kensho-technologies / sequence_align Goto Github PK

Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

License: Apache License 2.0

Rust 27.66% Shell 17.37% Python 54.97%

bioinformatics hirschberg natural-language-processing needleman-wunsch nlp pyo3 python rust sequence-alignment

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entn-at nick1udwig

sequence_align's Issues

Add Rust tests and coverage

Currently, testing is really just integration testing, where we call the Python code and verify the outputs are correct. We should add some tests on the Rust code directly (e.g., verifying alignment matrices are correct), as well as code coverage.

Add performance regression tests

Need to make sure changes don't unintentionally (or intentionally...?) slow down the code and/or increase memory usage.

Create documentation website

Likely just GitHub Pages, but worth looking into, even for a relatively simple toolkit.

Add Python 3.11 support

Codecov package removed

The codecov package just got removed from pypi, it needs to be removed from the dev dependencies and if we still want to use it, replace it with the new supported version: see here

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