Aging alignment with EMOD-Generic

[kfrey-idm]

Notes from Claude:

What it does: refactors Susceptibility (and its HIV/Malaria/STI/Vector subclasses) to stop tracking its own private age copy and instead read age live from parent->GetAge() (the IndividualHuman). Mostly mechanical signature cleanup (CreateSusceptibility/Initialize drop the now-redundant age parameter everywhere), plus some cosmetic reformatting. The regression baselines were regenerated wholesale (huge CSV/JSON diffs), which is the tell that this is not behavior-neutral.

Real behavioral differences found

• Age-desync when Enable_Immunity=false and infections are active, across all disease types. In main, IndividualHuman::Update() only calls susceptibility->Update(dt) (which advanced the local age) inside if(ImmunityEnabled()) during the infection sub-stepping loop, but calls it unconditionally in the no-infection branch. So whenever immunity was disabled and an individual had an active infection, Susceptibility's private age silently stopped advancing while IndividualHuman::m_age kept going — a permanent, uncorrected lag. In more_aging there's no private copy to desync; it always reads the live age. This changes age-dependent susceptibility math (maternal protection modifier, malaria BitingRiskAgeFactor, recalculateBloodCapacity, pyrogenic threshold vs. age) specifically for sims run with Enable_Immunity: 0 plus active infections.
• Age-freeze coupling changes when Enable_Aging=false. In main, Susceptibility::age incremented unconditionally on every Update() call regardless of the Enable_Aging config flag — so immune aging (maternal protection decay, malaria RBC-capacity growth, pyrogenic threshold drift, age-dependent biting risk) kept progressing even when chronological aging was turned off for the individual. In more_aging, since it now reads parent->GetAge() (which is only advanced inside if(IndividualHumanConfig::aging)), all of that immune/physiological aging now freezes along with chronological age. Any Malaria/Vector regression or user config that sets Enable_Aging: 0 will see a real behavior change here.

Other notable changes

• Susceptibility::IsImmune() and InitNewInfection() changed from LOG_WARN + safe no-op/false to release_assert(false). No current caller of these base-class virtuals in-tree.
• Node::LoadOtherDiseaseSpecificDistributions() call moved from before to after ExtractDataFromDemographics() in Node::SetParameters. No current override of this virtual exists anywhere in the tree, so it's a no-op today — but it's an ordering change a disease module overrides it and depends on ExtractDataFromDemographicshaving/not having run yet.
• Interface type narrowing: IIndividualHuman::GetAge()/GetMonteCarloWeight() changed double to float, and ISusceptibilityContext::getAge() was removed. The backing storage (m_age, m_mc_weight) was already float, so this isn't an actual precision loss, just the interface catching up to reality. Not a concern.
• Serialization: Susceptibility::age is still archived (ar.labelElement("age") & susceptibility.age, marked // REMOVE NEXT VERSION) but is now permanently 0.0f and unused — dead field kept only for checkpoint schema stability. Harmless, but means old checkpoints' age data is silently discarded on load, which is fine since nothing reads it anymore.

[Copilot]

Pull request overview

This PR aligns EMOD’s susceptibility “aging” behavior with EMOD-Generic by removing Susceptibility’s private age tracking and instead reading age directly from the owning IIndividualHumanContext (parent->GetAge()). It also propagates signature updates (dropping redundant age parameters) across disease-specific susceptibility subclasses and updates several interfaces to use float for age/MC weight.

Changes:

• Refactor Susceptibility (+ HIV/Malaria/STI/Vector subclasses) to stop maintaining an internal age copy; age-dependent calculations now use parent->GetAge().
• Update factory/initialize APIs to remove the age parameter and narrow age/MC weight interface return types from double to float.
• Adjust Node demographics distribution hooks to accept NodeDemographics* and move the “other disease distributions” hook to run after demographics extraction; regenerate regression baselines.

Reviewed changes

Copilot reviewed 31 out of 45 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
Regression/STI/86_STI_ReportRelationshipCensus/output/ReportRelationshipCensus.csv	Updated STI regression output baseline reflecting new age-alignment behavior.
Eradication/VectorToHumanAdapter.h	Interface return types updated (GetAge, GetMonteCarloWeight) to float.
Eradication/VectorToHumanAdapter.cpp	Implementation updated to match new float return types.
Eradication/SusceptibilityVector.h	Remove age parameter from factory/init; rename some age parameters for clarity.
Eradication/SusceptibilityVector.cpp	Use live parent age for biting-risk calculations; remove unused config accessor.
Eradication/SusceptibilitySTI.h	Remove age parameter from factory/init.
Eradication/SusceptibilitySTI.cpp	Wire factory/init to new signature (no explicit age).
Eradication/SusceptibilityMalaria.h	Remove age parameter from factory/init; make age-dependent helpers read from parent age.
Eradication/SusceptibilityMalaria.cpp	Convert malaria age-dependent logic to use parent->GetAge(); refactor innate variation selection.
Eradication/SusceptibilityHIV.h	Remove age parameter from factory/init.
Eradication/SusceptibilityHIV.cpp	Remove immune-age increment; rely on parent age and updated init signature.
Eradication/Susceptibility.h	Add IIndividualHumanContext include; remove getAge() from ISusceptibilityContext exposure; refactor initialization API.
Eradication/Susceptibility.cpp	Remove local age increment and getAge(); switch maternal/immune logic to parent age; tighten base virtuals with asserts.
Eradication/NodeEventContextHost.h	Minor formatting/cleanup.
Eradication/NodeEventContext.h	Forward declaration cleanup and formatting changes.
Eradication/NodeEventContext.cpp	Formatting cleanup; return explicit broadcaster interface pointer.
Eradication/Node.h	Change demographics distribution hooks to accept NodeDemographics*.
Eradication/Node.cpp	Call updated demographics distribution hooks with NodeDemographics* and adjust ordering.
Eradication/ISusceptibilityContext.h	Remove getAge() from susceptibility context interface.
Eradication/IndividualVector.cpp	Update susceptibility creation call to new signature (no explicit age).
Eradication/IndividualSTI.h	Friend/refcounting layout cleanup.
Eradication/IndividualSTI.cpp	Update STI susceptibility creation call; formatting cleanup.
Eradication/IndividualMalaria.cpp	Update malaria susceptibility creation call to new signature (no explicit age).
Eradication/IndividualHIV.cpp	Update HIV susceptibility creation call; formatting cleanup.
Eradication/IndividualEventContext.h	Update GetAge/GetMonteCarloWeight return types to float; formatting cleanup.
Eradication/Individual.h	Update individual event context accessors to float age/MC weight; minor API ordering/formatting.
Eradication/Individual.cpp	Rename parameters for clarity; some minor logic/formatting changes in migration duration helper.
Eradication/IIndividualHumanContext.h	Add GetAge() to context interface (as float).
Eradication/IIndividualHuman.h	Narrow interface return types for age/MC weight to float and reorder some accessors.
componentTests/IndividualHumanContextFake.h	Update fake to match interface type changes (float age/MC weight) and formatting.

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