Codebase Deep Dive

This section contains a detailed analysis of the Leaspy source code structure, explaining the interaction between Models, Algorithms, and Data.

Contents

• Architecture & Data Flow
  • High-Level Overview
  • Simplified workflow structure
  • Why This Architecture?
• ModelInterface
  • What is an Interface?
  • The Contract: Mandatory Capabilities
  • The Hierarchy: Interface, Base, and Concrete Models
  • Why Do We Need This?
  • Moving to Implementation: BaseModel
• BaseModel
  • The Bridge Between Model, Algorithm, and Data
  • Anatomy of fit(): The Three-Step Orchestration
  • From Abstract to Concrete: The Inheritance Chain
• StatefulModel
  • The “State” Concept
  • How StatefulModel Works
  • Developer Note: When to use which?
  • What comes next?
• McmcSaemCompatibleModel
  • The Optimization Contract
  • Other Responsibilities
  • The Algorithm Loop
• TimeReparametrizedModel
  • The Core Idea: Reparametrized Time
  • Variables Defined
  • What This Class Implements
  • What Comes Next
• RiemanianManifoldModel
  • Abstract Methods: What Subclasses Must Provide
  • Centering \(\xi\) (Speed Factor): Identifiability Fix
  • Variables Defined
  • What Comes Next
• LogisticModel
  • The Metric
  • The Model Equation
  • Variables Defined
  • Initialization (Mixin)
  • What Comes Next
• LogisticInitializationMixin
  • Why a Separate Mixin?
  • The Method: _compute_initial_values_for_model_parameters
  • Utility Functions
• Observation Models
  • The Abstract Base: ObservationModel
  • The Standard: GaussianObservationModel
• The Variables DAG
  • Why does Leaspy need a DAG?
  • What is a DAG, concretely?
  • The Logistic Model’s DAG
  • How VariablesDAG is built
  • Relation to State
• Variable Types
  • Class Hierarchy
  • Color Legend
  • An Illustrated Example — Temporal Variability
  • Variable Types
  • Decision at a Glance
• Declaring Variables: get_variables_specs()
  • The Pattern
  • The Inheritance Chain
  • What Happens Behind the Scenes
  • From Specs to State
  • Writing Your Own Layer
  • See Also
• Data & Dataset
  • Data: The User Interface
  • Dataset: The Computational Core
  • Where is Data Handled in the Code?
• Internal Vocabulary
  • Variable Types
  • Algorithmic Concepts
  • Software Architecture Terms