Installation

Build from this repository to get the current Rust algorithms and benchmark tools. The instructions below are the Linux source-build path used by CI. Other platforms may require different BLAS and compiler setup; these instructions do not establish Windows or macOS support.

Toolchain

Use Python 3.10 for the CI-tested environment, a stable Rust toolchain, and uv 0.12.23. The version pin lives in .uv-version and pyproject.toml. If uv manages its own installation, uv self update 0.12.23 selects that version.

On Debian or Ubuntu, install the native prerequisites:

sudo apt-get install libopenblas-dev libssl-dev gfortran pkg-config

Then clone and build:

git clone https://github.com/GeorgePearse/squeeze.git
cd squeeze
uv sync --frozen --extra dev --extra benchmark --no-install-project
uv run --no-sync maturin develop --release --features extension-module,ndarray-linalg/openblas-system

The two-step build installs locked Python dependencies before compiling the local extension against system OpenBLAS. Subsequent uv run --no-sync commands use that environment without replacing the manually built extension.

Check the installed backend

import squeeze

assert squeeze.PCA is not None, "Build the Rust extension first"
assert squeeze.NeighborMap is not None, "Rebuild for the new graph methods"
print(squeeze.__version__)
print(squeeze.__file__)

Run examples from the checkout with uv run --no-sync python your_script.py. If NeighborMap or SpectralMap is None, an old or missing compiled extension is being imported. Rebuild and check squeeze.__file__ before debugging parameters.

Optional dependencies

Extra	Purpose
benchmark	Matplotlib and pandas for benchmark charts and result tables
dev	Maturin, pytest, linting, and development utilities
plot	Additional Python plotting integrations
parametric	TensorFlow for the inherited ParametricUMAP implementation
test	Python test tooling

The core install does not enable TensorFlow. Documentation builds use a separate, small environment described in Contributing.