SIP350 Update carbon accounting + plant mortality

[Copilot]

Summary

• What: Revamp handling of the C pseudo-storage pool; add unit tests covering the changes
• Motivation: Current handling is broken.

NOTE: THIS REPLACES #353

How was this change tested?

New unit tests in tests/sipnet/test_modeling/:

• testPlantMortality.c — tests for initPlantSurvivalTracker and checkForMortality (plant stays alive, dies with/without litter pool, dies with nitrogen cycle, dead stays dead, plant re-emerges)
• testFluxCalculations.c — tests for calcWoodAndLeafFluxes (positive/negative NPP, leaf deficit case, accounting delta, additivity) and calcRootFluxes (positive/negative NPP with N resorption, additivity)
• testNitrogenCycle.c — added testUpdateNResorptionFlux for the new updateNResorptionFlux helper

All existing unit and smoke tests continue to pass.

Checklist

• ] Related issues are listed above. [PRs without an approved, related issue may not get reviewed.
• PR title has the issue number in it ("[#

[Alomir]

Looks good

[Copilot]

Pull request overview

This PR adjusts plant mortality event output behavior to respect the ctx.events flag (preventing computed-event writes when event output isn’t enabled), and adds new unit tests to validate plant mortality behavior and key flux calculations (including N resorption flux handling).

Changes:

• Guard PLANTDEATH computed event output behind ctx.events in checkForMortality().
• Add new unit tests for plant mortality transitions and for wood/leaf/root flux calculations (including accounting delta behavior).
• Extend nitrogen-cycle unit tests with coverage for updateNResorptionFlux() and register the new test binaries in the modeling test Makefile.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/sipnet/sipnet.c	Prevents computed plant-death event output when events are disabled (ctx.events == 0).
tests/sipnet/test_modeling/testPlantMortality.c	New unit tests covering initPlantSurvivalTracker() and checkForMortality() scenarios (alive/dead/re-emergence, litter/no-litter, N-cycle).
tests/sipnet/test_modeling/testFluxCalculations.c	New unit tests for calcWoodAndLeafFluxes() and calcRootFluxes(), including accounting-delta and negative-NPP cases.
tests/sipnet/test_modeling/testNitrogenCycle.c	Adds a focused unit test for updateNResorptionFlux() behavior (basic/additive/negative cases).
tests/sipnet/test_modeling/Makefile	Adds the new modeling test sources to the build/run list.

Suppressed comments (3)

tests/sipnet/test_modeling/testPlantMortality.c:243

• These context flags aren’t fully reset after the nitrogen-cycle test (which sets ctx.anaerobic/waterHResp=1), so this test can inherit unrelated context and become order-dependent. Reset the coupled flags here to keep the suite isolated.

int testMortalityReemergence(void) {
  int status = 0;
  logTest("Running testMortalityReemergence\n");

tests/sipnet/test_modeling/testPlantMortality.c:265

• This test only resets litterPool/nitrogenCycle, but earlier tests enable ctx.anaerobic/waterHResp. That makes the suite order-dependent and can cause surprises if mortality logic later consults those flags. Reset them here to keep tests independent.

int testMortalityWithAccountingDelta(void) {
  int status = 0;

tests/sipnet/test_modeling/testFluxCalculations.c:283

• After the negative-NPP root test enables litterPool/anaerobic/waterHResp, this test resets only ctx.nitrogenCycle. Reset the other coupled context flags too so this test remains independent of execution order.

  status |= checkFlux(fluxes.leafOffNResorption, 0.024,
                      "leafOffNResorption (negative NPP roots)");

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