Restructure documentation and add quickstart guide

[dehe1011]

Summary

This PR comprehensively restructures the TensorHEOM documentation to improve clarity and user experience. It introduces a new quickstart guide, expands the user guide with detailed examples, reorganizes the API documentation, and updates the main index page with better navigation and feature descriptions.

Key Changes

Documentation Structure

• New quickstart guide (docs/quickstart.rst): Provides the fastest path from installation to a working simulation, covering both high-level (calcTimeEvo) and low-level (main) APIs with minimal examples
• Expanded user guide (docs/guide/guide.rst): Transformed from a brief introduction into a comprehensive 300+ line guide with:
  • Four-step workflow overview with ASCII diagram
  • Three detailed examples (single qubit with broadband noise, realistic single-qubit simulation, two-qubit Bell state)
  • Results analysis section with evaluation functions
  • Bath decomposition explanation
  • Hierarchy depth and bond dimension tuning guidance
  • Redfield+ approximation documentation
  • HPC submission instructions
• Reorganized main index (docs/index.rst):
  • Added version, license, and GitHub links
  • Expanded feature list highlighting non-Markovian dynamics, tensor-train compression, Qiskit integration, and analysis tools
  • Added minimal example code
  • Restructured table of contents with clearer section grouping (Getting Started, User Guide, API Reference, About)
• Improved GUI documentation (docs/gui/gui.rst): Added launch instructions, better section organization, and improved figure captions
• Reorganized API documentation (docs/apidoc/apidoc.rst, docs/apidoc/functions.rst, docs/apidoc/classes.rst):
  • Split functions into "Top-level Functions" and "Classes & Module Functions"
  • Added subsections for high-level interface, physical-unit helpers, bath decomposition, and evaluation tools
  • Reordered classes by logical grouping (pulse types, tensor-train, circuit compilation, dynamics, HPC)

Configuration Updates

• Sphinx configuration (docs/conf.py):
  • Added static files path and logo configuration
  • Added theme options for better navigation (collapse_navigation, sticky_navigation)
  • Added GitHub context for "Edit on GitHub" links
  • Fixed typo: "Syntax highlighing" → "Syntax highlighting"

Source Code Updates

• Main module (ttheom/main.py): Fixed docstring typo in calcTimeEvo (dtFB unit: "fs" → "ps")
• Evaluation module (ttheom/evaluation/__init__.py): Added import for logarithmic_negativity module

Notable Implementation Details

• The quickstart guide uses the high-level calcTimeEvo API with physical units (GHz, ns, mK, µs, ps) for accessibility
• The user guide demonstrates the low-level main API with internal units and includes helper functions (prepareSystemArgs, prepareBathArgs, prepareGateArgs) for unit conversion
• Examples progress in complexity: single qubit → realistic single qubit → two-qubit entanglement
• Documentation now clearly distinguishes between quick-start (high-level) and in-depth (low-level) workflows

https://claude.ai/code/session_013BxsoSLohB7jw2D72nJRpx