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NEW_PATHWAY_CHECKLIST.md

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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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