CIP-0001: Documentation Improvements with Sphinx

author:

Neil Lawrence

created:

2025-07-09

id:

0001

last_updated:

2025-07-09

status:

in-progress

tags:

["cip", "documentation", "sphinx", "readme"]

title:

Documentation Improvements with Sphinx

CIP-0001: Documentation Improvements with Sphinx

Summary

This CIP proposes comprehensive documentation improvements for the MLAI package, including setting up Sphinx documentation generation, enhancing the README.md, and creating proper API documentation for all modules.

Motivation

The current documentation is minimal and insufficient for users and contributors. The README.md contains only a single sentence, and there’s no structured documentation system in place. This makes it difficult for:

  • New users to understand how to use the MLAI package

  • Contributors to understand the codebase structure

  • Educators to find relevant teaching materials

  • Developers to maintain and extend the codebase

A proper documentation system with Sphinx will provide:

  • Auto-generated API documentation

  • Structured tutorials and guides

  • Better discoverability of features

  • Professional presentation for educational use

Detailed Description

Current State Analysis

  • README.md contains only a single sentence description

  • No API documentation exists

  • No installation or usage instructions

  • No examples or tutorials

  • No contribution guidelines

Proposed Improvements

1. Enhanced README.md

  • Comprehensive project description

  • Installation instructions

  • Quick start guide with examples

  • Project structure overview

  • Contributing guidelines

  • License information

  • Links to documentation

2. Sphinx Documentation Setup

  • Configure Sphinx for Python documentation

  • Set up automatic API documentation generation

  • Create documentation structure with:

    • User guide

    • API reference

    • Tutorials

    • Installation guide

    • Contributing guide

3. Module Documentation

  • Add docstrings to all Python modules

  • Create tutorials for each major feature

  • Document the teaching/lecturing aspects

  • Include mathematical explanations where relevant

4. Documentation Hosting

  • Set up Read the Docs integration

  • Configure automatic documentation builds

  • Ensure documentation is accessible online

Implementation Plan

Phase 1: Foundation (Week 1)

  1. Set up Sphinx environment:

    • Install Sphinx and required extensions

    • Create docs/ directory structure

    • Configure conf.py for MLAI project

    • Set up basic documentation theme

  2. Enhance README.md:

    • Write comprehensive project description

    • Add installation instructions

    • Include quick start examples

    • Add project structure overview

Phase 2: Core Documentation

  1. Create documentation structure:

    • User guide with tutorials

    • API reference documentation

    • Installation and setup guide

    • Contributing guidelines

  2. Add module docstrings:

    • Document all public functions and classes

    • Add type hints where missing

    • Include usage examples in docstrings

Phase 3: Advanced Features

  1. Set up automatic documentation:

    • Configure GitHub Actions for doc builds

    • Set up Read the Docs integration

    • Add documentation badges to README

  2. Create tutorials:

    • Machine learning tutorial using MLAI

    • Gaussian Process tutorial

    • Deep GP tutorial

    • Mountain Car example tutorial

Phase 4: Polish and Launch

  1. Final review and testing:

    • Test all documentation links

    • Verify code examples work

    • Review for clarity and completeness

  2. Launch and announce:

    • Deploy to Read the Docs

    • Update all references to documentation

    • Announce to users and contributors

Backward Compatibility

This change is purely additive and will not affect any existing functionality. All existing code will continue to work as before. The only changes are:

  • Enhanced README.md (replaces existing minimal version)

  • Addition of documentation files and directories

  • Addition of documentation dependencies

Testing Strategy

  • Verify all code examples in documentation run successfully

  • Test documentation builds locally and on CI

  • Validate all internal links work correctly

  • Test Read the Docs integration

  • Review documentation with potential users

Implementation Status

  • [x] Set up Sphinx environment

  • [x] Enhance README.md

  • [x] Create documentation structure

  • [x] Add module docstrings

  • [x] Set up automatic documentation builds

  • [ ] Create tutorials

  • [x] Deploy to Read the Docs

  • [ ] Final review and testing

Progress Updates

2025-07-09

CIP created with proposed status.

2025-07-09

Major progress made on documentation improvements:

  • Sphinx Environment: Successfully set up Sphinx with autodoc, napoleon, mathjax, and other extensions

  • README.md: Completely rewritten with comprehensive project description, installation instructions, quick start guide, and contribution guidelines

  • Documentation Structure: Created full Sphinx documentation structure with user guide, API reference, tutorials, and contributing guides

  • Module Docstrings: Added comprehensive Sphinx-style docstrings to all functions and classes in mlai.py, including proper parameter types, return values, and examples

  • Automatic Documentation: Set up GitHub Actions workflows for building and deploying documentation to GitHub Pages

  • Read the Docs: Documentation is now accessible online through GitHub Pages

The core documentation infrastructure is now complete and functional. Remaining tasks include creating detailed tutorials and final review/testing.

References