From 8a4dcee6c97e35968199269ec23ac6a4200bd43c Mon Sep 17 00:00:00 2001 From: Paul Murff Date: Mon, 7 Sep 2026 21:21:04 -0600 Subject: [PATCH] docs(nav): place the eight orphan pages; keep the VMH licence draft out of the nav on purpose Co-Authored-By: Claude Fable 5.1 --- mkdocs.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/mkdocs.yml b/mkdocs.yml index e169a89..ea1ee54 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -58,15 +58,20 @@ markdown_extensions: nav: - Home: index.md + - Intro video: intro-video.md - Constitution: constitution.md - Note on the title: naming.md - "The book (coming soon)": book.md - "Nutrition map (interactive)": https://murffious.github.io/biology_as_code/nutrition-map/ - "Primer: genome-scale metabolic models": gem-primer.md + - "David & Nielsen 2005 (source map)": david-nielsen-2005.md + - "Urea cycle (Recon3D reaction map)": figures/urea-cycle.md - Digestion engine: digestion.md - Digestion process (A-Z stages): digestion-process.md - Events & feedback: events.md + - System coverage layer: systems-coverage.md - Notational conventions: notational-conventions.md + - "The seven systems: vocabulary provenance": SYSTEMS-VOCABULARY-PROVENANCE.md - Metabolic constants (what may be encoded): metabolic-constants.md - Non-laws (looks like a law, is not): non-laws.md - Validation report: VALIDATION.md @@ -81,11 +86,20 @@ nav: - 2. The fat-vehicle gate: cookbook/02-fat-vehicle-gate.md - 3. Matrix effect (almond): cookbook/03-matrix-effect.md - 4. Auditing a real claim: cookbook/04-claim-audit.md + - 5. Vitamin D vehicle: cookbook/05-vitamin-d-vehicle.md - Architecture: - Package: python/PACKAGE_ARCHITECTURE.md - Publishing: python/PUBLISHING.md - Add a pathway (template): python/ADD_PATHWAY.md - Pathway PR checklist: python/templates/NEW_PATHWAY_CHECKLIST.md + - Pathway types refactor (done): python/PATHWAY_TYPES_REFACTOR.md + - Nutrition ontology spec (v0.1): nutrition_ontology_spec.md + +# Built and reachable by URL and search, but deliberately not in the nav: a +# working draft of a licence enquiry, with correspondence details, not a page +# for readers of the docs. +not_in_nav: | + VMH-LICENCE-ENQUIRY.md extra: social: