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Contributing

Thank you for your interest in contributing to vrs-matcher!

Development setup

Install uv, then:

git clone https://github.com/ohsu-comp-bio/vrs-matcher.git
cd vrs-matcher
uv sync --all-groups

If you plan to run the real-data integration test, install the integration group and a local seqrepo data instance:

uv sync --group dev --group integration

# one-time seqrepo download (~10 GB, cached across runs)
scripts/setup_integration_data.sh

# required by tests/integration/conftest.py
export GA4GH_VRS_DATAPROXY_URI=seqrepo+file://$HOME/.local/share/seqrepo/2024-12-20

To use a different snapshot or root directory, set SEQREPO_INSTANCE and/or SEQREPO_ROOT before running scripts/setup_integration_data.sh.

Making changes

  1. Create a branch: git checkout -b your-feature
  2. Make your changes in src/vrs_matcher/
  3. Add or update tests in tests/
  4. Run the checks below and fix any failures before opening a PR

Checks

# Lint and format
uv run ruff check .
uv run ruff format .

# Tests
uv run pytest

# Optional integration test (network + local seqrepo required)
GA4GH_VRS_DATAPROXY_URI=seqrepo+file://$HOME/.local/share/seqrepo/2024-12-20 \
  RUN_INTEGRATION_TESTS=1 uv run pytest -m integration --run-integration

Pull requests

  • Keep PRs focused on a single change
  • Include tests for new behaviour
  • Ensure all checks pass