Contributing to STRdust

Thanks for your interest in contributing to STRdust! This document covers the development setup, workflow, and quality standards for the project.

Getting Started for Contributors

Prerequisites

• Rust toolchain (install via rustup)
• Git

First-Time Setup

1. Clone the repository:

git clone https://github.com/wdecoster/STRdust.git
cd STRdust

2. Install development tools and git hooks:

make setup        # Installs rustfmt, clippy, cargo-audit, cargo-outdated
make install-hooks # Installs pre-commit and pre-push hooks

The git hooks will automatically run quality checks before commits and pushes, catching issues early.

Development Workflow

Quick checks before committing:

make pre-commit   # Runs fmt, clippy, and tests

Full CI simulation before pushing:

make ci           # Runs fmt-check, clippy, and tests (same as CI)

Other useful commands:

make fmt          # Format code
make fmt-check    # Check formatting without modifying files
make clippy       # Run linter
make test         # Run tests
make build        # Build release binary
make build-musl   # Build static MUSL binary
make docs         # Generate and open documentation
make help         # Show all available targets

Testing

STRdust includes comprehensive tests, including specific tests for the --pathogenic functionality. Run tests with:

cargo test
# or
make test

Some tests depend on network access (testing the STRchive download functionality) and are skipped by default. They are gated on environment variables — set the variable and run cargo test as usual (no --ignored needed):

TEST_PATHOGENIC_NETWORK=1 cargo test   # cache/download behavior
TEST_PATHOGENIC_FULL=1 cargo test      # full --pathogenic workflow (slower)

Code Quality Standards

Formatting

Code must be formatted with rustfmt using the project's configuration (.rustfmt.toml):

• Max line width: 100 characters
• Edition: 2024
• Field init shorthand enabled

The pre-commit hook automatically runs formatting checks.

Linting

The project uses cargo clippy for linting with warnings treated as errors. Some clippy warnings are configured to be allowed in Cargo.toml:

• too_many_arguments: Allowed because bioinformatics functions often require many parameters for configuration

Run clippy with:

cargo clippy --all-targets --all-features -- -D warnings
# or
make clippy

Security

Security audits run automatically:

make audit        # Run cargo-audit for vulnerability scanning
make outdated     # Check for outdated dependencies

Dependency Management

This project uses Dependabot to automatically keep dependencies up to date. Dependabot is configured to:

• Check for Cargo dependency updates weekly on Mondays
• Check for GitHub Actions updates weekly
• Automatically create pull requests for dependency updates
• Group minor and patch updates together for easier review
• Auto-merge patch updates after tests pass
• Require manual review for major version updates

The Dependabot configuration can be found in .github/dependabot.yml.

Continuous Integration

The project uses GitHub Actions for CI/CD:

• Test workflow: Runs on all pushes and pull requests

  • Checks formatting (cargo fmt --check)
  • Runs clippy with -D warnings
  • Runs full test suite
  • Separate job for MUSL static binary build and test
  • Uses cargo caching for faster builds

• Security workflow: Runs weekly and on every push/PR

  • Security audit with cargo-audit
  • Outdated dependency checks
  • License and security policy enforcement with cargo-deny

• Dependabot workflow: Automatically tests and merges safe dependency updates

• Publish workflow: Creates releases for Linux and macOS when tags are pushed

All CI checks can be simulated locally with make ci before pushing.