Installation

Install

# Clone the repository
git clone https://github.com/devsystemslab/phenocoder.git
cd phenocoder

# Install with uv (recommended)
uv pip install .

# Or with pip
pip install .

Requirements

  • Python >= 3.10, < 3.13

  • TensorFlow >= 2.19.0 (CUDA on Linux, Metal on macOS)

  • SpatialData >= 0.5.0

  • Additional dependencies listed in pyproject.toml

Phenocoder is built on Keras 3 with the TensorFlow backend. On Linux the full CUDA stack is installed (tensorflow[and-cuda]); on macOS GPU acceleration is provided through tensorflow-metal.

Development install

From a clone of the repository (see above), install in editable mode with the dev extras:

# Install dev dependencies
uv pip install -e ".[dev]"

# Run tests
pytest tests/

# Format code
ruff format .

# Lint
ruff check .

Building the docs

uv pip install -e ".[docs]"
sphinx-build -b html docs docs/_build/html