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 Download.

Requirements

• Python >= 3.11

• numpy >= 1.24

• scipy >= 1.10

• matplotlib >= 3.7

• PyQt5 >= 5.15

With conda (recommended)

conda env create -f environment.yml
conda activate pygra

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

conda activate oxdna
pip install -e .

With pip

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:

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

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.