Installation#

Requirements#

  • Python 3.7 or newer (see requires-python in pyproject.toml).

  • A normal scientific Python environment; heavy lifting for several solvers uses Numba (installed with the package).

Install the package#

From PyPI (when a release is published):

pip install phypanda

From a clone of the repository (editable install recommended for development):

cd panda
python -m venv .venv
source .venv/bin/activate   # Windows: .venv\Scripts\activate
pip install -e .

Optional extras#

Run the test suite (pytest):

pip install -e ".[dev]"
pytest

Build this documentation (Sphinx + PyData theme):

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

Open docs/build/html/index.html in a browser.

Dependencies (automatic with pip install phypanda)#

These are declared in pyproject.toml and pulled in by pip:

Package

Role in phypanda

phylozoo

Directed phylogenetic networks, I/O, subnetworks.

networkx

Graph algorithms shared with phylozoo / scanwidth.

scanwidth

Edge- and node-scanwidth, tree extensions, NSW / XP hooks.

numba

JIT-accelerated child merges inside several DPs (can be disabled where supported).