ophac – Order Preserving Hierarchical Agglomerative Clustering

Version: 0.5.2 Python: 3.10+

This library implements the algorithms described in the article Order-Preserving Hierarchical Clustering. It provides functionality for performing order-preserving hierarchical agglomerative clustering on partially ordered sets.

See the ophac wiki for usage examples and additional context (linked from the old Bitbucket repository).

License

This project is released under the GNU Lesser General Public License v3.0.

Requirements

ophac requires:

• Python 3.10 or newer
• numpy (runtime)
• scipy is optional, and only required for plotting-related utilities

From PyPI (recommended)

Install the core package:

pip install ophac

If you want to use the optional plotting features, install with extras:

pip install ophac[plot]

Local Installation (for development)

Use a virtual environment to avoid polluting your system Python:

python -m venv venv
source venv/bin/activate
pip install -e ".[plot]"  # omit [plot] if plotting is not needed

Building from Source (for unsupported platforms)

If you're on a platform without a prebuilt wheel (e.g., unusual Linux distro or Python version), pip will try to build ophac from source.

You'll need:

• A C++17-compatible compiler (e.g., GCC ≥ 7, Clang ≥ 5, or MSVC ≥ 2017)
• Python development headers (e.g., python3-dev)
• Build tools like make, cmake (if required)

Ensure pip, setuptools, and wheel are up to date:

pip install --upgrade pip setuptools wheel

Then install:

pip install ophac

If building fails, you can clone the repository and install locally:

git clone https://github.com/danielbakkelund/ophac.git
cd ophac
pip install .

Optional Plotting

Some functions provide visualization support (e.g., dendrograms). To enable these, install with the plot extra:

pip install ophac[plot]

This will install scipy as an additional dependency.