Contributing¶

Development setup¶

git clone https://github.com/semenko/rseqc-redux.git
cd rseqc-redux
uv sync

Running tests¶

# All tests
uv run pytest

# Single test file
uv run pytest tests/test_BED.py

# Single test with verbose output
uv run pytest tests/test_BED.py::test_parse_bed_line -v

# With coverage
uv run pytest --cov=rseqc --cov=scripts

Linting and formatting¶

# Check lint
uv run ruff check .

# Auto-fix lint issues
uv run ruff check . --fix

# Format code
uv run ruff format .

Type checking¶

uv run mypy rseqc/

Building docs locally¶

uv sync --group docs
uv run mkdocs serve

Then open http://localhost:8000.

Guidelines¶

Write tests before changing behavior
When fixing a bug, add a regression test first
Target Python 3.10+
Keep CI green: ruff check, ruff format --check, mypy, pytest