# Installation

```bash
pip install harpy-analysis
```

**With extras**

```bash
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**

```bash
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](contributing.md).

```bash
# 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
```