mkdocs.yml

site_name: TNFR Python Engine
site_description: Canonical documentation for the TNFR Python Engine
site_url: https://fermga.github.io/TNFR-Python-Engine/
repo_url: https://github.com/fermga/TNFR-Python-Engine
repo_name: fermga/TNFR-Python-Engine
docs_dir: build/docs-source
site_dir: site
strict: true

# These repository-owned guides/configurations are intentionally staged. Keep
# their paths so relative links work in both GitHub and the generated site.
exclude_docs: |
  !.github/
  !.github/**
  !.pre-commit-config.yaml

theme:
  name: material
  language: en
  features:
    - navigation.indexes
    - navigation.sections
    - content.code.copy

plugins:
  - search

markdown_extensions:
  - attr_list
  - md_in_html
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - tables
  - pymdownx.arithmatex:
      generic: true
  - toc:
      permalink: true

extra_javascript:
  - docs/assets/mathjax.js
  - https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-chtml.js

nav:
  - Home: index.md
  - Contributor and agent instructions: AGENTS.md
  - Architecture: ARCHITECTURE.md
# BEGIN GENERATED DOCS NAVIGATION
  - "Technical documentation":
      - "Documentation map": docs/README.md
      - "Usage guides":
          - "CLI and SDK": docs/CLI_AND_SDK.md
          - "Regional and relational SDK": docs/guides/REGIONAL_AND_RELATIONAL.md
          - "Observational interfaces": docs/STRUCTURAL_INTERFACE_THEORY.md
          - "Optional Torch backend": docs/TORCH_BACKEND.md
      - "Contracts and diagnostics":
          - "API contracts": docs/API_CONTRACTS.md
          - "Relational dynamics": docs/contracts/RELATIONAL_DYNAMICS.md
          - "Operator events": docs/contracts/OPERATOR_EVENTS.md
          - "Structural fields": docs/STRUCTURAL_FIELDS_TETRAD.md
# END GENERATED DOCS NAVIGATION
# BEGIN GENERATED THEORY NAVIGATION
  - "Theory and research":
      - "Reading routes and implementation map": theory/README.md
      - "State and laws":
          - "Fundamental theory": theory/FUNDAMENTAL_THEORY.md
          - "Parameter foundations": theory/NODAL_PARAMETER_FOUNDATIONS.md
          - "Relation foundations": theory/nodal/RELATION_FOUNDATIONS.md
          - "Pressure premises": theory/nodal/PRESSURE_CONSTITUTIVE_SCOPE.md
          - "Joint parameter response": theory/nodal/JOINT_PARAMETER_RESPONSE.md
          - "Glossary": theory/GLOSSARY.md
      - "Form, phase and coherent patterns":
          - "Inherited form dynamics": theory/nodal/INHERITED_FORM_DYNAMICS.md
          - "Phase-to-form exchange": theory/nodal/PHASE_FORM_EXCHANGE.md
          - "Primitive phase closure": theory/nodal/PRIMITIVE_PHASE_CLOSURE.md
          - "Derived form phase": theory/nodal/DERIVED_FORM_PHASE.md
          - "Relational exchange, recovery and formation": theory/nodal/RELATIONAL_EXCHANGE_ADMISSION.md
          - "Relational pattern composition": theory/nodal/RELATIONAL_PATTERN_COMPOSITION.md
          - "Relational pattern memory": theory/nodal/RELATIONAL_PATTERN_MEMORY.md
          - "Emergence and ontology": theory/EMERGENT_ONTOLOGY.md
      - "Transport, memory and clocks":
          - "EPI diffusion stability": theory/TNFR_DIFFUSION_STABILITY_THEOREM.md
          - "Directed nonnormal dynamics": theory/TNFR_DIRECTED_NONNORMAL_DYNAMICS.md
          - "Derived EPI memory": theory/DERIVED_EPI_MEMORY.md
          - "Capacity and localization": theory/CAPACITY_LOCALIZATION_BALANCE.md
          - "Cycle support dynamics": theory/CYCLE_SUPPORT_DYNAMICS.md
          - "Cycle memory relaxation": theory/CYCLE_MEMORY_RELAXATION.md
          - "Forced support balance": theory/FORCED_SUPPORT_BALANCE.md
          - "REMESH fixed-delay models": theory/REMESH_INFINITY_DERIVATION.md
          - "Scale, geometry and bridge": theory/TNFR_SCALE_GEOMETRY_AND_BRIDGE.md
      - "Operators, grammar and support events":
          - "Structural operators": theory/STRUCTURAL_OPERATORS.md
          - "Unified grammar": theory/UNIFIED_GRAMMAR_RULES.md
          - "Diagnostic and grammar scope": theory/DIAGNOSTIC_AND_GRAMMAR_SCOPE.md
          - "Coupling and winding": theory/COUPLING_WINDING_PERSISTENCE.md
          - "Coherent pattern contact": theory/COHERENT_PATTERN_CONTACT.md
          - "THOL pressure feedback": theory/THOL_PRESSURE_FEEDBACK.md
          - "THOL birth and transport": theory/THOL_BIRTH_AND_TRANSPORT.md
          - "Child coupling feedback": theory/CHILD_COUPLING_FEEDBACK.md
      - "Diagnostics and geometry":
          - "Minimal structural degrees": theory/MINIMAL_STRUCTURAL_DEGREES.md
          - "Structural conservation diagnostics": theory/STRUCTURAL_CONSERVATION_THEOREM.md
          - "Stability and dynamics diagnostics": theory/STRUCTURAL_STABILITY_AND_DYNAMICS.md
          - "Extended fields": theory/EXTENDED_FIELDS_AND_DERIVED_QUANTITIES.md
      - "Auxiliary models and physical comparisons":
          - "Variational and exchange models": theory/TNFR_VARIATIONAL_PRINCIPLE.md
          - "Dissipative/open-system models": theory/DISSIPATIVE_AND_OPEN_SYSTEMS.md
          - "Gauge and polarization constructions": theory/GAUGE_SYMMETRY_AND_UNIFICATION.md
          - "Physical phenomena atlas": theory/PHYSICAL_REGIME_CORRESPONDENCES.md
      - "Arithmetic and applications":
          - "Number theory": theory/TNFR_NUMBER_THEORY.md
          - "Structural observability — R1": theory/TNFR_STRUCTURAL_OBSERVABILITY.md
          - "Arithmetic dynamics — R2": theory/TNFR_ARITHMETIC_DYNAMICS.md
          - "CRT composition — R3": theory/TNFR_CRT_FRACTALITY.md
          - "p-adic dynamics — R4": theory/TNFR_PADIC_DYNAMICS.md
          - "Algebraic number fields — R5": theory/TNFR_ALGEBRAIC_NUMBER_FIELDS.md
          - "Additive dynamics — R6": theory/TNFR_ADDITIVE_DYNAMICS.md
          - "Arithmetic pressure — R7": theory/TNFR_ARITHMETIC_PRESSURE.md
          - "Arithmetic operators — R8": theory/TNFR_ARITHMETIC_OPERATORS.md
          - "Riemann scope": theory/TNFR_RIEMANN_RESEARCH_NOTES.md
          - "Prime-ladder atlas": theory/NUCLEUS_A_PRIME_LADDER_ATLAS.md
          - "Equivariance obstructions": theory/NUCLEUS_B_EQUIVARIANCE_OBSTRUCTIONS.md
          - "Applied structural analysis": theory/APPLIED_STRUCTURAL_ANALYSIS.md
      - "Research, measurement and parked evidence":
          - "Execution plan": theory/research/FIVE_STAGE_EXECUTION_PLAN.md
          - "Research strategy": theory/NODAL_RESEARCH_STRATEGY.md
          - "Passive transport protocol": theory/research/PASSIVE_TRANSPORT_PROTOCOL.md
          - "Regional phase/amplitude protocol": theory/research/PHASE_AMPLITUDE_MEASUREMENT_PROTOCOL.md
          - "TCLab exploratory protocol": theory/research/TCLAB_EXPLORATORY_PROTOCOL.md
          - "C6 mechanism audit": theory/C6_RESEARCH_MECHANISM_AUDIT.md
# END GENERATED THEORY NAVIGATION
      - Historical archive: theory/research/archive/README.md
      - Retired programme boundaries: theory/research/archive/RETIRED_PROGRAMME_BOUNDARIES.md
  - Examples: examples/README.md
  - Benchmarks: benchmarks/README.md
  - Applications:
      - Scope and retained projects: applications/README.md
      - Factorization lab: applications/factorization-lab/README.md
      - Primality: applications/primality-test/README.md
  - Development:
      - Testing: TESTING.md
      - Contributing: CONTRIBUTING.md
      - Security: SECURITY.md
      - Workflows: .github/WORKFLOWS.md
      - Repository scripts: scripts/README.md