New pathway PR checklist

Copy this into the PR description and fill every box.
Guide: docs/python/ADD_PATHWAY.md

Identity

Field	Value
Pathway name (snake_case)	________________
Module path	src/biology_as_code/pathways/________.py
New module or extend existing?	new / extend
Clinical or teaching hook (one line)
Links to existing graphs (if any)	e.g. urea_cycle

Code

• [ ] Graph built (nodes + edges); endpoints valid
• [ ] description written (FLOW teaching, not medical advice claim)
• [ ] references listed or explicitly “topology-only / textbook standard”
• [ ] get_*_registry() factory + list_all or .pathways
• [ ] Wired in pathways/registry.py → pathway_loaders() only
• [ ] No directory that shadows a .py name

Mechanisms (if used)

• [ ] N/A — no mechanism_id on edges
• [ ] New ids registered in metabolic_mechanisms.py
• [ ] Every edge mechanism_id resolves

Export & mermaid

• [ ] Ran PYTHONPATH=src python3 scripts/export_pathway_packs.py
• [ ] packs/<name>/pathway.mermaid present (flowchart + edges)
• [ ] packs/<name>/tests.md + README.md present
• [ ] Did not hand-edit auto mermaid

Docs

• [ ] packs/COVERAGE.md row added / textbook gap updated
• [ ] CHANGELOG.md entry (if release-facing)
• [ ] README “what's inside” (optional)

Tests

• [ ] Discoverable: get_pathway("<name>") works
• [ ] Dedicated test file or invariants covered by existing suite
• [ ] PYTHONPATH=src python3 tests/test_pathway_packs.py passes
• [ ] PYTHONPATH=src python3 scripts/check_pathway_integration.py --pathway <name> exits 0

Boundaries

• [ ] No product meal score / vendor-variable / proprietary engine
• [ ] No invented citations or fabricated magnitudes
• [ ] Zero new runtime dependencies

Reviewer notes

What should a reviewer look at first? Teaching point? Clinical enzyme? Link to urea?

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