Contributing¶

Contributions to Amplirust are welcome!

Development Setup¶

# Clone the repository
git clone https://github.com/erdikilic/amplirust.git
cd amplirust

# Build
RUSTFLAGS="-C target-cpu=native" cargo build --release

# Run tests
cargo test

Code Quality¶

CI enforces a quality gate on every push and pull request. Before submitting changes, ensure your code passes all checks locally:

# Format code
cargo fmt --all

# Run linter (pedantic lints are configured in Cargo.toml)
cargo clippy --all-targets -- -D warnings

# Audit dependencies for security vulnerabilities and license issues
cargo deny check

# Run tests with both parser backends
cargo test
cargo test --no-default-features --features parser_needletail

Testing¶

Unit & integration tests¶

cargo test
cargo test --no-default-features --features parser_needletail

Fuzz testing¶

Requires a nightly toolchain and cargo-fuzz:

cargo install cargo-fuzz

# Run a target (runs until stopped with Ctrl-C)
cargo +nightly fuzz run fuzz_fasta

# Available targets: fuzz_fasta, fuzz_genbank_streaming, fuzz_genbank_slice,
#                    fuzz_primer_csv, fuzz_primer_matcher
cargo +nightly fuzz list

Mutation testing¶

Requires cargo-mutants:

cargo install cargo-mutants

cargo mutants

Configuration is in .cargo/mutants.toml.

Benchmarks¶

Requires Criterion (already a dev-dependency):

# Run all benchmarks
cargo bench

# Run a specific suite
cargo bench --bench matching
cargo bench --bench parsing
cargo bench --bench pipeline
cargo bench --bench circular

Validation against UCSC isPCR¶

The script scripts/validate_ispcr.sh compares amplirust output against the gold-standard UCSC isPCR tool. It requires isPcr on your PATH and downloads the E. coli K-12 genome:

bash scripts/validate_ispcr.sh

Feature Flags¶

Amplirust uses feature flags for FASTA parser selection:

parser_seqio (default) -- uses the seq_io parser
parser_needletail -- uses the needletail parser

Test with both parsers when making changes to input handling:

cargo test
cargo test --no-default-features --features parser_needletail

Submitting Changes¶

Fork the repository
Create a feature branch (git checkout -b feature/my-change)
Make your changes and add tests
Ensure all CI checks pass: cargo fmt --all, cargo clippy --all-targets -- -D warnings, cargo deny check, and cargo test (with both parser features)
Open a pull request against main

License¶

Amplirust is licensed under the MIT License.