scikit-bio-benchmarks

Performance benchmarks for the scikit-bio library.

Overview

This repository contains performance benchmarks for scikit-bio using ASV (airspeed velocity). The benchmarks track performance across different releases to identify regressions and improvements over time.

🔗 View Live Results: https://scikit.bio/scikit-bio-benchmarks

Features

• Benchmarking of scikit-bio releases
• Performance tracking across versions
• Interactive web interface for exploring results
• GitHub Actions integration for automated deployment

Contributing

We welcome contributions! Please:

1. Fork the repository
2. Create a feature branch
3. Add your benchmarks following existing patterns
4. Test locally
5. Submit a pull request

For benchmark ideas, see the scikit-bio documentation or check existing GitHub issues.

Local Development

1. Clone the repository:

   # or clone your own fork of the repository
   git clone https://github.com/scikit-bio/scikit-bio-benchmarks.git
   cd scikit-bio-benchmarks
   

2. Install dependencies:

   pip install asv
   pip install scikit-bio
   

3. Run benchmarks:

   # Quick benchmarks for current version
   asv run --quick
   
   # Benchmark specific version
   asv run 0.6.3^!
   

4. Generate and view results:

   asv publish
   asv preview
   

Triggering Benchmarking

This repository uses GitHub Actions to automatically benchmark new scikit-bio releases:

1. Manual Trigger: Go to Actions → "Benchmark Specific Releases" → "Run workflow"
2. Add New Version: Enter the new release version (e.g., 0.6.4)
3. Deploy: Results are automatically published to GitHub Pages

The workflow will:

• Add the new version to versions.txt
• Run benchmarks for the specified version
• Generate HTML reports
• Deploy to GitHub Pages
• Commit the updated version list

Configuration

Key configuration files:

• asv.conf.json: ASV configuration and build settings
• versions.txt: List of scikit-bio versions to benchmark
• .github/workflows/benchmark.yml: Automated benchmarking workflow

Resources

• ASV Documentation
• scikit-bio Documentation
• GitHub Actions Documentation

License

scikit-bio-benchmarks is available under the new BSD license. See LICENSE.txt for scikit-bio-benchmarks's license.