Installation

PhyloGNN is a Python package requiring Python 3.12 or newer. Install from a local checkout with the smallest extra set that matches your task.

Core package

Use the core install when you need ete3.Tree objects, feature engineering, graph conversion, models, and local training. This includes the public PyTorch, PyTorch Geometric, torch-scatter, ETE3, NumPy, and tqdm runtime dependencies.

python -m pip install -e .

Development tools

Use the development extra for tests, linting, and formatting.

python -m pip install -e ".[dev]"

Documentation tools

Use the documentation extra to build this local Sphinx site. It adds Sphinx and the Read the Docs HTML theme, but does not make either package a runtime dependency.

python -m pip install -e ".[docs]"
python -m sphinx -b html -n -W --keep-going docs/source docs/_build/html

Optional tree I/O

The core tree workflow works with ete3.Tree objects. File workflows that read NEXUS or BEAST-style trees through DendroPy require the beast extra.

python -m pip install -e ".[beast]"

Optional experiment tracking

Weights & Biases tracking is isolated behind the wandb extra and is only needed when tracking is enabled.

python -m pip install -e ".[wandb]"

Everything optional

Use the all extra for optional tree I/O, workflow helpers, and tracking. It does not include development or documentation tooling.

python -m pip install -e ".[all]"

Next steps

Continue with the Quickstart as the first tutorial. Use Graph Conversion when you need to interpret the graph fields produced by conversion.