Installation

pip install harpy-analysis

With extras

pip install "harpy-analysis[extra]"

[extra] installs optional dependencies for:

• Segmentation: cellpose

• OpenCV support: opencv-python-headless

• FlowSOM Clustering: flowsom, scikit-learn

• Vitessce: harpy-vitessce

• Notebook workflows: ipywidgets, tqdm, bokeh, textalloc, joypy, supervenn, nbconvert, ipython

• CLI workflows: hydra-core, hydra-colorlog, submitit, hydra-submitit-launcher

With extras and napari

pip install "harpy-analysis[extra,napari]"

[napari] adds:

• napari[all]

• napari-harpy

• napari-spatialdata

Only for developers. Clone this repository locally, install the .[dev] instead of the .[extra] dependencies and read the contribution guide.

# Clone repository from GitHub
uv venv --python=3.12  # create venv using uv, set python version (>=3.11)
source .venv/bin/activate  # activate the virtual environment
uv pip install -e '.[dev]'  # editable install with dev tooling
python -c 'import harpy; print(harpy.__version__)'  # check if the package is installed
# make changes
python -m pytest  # run the tests