Installation

pip install maldibatchkit

maldiamrkit is a core dependency and is installed automatically - BatchAwareWarping reuses maldiamrkit.alignment.Warping under the hood, and MaldiSetAdapter bridges to maldiamrkit.MaldiSet for end-to-end AMR workflows.

Optional: Visualisation Extras

For UMAP before/after plots and the diagnostic summary figures:

pip install maldibatchkit[viz]

This pulls in umap-learn and seaborn. All plotting functions use lazy imports, so matplotlib / umap are only required when a plot is actually rendered.

Development Installation

git clone https://github.com/EttoreRocchi/MaldiBatchKit.git
cd MaldiBatchKit
pip install -e ".[dev,viz]"
pre-commit install

See Contributing for coding conventions, testing, and PR guidelines.

Documentation Build

To build the documentation locally:

pip install -e ".[docs,viz]"
make -C docs html

The rendered site lands in docs/build/html/index.html.