Contributing

Contributing

Bug reports, questions and pull requests are welcome. See CONTRIBUTING.md for how to report a bug, set up a development environment, open a pull request and make a release, and the code of conduct.

Continuous integration

• Lint with ruff, and tests on Python 3.10, 3.12 and 3.14, for every push and pull request.
• The end-to-end tests run Seal on synthetic genomes and reads with known spoligotypes.
• Coverage is uploaded to Codecov from the Python 3.12 job with the CODECOV_TOKEN secret.
• Dependabot opens one pull request per month to update the GitHub Actions used by the workflows.

Editing this wiki

This wiki is maintained in the wiki/ folder of the main repository and published to the GitHub wiki automatically when changes are pushed to main. Do not edit the wiki on GitHub directly: changes would be overwritten. Edit the files in wiki/ and open a pull request instead.

• Page file names become page titles: Output-files.md → "Output files".
• Link to other pages without the extension: [Usage](Usage).
• _Sidebar.md is the navigation shown on every page.
• Images are stored in the repository's assets/ folder and linked with their https://raw.githubusercontent.com/duceppemo/spoligotyper/main/assets/... URL.

Logo

assets/logo_source.svg is the original logo. Its text needs the Sora font, so assets/make_logo.py converts it to outlines and writes assets/logo.svg, assets/logo_dark.svg (for dark backgrounds) and the bitmap used in the PDF report, spoligotyper/data/logo.png. See the script for its requirements.