multiway-alignment 0.0.1

Quantifying multiway (higher-order) alignment with mutual information

multiway-alignment

This repository implements an algorithm for quantifying multiway alignment or higher-order alignment, that is, the alignment across n different dimensions. You can refer to the slide deck for the original idea.

Structure of the repo

• \multiway_alignment\: source code
• \tests\: tests for the source code

Installing the package

From PIP

This package can be installed directly from the Python Package Index (PyPI) using pip from the command-line interface by executing the following command:

$ pip install multiway-alignment

Build from source

Alternatively, the package can be installed by first cloning the repository containing the source code and then installing the package locally in a chosen directory:

$ git clone [e-mail]:letiziaia/multiway-alignment.git
$ cd multiway-alignment
$ pip install .

Setting up the development environment

You should have python >= 3.10 and pipenv installed.

# install dependencies (including dev)
$ pipenv install --dev

# activate environment
$ pipenv shell

Formatting

The project uses Black, flake8 and ruff code linting. All the code can be formatted by running python3 -m black . in root dir. Additional issues can be found by running python3 -m flake8 . and python3 -m ruff check . in root dir.

Tests

This code is built and tested for python 3.10, 3.11, and 3.12.