Contributing

Contributions are very welcome, especially curated rule datasets, bug reports, reproducible test cases, and code improvements.

Bug reports and feature requests

Open an issue on GitHub with:

• A clear description of the problem or feature
• Steps to reproduce (for bugs)
• Expected vs. actual behavior
• ResPro version and Python version

Pull requests

1. Fork the repository.
2. Create a feature branch.
3. Make your changes with tests.
4. Open a pull request against the master branch.

Curated rule datasets are especially welcome — see Database Preparation and Rules TSV Format for the expected file formats.

Design principles

These principles guide development and code review:

• CLI-first — backend changes must remain usable through respro.
• Core independence — domain logic lives in respro/, not in web-only layers.
• Deterministic outputs — reporting and regeneration flows must be reproducible.
• Framework-first design — the project database is the stable internal reference layer for profiling.
• Codon-aware — resistance interpretation stays amino-acid-centered.
• Fail fast — require data to be present; no silent fallbacks or compatibility shims.
• Thin CLI handlers — orchestration belongs in respro/cli/; reusable logic belongs in package modules (respro/core/, respro/io/, respro/db/, respro/report/).

Module layout

• respro/cli — CLI command registration and orchestration
• respro/core — reference-normalized profiling, amino-acid interpretation, and rule matching
• respro/io — format-specific parsing (GenBank, VCF, FASTA, TSV) and external data retrieval
• respro/db — schema, migrations, and persistence/query helpers
• respro/report — HTML/JSON/TSV/PDF export and plotting
• web/backend — FastAPI API, job queue, and startup config
• web/frontend — React frontend

Local quality gates

python -m pytest

Direct contact

For direct contact, email Jonas Fuchs.