rosalind

Solutions to the Rosalind problems in python as a command line app.

I'm trying not to use Biopython (whilst also not attempting to rewrite this from scratch!)

Some build details that I'm playing with while putting this together:

• CLI built using Poetry & Typer based on this blog post
• GitLab CI based on this medium blog post
• black for code formatting
• flake8 for code linting
• Pre-commit hook for formatting with black using pre-commit based on black docs
• Coverage and coverage reports with pytest-cov
• Snapshots of test output with snapshottest
• GitHub CI based with github actions

Install

You can install with pip:

pip3 install rosalind

Examples

rosalind dna rosalind_dna.txt

Testing

You can run tests using poetry. For example, to test a function with the test data, run something like:

poetry run rosalind fib tests/data/test_fib.txt

To run all tests and calculate coverage run:

poetry run pytest --cov rosalind