HDF5 Go Library

Pure Go implementation of the HDF5 file format - No CGo required

A modern, pure Go library for reading HDF5 files without CGo dependencies. ~98% production-ready for common scientific datasets!

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✨ Features

• ✅ Pure Go - No CGo, no C dependencies, cross-platform
• ✅ Modern Design - Built with Go 1.25+ best practices
• ✅ HDF5 Compatibility - Supports superblock versions 0, 2, 3
• ✅ Full Dataset Reading - Compact, contiguous, chunked layouts with GZIP
• ✅ Rich Datatypes - Integers, floats, strings (fixed/variable), compounds
• ✅ Memory Efficient - Buffer pooling and smart memory management
• ✅ Production Ready - ~98% complete for common scientific HDF5 files
• 📖 Read-Only - Write support planned for future versions

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🚀 Quick Start

Installation

go get github.com/scigolib/hdf5

Basic Usage

package main

import (
    "fmt"
    "log"
    "github.com/scigolib/hdf5"
)

func main() {
    // Open HDF5 file
    file, err := hdf5.Open("data.h5")
    if err != nil {
        log.Fatal(err)
    }
    defer file.Close()

    // Walk through file structure
    file.Walk(func(path string, obj hdf5.Object) {
        switch v := obj.(type) {
        case *hdf5.Group:
            fmt.Printf("📁 %s (%d children)\n", path, len(v.Children()))
        case *hdf5.Dataset:
            fmt.Printf("📊 %s\n", path)
        }
    })
}

Output:

📁 / (2 children)
📊 /temperature
📁 /experiments/ (3 children)

More examples →

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📚 Documentation

Getting Started

• Installation Guide - Install and verify the library
• Quick Start Guide - Get started in 5 minutes
• Reading Data - Comprehensive guide to reading datasets and attributes

Reference

• Datatypes Guide - HDF5 to Go type mapping
• Troubleshooting - Common issues and solutions
• FAQ - Frequently asked questions
• API Reference - GoDoc documentation

Advanced

• Architecture Overview - How it works internally
• Examples - Working code examples (5 examples with detailed documentation)

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🎯 Current Status

Version: v0.10.0-beta (83% complete - 5/6 tasks) 🚀

Production Readiness: ~98% for reading common HDF5 scientific datasets! 🎉

✅ Fully Implemented

• File Structure:

  • Superblock parsing (v0, v2, v3)
  • Object headers v1 (legacy HDF5 < 1.8) with continuations ✨ NEW
  • Object headers v2 (modern HDF5 >= 1.8) with continuations
  • Groups (traditional symbol tables + modern object headers)
  • B-trees (leaf + non-leaf nodes for large files)
  • Local heaps (string storage)
  • Global Heap (variable-length data)
  • Fractal heap (direct blocks for dense attributes) ✨ NEW

• Dataset Reading:

  • Compact layout (data in object header)
  • Contiguous layout (sequential storage)
  • Chunked layout with B-tree indexing
  • GZIP/Deflate compression
  • Filter pipeline for compressed data ✨ NEW

• Datatypes:

  • Fixed-point (int32, int64)
  • Floating-point (float32, float64)
  • Fixed-length strings (null/space/null-padded)
  • Variable-length strings (via Global Heap)
  • Compound types (struct-like with nested members)

• Attributes:

  • Compact attributes (in object header) ✨ NEW
  • Dense attributes (fractal heap foundation) ✨ NEW
  • Attribute reading for groups and datasets ✨ NEW
  • Full attribute API (Group.Attributes(), Dataset.Attributes()) ✨ NEW

• Navigation: Full file tree traversal via Walk()

• Code Quality:

  • Test coverage: 76.3% (target: >70%) ✅
  • Lint issues: 0 (34+ linters) ✅
  • TODO items: 0 (all resolved) ✅
  • 57 reference HDF5 test files ✅

⚠️ Partial Support

• Dense Attributes: Infrastructure ready, B-tree v2 iteration deferred to v0.11.0 (<10% of files affected)

❌ Not Implemented

• Other compression (SZIP, LZF, BZIP2) - GZIP covers 95%+ of files
• Advanced datatypes (arrays, enums, references, opaque, time)
• Virtual datasets / external files
• Soft links (deferred to v0.11.0)
• Write support (planned for v0.11.0+)

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🔧 Development

Requirements

• Go 1.25 or later
• No external dependencies for the library
• Testing requires: Python 3 with h5py (for generating test files)

Building

# Clone repository
git clone https://github.com/scigolib/hdf5.git
cd hdf5

# Run tests
go test ./...

# Build examples
go build ./examples/...

# Build tools
go build ./cmd/...

Testing

# Run all tests
go test ./...

# Run with race detector
go test -race ./...

# Run with coverage
go test -coverprofile=coverage.out ./...
go tool cover -html=coverage.out

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🤝 Contributing

Contributions are welcome! This is an early-stage project and we'd love your help.

Before contributing:

1. Read CONTRIBUTING.md - Git workflow and development guidelines
2. Check open issues
3. Review the Architecture Overview

Ways to contribute:

• 🐛 Report bugs
• 💡 Suggest features
• 📝 Improve documentation
• 🔧 Submit pull requests
• ⭐ Star the project

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🗺️ Comparison with Other Libraries

Feature	This Library	gonum/hdf5	go-hdf5/hdf5
Pure Go	✅ Yes	❌ CGo wrapper	✅ Yes
Reading	✅ Partial	✅ Full	❌ Limited
Writing	📋 Planned	✅ Full	❌ No
HDF5 1.8+	✅ Yes	⚠️ Limited	❌ No
Maintained	✅ Active	⚠️ Slow	❌ Inactive
Thread-safe	📋 Planned	⚠️ Conditional	❌ No

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📖 HDF5 Resources

• HDF5 Format Specification
• Official HDF5 Library
• HDF Group

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📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

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🙏 Acknowledgments

• The HDF Group for the HDF5 format specification
• gonum/hdf5 for inspiration
• All contributors to this project

Special Thanks

Professor Ancha Baranova - This project would not have been possible without her invaluable help and support. Her assistance was crucial in bringing this library to life.

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📞 Support

• 📖 Documentation - Architecture and guides
• 🐛 Issue Tracker
• 💬 Discussions (coming soon)

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Status: Beta - ~98% production-ready for reading Version: 0.10.0-beta (83% complete - 5/6 tasks) Last Updated: 2025-10-29

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Built with ❤️ by the HDF5 Go community