LabTrust-Gym/mkdocs.yml at main · fraware/LabTrust-Gym · GitHub

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# MkDocs config for LabTrust-Gym documentation site
site_name: LabTrust-Gym
site_description: Multi-agent environment for a self-driving hospital lab (PettingZoo/Gym style) with trust skeleton
site_url: https://fraware.github.io/LabTrust-Gym/
repo_url: https://github.com/fraware/LabTrust-Gym
repo_name: fraware/LabTrust-Gym
edit_uri: edit/main/docs/

docs_dir: docs
strict: true

theme:
  name: readthedocs
  highlightjs: true

nav:
  - Overview: getting-started/index.md
  - Getting started:
    - getting-started/index.md
    - Installation: getting-started/installation.md
    - Build your own agent: getting-started/build_your_own_agent.md
    - Example agents: getting-started/example_agents.md
    - Example experiments: getting-started/example_experiments.md
    - Forker guide: getting-started/forkers.md
    - Quick demos: getting-started/quick_demos.md
    - Troubleshooting: getting-started/troubleshooting.md
    - Demo readiness: getting-started/demo_readiness.md
    - Windows setup: getting-started/windows_setup.md
    - Environment and .env: getting-started/env_and_dotenv.md
  - Architecture:
    - architecture/index.md
    - Architecture: architecture/architecture.md
    - Systems and threat model: architecture/systems_and_threat_model.md
    - Threat model: architecture/threat_model.md
    - Diagrams: architecture/diagrams.md
    - Workflow and domain spec: architecture/workflow_domain_spec.md
    - Design choices: architecture/design_choices.md
    - Hospital lab workflow: architecture/hospital_lab_workflow.md
    - Simulation and LLM agentic: architecture/simulation_llm_agentic.md
    - System overview: architecture/system_overview.md
    - Design artifacts: architecture/design/README.md
  - Policy and invariants:
    - policy/index.md
    - Policy pack and schemas: policy/policy_pack.md
    - Coordination policy: policy/coordination_policy.md
    - Calibration guide: policy/calibration_guide.md
    - Invariant registry: policy/invariants_registry.md
    - Enforcement: policy/enforcement.md
  - Coordination:
    - coordination/index.md
    - Coordination methods: coordination/coordination_methods.md
    - Coordination method contract: coordination/coordination_method_contract.md
    - Coordination scale: coordination/coordination_scale.md
    - Coordination matrix: coordination/coordination_matrix.md
    - Coordination matrix contract: coordination/coordination_matrix_contract.md
    - Coordination studies: coordination/coordination_studies.md
    - Coordination benchmark card: coordination/coordination_benchmark_card.md
    - Generalization and limits: coordination/generalization_and_limits.md
    - Coordination and env: coordination/coordination_and_env.md
    - Coordination methods how they work: coordination/coordination_methods_how_they_work.md
    - Handoff protocol: coordination/handoff_protocol.md
    - Multi-LLM protocols: coordination/multi_llm_protocols.md
    - Phase 5 LLM upgrades: coordination/phase5_llm_upgrades.md
    - Coordination methods audit: coordination/coordination_methods_audit.md
    - Fidelity notes: coordination/fidelity_notes.md
    - Learning methods implementation strategy: coordination/learning_methods_implementation_strategy.md
  - Benchmarks and studies:
    - benchmarks/index.md
    - Benchmarks: benchmarks/benchmarks.md
    - Benchmark card: benchmarks/benchmark_card.md
    - Official benchmark pack: benchmarks/official_benchmark_pack.md
    - Hospital lab full pipeline: benchmarks/hospital_lab_full_pipeline.md
    - Hospital lab full pipeline results: benchmarks/hospital_lab_full_pipeline_results_report.md
    - Hospital lab metrics: benchmarks/hospital_lab_metrics.md
    - Throughput comparison: benchmarks/throughput_comparison.md
    - Determinism contract: benchmarks/determinism_contract.md
    - Studies and plots: benchmarks/studies.md
    - Scale and operational limits: benchmarks/scale_operational_limits.md
    - Uncertainty quantification: benchmarks/uncertainty_quantification.md
    - Reproduce: benchmarks/reproduce.md
    - LLM Coordination Protocol: benchmarks/llm_coordination_protocol.md
    - Paper claims: benchmarks/PAPER_CLAIMS.md
    - Paper provenance: benchmarks/paper/README.md
    - Evaluation checklist: benchmarks/evaluation_checklist.md
  - Contracts:
    - contracts/index.md
    - Frozen contracts: contracts/frozen_contracts.md
    - Injector get_metrics contract: contracts/injector_get_metrics_contract.md
    - Scripted baseline contract: contracts/scripted_baseline_contract.md
    - UI data contract: contracts/ui_data_contract.md
    - Risk register contract: contracts/risk_register_contract.v0.1.md
    - Queue contract: contracts/queue_contract.v0.1.md
    - CLI contract: contracts/cli_contract.md
    - Metrics contract: contracts/metrics_contract.md
    - Cross-provider contract: contracts/cross_provider_contract.md
  - Risk and security:
    - risk-and-security/index.md
    - Trust verification: risk-and-security/trust_verification.md
    - Risk register: risk-and-security/risk_register.md
    - Risk register viewer: risk-and-security/risk_register_viewer.md
    - Risk injections: risk-and-security/risk_injections.md
    - Security attack suite: risk-and-security/security_attack_suite.md
    - Security monitoring: risk-and-security/security_monitoring.md
    - Security detection design: risk-and-security/security_detection_design.md
    - Prompt-injection defense: risk-and-security/prompt_injection_defense.md
    - Security controls (online): risk-and-security/security_online.md
    - Output controls: risk-and-security/output_controls.md
    - Gate and required bench: risk-and-security/gate_and_required_bench.md
    - LLM live security testing: risk-and-security/llm_live_security_testing.md
    - Security flows and entry points: risk-and-security/security_flows_and_entry_points.md
    - Supply chain integrity: risk-and-security/supply_chain_integrity.md
    - Tool registry SBOM attestation: risk-and-security/tool_registry_sbom_attestation.md
    - Method and pack matrix: risk-and-security/method_and_pack_matrix.md
    - Partner calibration: risk-and-security/partner_calibration.md
  - Export:
    - export/index.md
    - FHIR R4 export: export/fhir_export.md
  - Agents and baselines:
    - agents/index.md
    - LLM baselines: agents/llm_baselines.md
    - Live LLM: agents/llm_live.md
    - MARL baselines: agents/marl_baselines.md
    - MARL multi-agent design: agents/marl_multi_agent_design.md
    - PettingZoo API: agents/pettingzoo_api.md
    - Scripted baselines: agents/scripted_baselines.md
    - Extension development: agents/extension_development.md
  - Operations:
    - operations/index.md
    - CI: operations/ci.md
    - Releasing: operations/releasing.md
    - Ops runbook: operations/ops_runbook.md
    - "How-to: Add coordination method": operations/howto_add_coordination_method.md
    - "How-to: Add risk injection": operations/howto_add_injection.md
    - "How-to: Tune selection policy": operations/howto_selection_policy.md
    - "How-to: Security and gate failures": operations/howto_security_gate_failures.md
    - Operators summary: operations/operators_summary.md
    - Production runbook: operations/production_runbook.md
    - Reviewer runbook: operations/reviewer_runbook.md
  - Reference:
    - reference/index.md
    - Glossary: reference/glossary.md
    - Use cases and impact: reference/use_cases_and_impact.md
    - LabTrust Portal context: labtrust-portal-context.md
    - Repository structure: reference/repository_structure.md
    - Documentation standards: reference/documentation_standards.md
    - Code style and lint: reference/code_style_and_lint.md
    - State of the art and limits: reference/state_of_the_art_and_limits.md
    - Outputs and results: reference/outputs_and_results.md
    - Frontend handoff (UI bundle): reference/frontend_handoff_ui_bundle.md
    - Episode viewer: reference/episode_viewer.md
    - LLM coord trials: reference/llm_coord_trials.md
    - Plan results coordination: reference/plan_results_coordination.md
    - Public API: reference/public_api.md
    - Lab profile reference: reference/lab_profile_reference.md
    - Observability: reference/observability.md
    - Online mode: reference/online_mode.md
    - Testing strategy: reference/testing_strategy.md
    - Presentation and demo guide: presentation_labtrust_gym.md
  - API Reference: api/index.md

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            show_source: true
            show_root_heading: true
            show_symbol_type_heading: true
            docstring_style: google
            members_order: source

markdown_extensions:
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  - pymdownx.snippets
  - pymdownx.superfences