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Contributing to fg-sra

Development Setup

Prerequisites

  • Rust (stable toolchain, see rust-toolchain.toml)
  • CMake (for building the vendored ncbi-vdb C library)

Building

git clone --recurse-submodules https://github.com/fg-labs/fg-sra
cd fg-sra
cargo build --release

Install Git Hooks

We use pre-commit hooks to ensure code quality. Install them after cloning:

./scripts/install-hooks.sh

This installs hooks (via symlink, so updates propagate automatically) that run before each commit:

  • cargo ci-fmt - Check code formatting
  • cargo ci-lint - Run clippy lints (pedantic)

Running Checks Manually

# Format check (fails if formatting differs)
cargo ci-fmt

# Lint check (fails on any warnings, pedantic enabled)
cargo ci-lint

# Run all tests (uses nextest)
cargo ci-test

Code Style

  • Run cargo fmt before committing
  • Fix all clippy warnings (including pedantic)
  • Add backticks around identifiers in doc comments (e.g., `read_name`)

Testing

All new features should include tests. Run the full test suite with:

cargo ci-test

Integration tests that require network access to resolve SRA accessions are marked #[ignore] and can be run with:

cargo test -- --ignored

Pull Requests

  1. Ensure all CI checks pass (cargo ci-fmt, cargo ci-lint, cargo ci-test)
  2. Keep PRs focused and reasonably sized
  3. Include tests for new functionality