Installation

Requirements

Python 3.10 or later
A conda environment is strongly recommended due to the number of spatial biology dependencies

Download the environment.yml file and run:

conda env create -f environment.yml
conda activate maldi
pip install goatpy

This installs all required and optional dependencies, including napari for visualisation.

For a minimal install without napari:

pip install goatpy

With napari support:

pip install "goatpy[napari]"

pip install git+https://github.com/agc888/goatpy.git

Extra	What it adds
`napari`	Interactive visualisation via napari and napari-spatialdata
`docs`	Sphinx documentation build dependencies
`dev`	Testing, linting, and formatting tools

Whole-slide image formats require openslide:

conda install -c conda-forge openslide openslide-python