Documentation Coverage Matrix

This page records the public documentation surface for the repository. It is intentionally practical: users should be able to install, learn, run notebooks, run demos, inspect APIs, and move to production without searching the source tree.

This is the quality gate document for documentation discoverability. If a user can operate the product, onboard a new domainpack, and audit decisions without consulting source code, then the public documentation surface is complete for that user path.

The counts and mappings below should therefore be treated as a release input, not as static inventory. When implementation coverage expands (new adapters, modules, frontier surfaces), the matrix must be updated before release and before any roadmap milestone is announced.

Owner model

• Maintainers: keep this page aligned with mkdocs.yml and API source exports.
• Release owners: verify that any feature or benchmark launch includes matching documentation entries here.
• Contributors: when touching a public surface, add/update the corresponding documentation row in the same change to avoid “code-first” drift.

How to use this as a release gate

This matrix is a production-readiness artifact, not a documentation convenience index. It is used to answer three operational questions before a milestone:

• Can a user reproduce the same path from install to first successful run without reading source?
• Is every advertised runtime path represented in API pages, guides, and walkthroughs?
• Do docs indicate where implementation evidence stops and claim scope begins?

Before release, the page is validated by:

1. mkdocs build --strict --clean (navigation completeness),
2. the API navigation coverage test (tests/test_api_docs_navigation.py),
3. roadmap and release note linkage for each externally announced capability.

If any major path lacks onboarding/tutorial coverage, that path is treated as documentation incomplete even if code exists and tests pass.

Current Inventory

Surface	Current coverage	Entry point
Onboarding	Role route, first-hour checklist, repository map	Onboarding Handbook
Installation	Package extras, local development install, quick checks	Installation
Quickstart	Minimal Python and CLI run path	Quickstart
Tutorials	Seven task-oriented tutorials	New Domain Checklist
Guides	Runtime, production, testing, adapters, backend, notebooks	Guides
Contributor onboarding	setup, repository map, checks, documentation duties	Contributor Onboarding
API reference	67 MkDocs API pages, all wired into navigation	API Reference
Domainpacks	36 domainpacks documented in the gallery	Domainpack Gallery
Notebooks	19 notebook workflows	Notebooks & Demos
Notebook CI matrix	per-notebook extras and execution expectations	Notebook Execution Matrix
Examples	28 terminal-first Python examples	Notebooks & Demos
Interactive demos	Streamlit tools, browser WASM demo, CLI demo	Interactive Tools
Validation	V&V report, study protocol, testing guide	V&V Report
Roadmap	public stable, active, deferred, and research tracks	Public Roadmap

Counts above are derived from the repository tree at the time this page was updated: 36 domainpack directories, 28 examples/*.py scripts, 19 notebooks, and 67 files under docs/reference/api/. tests/test_api_docs_navigation.py guards that every API reference page is listed in mkdocs.yml and that every maintained public source module has a mkdocstrings directive in the API reference. Generated protobuf stubs are covered through the gRPC facade rather than direct autodoc.

The current source inventory contains 204 maintained public Python modules under src/scpn_phase_orchestrator/. API-reference coverage is complete for those modules through package-level or detailed mkdocstrings pages, excluding generated protobuf stubs. Module-level docstrings are still being tightened: the root package now documents the frozen top-level import surface, and new or touched public modules should carry a module docstring that states the stable contract, backend assumptions, and failure-mode policy.

API Documentation Policy

Public APIs are documented at one of two levels:

• Package-level pages document the public module surface through mkdocstrings and a short pipeline explanation.
• Detailed pages document numerically or operationally important modules with theory, usage examples, backend notes, benchmarks, and validation commands.

Private backend probes and experimental auxiliary-backend shim modules are not listed as user-facing APIs unless they expose a stable public contract. They are covered through the owning package page and backend strategy guides.

Module docstrings are required for new public modules. Existing public modules without module-level docstrings are treated as documentation debt, not as a reason to weaken the mkdocstrings coverage gate. When touching such a module, add the module docstring in the same change instead of spreading generic one-line docstrings across unrelated code.

CI also runs interrogate src/scpn_phase_orchestrator --fail-under 100 in the lint job, with generated gRPC stubs excluded and __init__/dunder methods exempted. That ratchet keeps the maintained source tree from regressing below the documented 100% docstring floor.

v0.6.0 Code-to-Documentation Reconciliation

Reader-facing evidence flow

The documentation matrix is used as a practical chain-of-custody structure:

• onboarding starts with operational objective and install path,
• guides and tutorials map each objective to a validated execution path,
• API pages define the stable contract for each executable surface,
• release and validation references define what can be claimed after tests pass.

Every new external statement should have a corresponding trace from source code to test evidence to documentation path. This avoids splitting implementation detail across files and helps new reviewers understand both expected behavior and evidence boundaries in one pass.

The v0.6.0 release preparation reconciled the changed source tree against the public documentation surface using git diff --name-only v0.5.11..HEAD.

Reconciliation item	Result
Changed Python modules under src/scpn_phase_orchestrator/	396
Changed public modules matched by reference, guide, tutorial, example, README, or changelog text	232
Changed modules intentionally excluded as package initialisers, generated gRPC/protobuf stubs, or experimental accelerator implementation mirrors	125
Residual unmatched changed modules after exclusions	39

The 39 residual modules are private auxiliary backend shims:

• coupling shims: _hodge_go, _hodge_julia, _hodge_mojo, _spectral_go, _spectral_julia, _spectral_mojo;
• monitor shims: _psychedelic_go, _psychedelic_julia, _psychedelic_mojo;
• UPDE shims: _basin_stability_*, _envelope_*, _geometric_*, _hypergraph_*, _inertial_*, _market_*, _reduction_*, _simplicial_*, _splitting_*, and _swarmalator_* for Go, Julia, and Mojo.

These files are not standalone public APIs. They are implementation mirrors for the documented public dispatchers and are covered by:

• Backend Fallback Chain, which defines the fallback and demotion policy;
• Backend Strategy, which defines support tiers and promotion criteria;
• the owning API pages for coupling, monitor, and UPDE functions.

No release-blocking public documentation gaps remain from this reconciliation.

API Coverage Summary

Package or surface	Public page	Detailed pages
Core package, exceptions, compatibility	Core	CLI reference
Binding specs and resolution	Binding	schema, defaults, tutorials
UPDE engines	UPDE	basin stability, bifurcation, delay, engine, envelope, geometric, hypergraph, inertial, market, order parameters, PAC, reduction, simplicial, splitting, stochastic, Stuart-Landau, swarmalator
Coupling	Coupling	attention residuals, connectome, prior, transfer entropy adaptive
Monitors	Monitor	chimera, dimension, entropy production, EVS, ITPC, Lyapunov, NPE, recurrence, sleep staging, transfer entropy, winding
Supervisor	Supervisor	policy DSL, regime manager, boundary contract
Adapters	Adapters	production, observability, hardware deployment
SSGF	SSGF	carrier, ethical cost
Autotune	Autotune	SINDy, coupling estimation, phase extraction, frequency ID
Neural network layers	nn API	full nn reference and physics validation plan
Visualisation and reporting	Visualisation, Reporting	interactive tools
QueueWaves application	QueueWaves	QueueWaves guide and production guide

Notebook And Demo Policy

Every notebook or demo should state:

• the domainpack or API surface it exercises;
• the command or UI path to run it;
• whether it is CI-executed or local-only;
• optional dependencies, if any;
• a nearby production path when applicable.

The current notebook/demo inventory is listed in Notebooks & Demos.

Maintenance Checklist

When adding a module, domainpack, notebook, or demo:

• Add or update the relevant API reference page.
• Add or update the module docstring for public modules.
• Add a guide, tutorial, notebook, or example that shows the user path.
• Add the page to mkdocs.yml.
• Update this matrix if counts or coverage categories change.
• Run mkdocs build --strict --clean.

Reader-path coverage map

Different teams read the repository for different outcomes. The table below maps the same surface to the most common operational intent.

Reader goal	Primary source path	Supporting evidence pages
first-run success	getting-started/quickstart.md	getting-started/installation.md, getting-started/hello_world.md
evidence-first adoption	getting-started/executive_overview.md	VALIDATION_REPORT.md, guide/production.md, guide/notebook_to_production.md
API integration	reference/api/index.md	guide/studio.md, reference/api/core.md, reference/api/queuewaves.md
operations and runtime rollout	guide/production.md	guide/queuewaves.md, guide/hardware_deployment.md, guide/rust_ffi.md
formal or safety review	reference/api/upde_pha_c_formal_obligation.md	formal/kinematic_safety.md, guide/backend_review_gate.md, RELEASE_HYGIENE.md

This map is used to avoid documentation dead zones where one role has all required facts and another role receives only implementation hints.

Documentation debt policy for new work

For any merge request that ships a new capability in production scope:

• add or update at least one getting-started page for first-time operators,
• ensure the API reference links to the touched module,
• add or update a test or benchmark reference if performance, safety, or numerics change,
• update this matrix before merge.

Missing one of those checkpoints blocks release-signoff unless the change is explicitly tagged as review-only.