Installation

Installation

Install from PyPI

Install PhyloGeoPlot using:

pip install phylogeoplot

PhyloGeoPlot requires Python 3.10 or later.

The required Python dependencies are installed automatically by pip.

Main dependencies

PhyloGeoPlot relies on:

• Biopython
• Cartopy
• Rasterio
• Matplotlib
• Pandas
• NumPy
• scikit-image

Additional transitive dependencies may be installed automatically by these packages.

Verify the installation

python -c "import phylogeoplot; print('PhyloGeoPlot installation OK')"

Verify the main visualization module:

python -c "from phylogeoplot.visualisation.tree_to_map_raster import PhyloGeoPlotter; print('Visualization module OK')"

Development installation

Clone the GitHub repository:

git clone https://github.com/tahiri-lab/PhyloGeoPlot.git
cd PhyloGeoPlot

Install the package in editable mode with development dependencies:

pip install -e ".[dev]"

Development dependencies currently include:

• pytest
• Jupyter

Virtual environment

Using a virtual environment is recommended.

Windows PowerShell

python -m venv .venv
.\.venv\Scripts\Activate.ps1
pip install phylogeoplot

Linux or macOS

python -m venv .venv
source .venv/bin/activate
pip install phylogeoplot

Platform considerations

Cartopy and Rasterio depend on geospatial libraries. Current Python distributions generally provide precompiled wheels for supported platforms, so installation through pip should normally install the required components automatically.

If installation problems occur, see Troubleshooting.