Create documentation and tutorials

[jeremymanning]

Summary

Create comprehensive documentation and tutorials for the HTFA toolbox.

Tasks

Documentation

• Set up Sphinx documentation framework
• Write API documentation for all classes and methods
• Create installation and quick start guides
• Add theoretical background and algorithm explanations
• Write troubleshooting and FAQ sections
• Set up automated documentation deployment

Tutorials

• Create basic TFA usage tutorial (single subject)
• Create HTFA tutorial for multi-subject analysis
• Add visualization examples using matplotlib
• Create performance optimization guide
• Add real-world neuroimaging data examples
• Create Jupyter notebook tutorials

Sample Data

• Curate small sample neuroimaging datasets
• Create synthetic data generation examples
• Add data loading and preprocessing utilities
• Document data format requirements

Documentation Framework

• Use Sphinx with RTD theme
• Host on Read the Docs
• Include notebook tutorials via nbsphinx
• Automated API docs from docstrings

Acceptance Criteria

• Complete API documentation
• At least 3 comprehensive tutorials
• Documentation builds without errors
• Tutorials run successfully with sample data

[jeremymanning]

Status Update: Documentation foundation in place 📚

Current Documentation:

• Comprehensive docstrings in all modules
• Type hints throughout codebase
• Example usage in test files
• CLAUDE.md with architecture overview

Still Needed:

• User-facing tutorial notebooks
• API reference documentation
• Installation guide
• Example datasets and use cases

The code is well-documented internally. External documentation and tutorials would be valuable additions for user adoption.