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docs(nav): place the eight orphan pages #34

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14 changes: 14 additions & 0 deletions mkdocs.yml
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Expand Up @@ -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
Expand All @@ -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:
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