From 5ae2652609a15aa52fa5fb38c3773a719951f18c Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Wed, 18 Dec 2024 18:05:39 -0500
Subject: [PATCH 01/34] Adds event handler infrastructure with simple passing
 test

---
 Makefile                                   |  40 +++-
 events.c                                   | 227 +++++++++++++++++++++
 events.h                                   |  67 ++++++
 frontend.c                                 |  11 +
 modelStructures.h                          |  17 ++
 sipnet.c                                   |  57 ++++--
 sipnet.h                                   |   4 +
 tests/sipnet/test_events/Makefile          |  27 +++
 tests/sipnet/test_events/infra_events.in   |   5 +
 tests/sipnet/test_events/modelStructures.h |  17 ++
 tests/sipnet/test_events/testEventInfra.c  | 152 ++++++++++++++
 tests/sipnet/utils.h                       |  37 ++++
 tests/test.template                        |  37 ++++
 13 files changed, 676 insertions(+), 22 deletions(-)
 create mode 100644 events.c
 create mode 100644 events.h
 create mode 100644 modelStructures.h
 create mode 100644 tests/sipnet/test_events/Makefile
 create mode 100644 tests/sipnet/test_events/infra_events.in
 create mode 100644 tests/sipnet/test_events/modelStructures.h
 create mode 100644 tests/sipnet/test_events/testEventInfra.c
 create mode 100644 tests/sipnet/utils.h
 create mode 100644 tests/test.template

diff --git a/Makefile b/Makefile
index 200df75d..9b2a37c3 100755
--- a/Makefile
+++ b/Makefile
@@ -1,15 +1,16 @@
 CC=gcc
 LD=gcc
+AR=ar
 CFLAGS=-Wall
 LIBLINKS=-lm
 
-ESTIMATE_CFILES=sipnet.c ml-metro5.c ml-metrorun.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c
+ESTIMATE_CFILES=sipnet.c ml-metro5.c ml-metrorun.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c events.c
 ESTIMATE_OFILES=$(ESTIMATE_CFILES:.c=.o)
 
-SENSTEST_CFILES=sipnet.c sensTest.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c
+SENSTEST_CFILES=sipnet.c sensTest.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c events.c
 SENSTEST_OFILES=$(SENSTEST_CFILES:.c=.o)
 
-SIPNET_CFILES=sipnet.c frontend.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c
+SIPNET_CFILES=sipnet.c frontend.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c events.c
 SIPNET_OFILES=$(SIPNET_CFILES:.c=.o)
 
 TRANSPOSE_CFILES=transpose.c util.c
@@ -42,10 +43,41 @@ clean:
 #clean:
 #	rm -f $(ESTIMATE_OFILES) $(SENSTEST_OFILES) $(SIPNET_OFILES) $(TRANSPOSE_OFILES) $(SUBSET_DATA_OFILES) estimate sensTest  sipnet transpose subsetData
 
+#
+# UNIT TESTS
+SIPNET_TEST_DIRS:=$(shell find tests/sipnet -type d -mindepth 1 -maxdepth 1)
+SIPNET_TEST_DIRS_CLEAN:= $(addsuffix .clean, $(SIPNET_TEST_DIRS))
+SIPNET_LIB=libsipnet.a
+
+$(SIPNET_LIB): $(SIPNET_LIB)($(SIPNET_OFILES))
+	ranlib $(SIPNET_LIB)
+
+test: pretest $(SIPNET_TEST_DIRS) posttest $(SIPNET_LIB)
+
+pretest:
+	cp modelStructures.h modelStructures.orig.h
+
+# The dash in the build command tells make to continue if there are errors, allowing cleanup
+$(SIPNET_TEST_DIRS): pretest $(SIPNET_LIB)
+	cp $@/modelStructures.h modelStructures.h
+	-$(MAKE) -C $@
+
+# This is far from infallible, as model_structures.h will be in a bad place if a test
+# build step fails in a non-catchable way
+posttest: $(SIPNET_TEST_DIRS)
+	mv modelStructures.orig.h modelStructures.h
+
+testclean: $(SIPNET_TEST_DIRS_CLEAN)
+	rm -f $(SIPNET_LIB)
+
+$(SIPNET_TEST_DIRS_CLEAN):
+	$(MAKE) -C $(basename $@) clean
+
+.PHONY: all test $(SIPNET_TEST_DIRS) pretest posttest $(SIPNET_LIB) testclean $(SIPNET_TEST_DIRS_CLEAN)
+
 
 #This target automatically builds dependencies.
 depend::
 	makedepend $(CFILES)
 
 # DO NOT DELETE THIS LINE -- make depend depends on it.
-
diff --git a/events.c b/events.c
new file mode 100644
index 00000000..b8c48cc7
--- /dev/null
+++ b/events.c
@@ -0,0 +1,227 @@
+//
+// events.c
+//
+
+#include "events.h"
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include "util.h"
+
+void printEvent(EventNode* event);
+
+EventNode* createEventNode(
+    int loc, int year, int day, int eventType, char* eventParamsStr
+) {
+  EventNode *event = (EventNode*)malloc(sizeof(EventNode));
+  event->loc = loc;
+  event->year = year;
+  event->day = day;
+  event->type = eventType;
+
+  switch (eventType) {
+    case HARVEST:
+      {
+        double fracRA, fracRB, fracTA, fracTB;
+        HarvestParams *params = (HarvestParams*)malloc(sizeof(HarvestParams));
+        sscanf(eventParamsStr, "%lf %lf %lf %lf", &fracRA, &fracRB, &fracTA, &fracTB);
+        params->fractionRemovedAbove = fracRA;
+        params->fractionRemovedBelow = fracRB;
+        params->fractionTransferredAbove = fracTA;
+        params->fractionTransferredBelow = fracTB;
+        event->eventParams = params;
+      }
+      break;
+    case IRRIGATION:
+      {
+        double amountAdded;
+        int location;
+        IrrigationParams *params = (IrrigationParams*)malloc(sizeof(IrrigationParams));
+        sscanf(eventParamsStr, "%lf %d", &amountAdded, &location);
+        params->amountAdded = amountAdded;
+        params->location = location;
+        event->eventParams = params;
+      }
+      break;
+    case FERTILIZATION:
+      {
+        // If/when we try two N pools, enable the additional nh4_no3_frac param (likely via
+        // compiler switch)
+        double orgN, orgC, minN;
+        // double nh4_no3_frac;
+        FertilizationParams *params = (FertilizationParams*)malloc(sizeof(FertilizationParams));
+        sscanf(eventParamsStr, "%lf %lf %lf", &orgN, &orgC, &minN);
+        // scanf(eventParamsStr, "%lf %lf %lf %lf", &org_N, &org_C, &min_N, &nh4_no3_frac);
+        params->orgN = orgN;
+        params->orgC = orgC;
+        params->minN = minN;
+        // params->nh4_no3_frac = nh4_nos_frac;
+        event->eventParams = params;
+      }
+      break;
+    case PLANTING:
+      {
+        int emergenceLag;
+        double addedC, addedN;
+        PlantingParams *params = (PlantingParams*)malloc(sizeof(PlantingParams));
+        sscanf(eventParamsStr, "%d %lf %lf", &emergenceLag, &addedC, &addedN);
+        params->emergenceLag = emergenceLag;
+        params->addedC = addedC;
+        params->addedN = addedN;
+        event->eventParams = params;
+      }
+      break;
+    case TILLAGE:
+      {
+        double fracLT, somDM, litterDM;
+        TillageParams *params = (TillageParams*)malloc(sizeof(TillageParams));
+        sscanf(eventParamsStr, "%lf %lf %lf", &fracLT, &somDM, &litterDM);
+        params->fractionLitterTransferred = fracLT;
+        params->somDecompModifier = somDM;
+        params->litterDecompModifier = litterDM;
+        event->eventParams = params;
+      }
+      break;
+    default:
+      // Unknown type, error and exit
+      printf("Error reading from event file: unknown event type %d\n", eventType);
+      exit(1);
+  }
+
+  event->nextEvent = NULL;
+  return event;
+}
+
+enum EventType getEventType(char *eventTypeStr) {
+  if (strcmp(eventTypeStr, "irrig") == 0) {
+    return IRRIGATION;
+  } else if (strcmp(eventTypeStr, "fert") == 0) {
+    return FERTILIZATION;
+  } else if (strcmp(eventTypeStr, "plant") == 0) {
+    return PLANTING;
+  } else if (strcmp(eventTypeStr, "till") == 0) {
+    return TILLAGE;
+  } else if (strcmp(eventTypeStr, "harv") == 0) {
+    return HARVEST;
+  }
+  return UNKNOWN_EVENT;
+}
+
+EventNode** readEventData(char *eventFile, int numLocs) {
+  int loc, year, day, eventType;
+  int currLoc, currYear, currDay;
+  int EVENT_LINE_SIZE = 1024;
+  int numBytes;
+  char *eventParamsStr;
+  char eventTypeStr[20];
+  char line[EVENT_LINE_SIZE];
+  EventNode *curr, *next;
+
+  printf("Begin reading event data from file %s\n", eventFile);
+
+  EventNode** events = (EventNode**)calloc(sizeof(EventNode*), numLocs * sizeof(EventNode*));
+  // status of the read
+  FILE *in = openFile(eventFile, "r");
+
+  if (fgets(line, EVENT_LINE_SIZE, in) == NULL) {
+    printf("Error: no event data in %s\n", eventFile);
+    exit(1);
+  }
+  sscanf(line, "%d %d %d %s %n", &loc, &year, &day, eventTypeStr, &numBytes);
+  eventParamsStr = line + numBytes;
+
+  eventType = getEventType(eventTypeStr);
+  if (eventType == UNKNOWN_EVENT) {
+    printf("Error: unknown event type %s\n", eventTypeStr);
+    exit(1);
+  }
+  printf("Found event type %d (%s)\n", eventType, eventTypeStr);
+
+  next = createEventNode(loc, year, day, eventType, eventParamsStr);
+  events[loc] = next;
+  currLoc = loc;
+  currYear = year;
+  currDay = day;
+
+  printf("Found events:\n");
+  printEvent(next);
+
+  while (fgets(line, EVENT_LINE_SIZE, in) != NULL) {
+    // We have another event
+    curr = next;
+    sscanf(line, "%d %d %d %s %n", &loc, &year, &day, eventTypeStr, &numBytes);
+    eventParamsStr = line + numBytes;
+
+    eventType = getEventType(eventTypeStr);
+    if (eventType == UNKNOWN_EVENT) {
+      printf("Error: unknown event type %s\n", eventTypeStr);
+      exit(1);
+    }
+
+    // make sure location and time are non-decreasing
+    if (loc < currLoc) {
+      printf("Error reading event file: was reading location %d, trying to read location %d\n", currLoc, loc);
+      printf("Event records for a given location should be contiguous, and locations should be in ascending order\n");
+      exit(1);
+    }
+    if ((loc == currLoc) && ((year < currYear) || (day < currDay))) {
+      printf("Error reading event file: for location %d, last event was at (%d, %d) ", currLoc, currYear, currDay);
+      printf("next event is at (%d, %d)\n", year, day);
+      printf("Event records for a given location should be in time-ascending order\n");
+      exit(1);
+    }
+
+    next = createEventNode(loc, year, day, eventType, eventParamsStr);
+    printEvent(next);
+    if (currLoc == loc) {
+      // Same location, add the new event to this location's list
+      curr->nextEvent = next;
+    }
+    else {
+      // New location, update location and start a new list
+      currLoc = loc;
+      events[currLoc] = next;
+    }
+  }
+
+  fclose(in);
+  return events;
+}
+
+void printEvent(EventNode *event) {
+  if (event == NULL) {
+    return;
+  }
+  int loc = event->loc;
+  int year = event->year;
+  int day = event->day;
+  switch (event->type) {
+    case IRRIGATION:
+      printf("IRRIGATION at loc %d on %d %d, ", loc, year, day);
+      IrrigationParams *const iParams = (IrrigationParams*)event->eventParams;
+      printf("with params: amount added %4.2f\n", iParams->amountAdded);
+      break;
+    case FERTILIZATION:
+      printf("FERTILIZATION at loc %d on %d %d, ", loc, year, day);
+      FertilizationParams *const fParams = (FertilizationParams*)event->eventParams;
+      printf("with params: org N %4.2f, org C %4.2f, min N %4.2f\n", fParams->orgN, fParams->orgC, fParams->minN);
+      break;
+    case PLANTING:
+      printf("PLANTING at loc %d on %d %d, ", loc, year, day);
+      PlantingParams *const pParams = (PlantingParams*)event->eventParams;
+      printf("with params: emergence lag %d, added C %4.2f, added N %4.2f\n", pParams->emergenceLag, pParams->addedC, pParams->addedN);
+      break;
+    case TILLAGE:
+      printf("TILLAGE at loc %d on %d %d, ", loc, year, day);
+      TillageParams *const tParams = (TillageParams*)event->eventParams;
+      printf("with params: frac litter transferred %4.2f, som decomp modifier %4.2f, litter decomp modifier %4.2f\n", tParams->fractionLitterTransferred, tParams->somDecompModifier, tParams->litterDecompModifier);
+      break;
+    case HARVEST:
+      printf("HARVEST at loc %d on %d %d, ", loc, year, day);
+      HarvestParams *const hParams = (HarvestParams*)event->eventParams;
+      printf("with params: frac removed above %4.2f, frac removed below %4.2f, frac transferred above %4.2f, frac transferred below %4.2f\n", hParams->fractionRemovedAbove, hParams->fractionRemovedBelow, hParams->fractionTransferredAbove, hParams->fractionTransferredBelow);
+      break;
+    default:
+      printf("Error printing event: unknown type %d\n", event->type);
+  }
+}
diff --git a/events.h b/events.h
new file mode 100644
index 00000000..de027a64
--- /dev/null
+++ b/events.h
@@ -0,0 +1,67 @@
+//
+// Created by Michael J Longfritz on 11/8/24.
+//
+
+#ifndef EVENTS_H
+#define EVENTS_H
+
+#include "modelStructures.h"
+
+enum EventType {
+  FERTILIZATION,
+  HARVEST,
+  IRRIGATION,
+  PLANTING,
+  TILLAGE,
+  UNKNOWN_EVENT
+};
+
+typedef struct HarvestParams {
+  double fractionRemovedAbove;
+  double fractionRemovedBelow;
+  double fractionTransferredAbove; // to surface litter pool
+  double fractionTransferredBelow; // to soil litter pool
+} HarvestParams;
+
+typedef struct IrrigationParams {
+  double amountAdded;
+  int location; // 0=canopy, 1=soil
+} IrrigationParams;
+
+typedef struct FertilizationParams {
+  double orgN;
+  double orgC;
+  double minN;
+  //double nh4_no3_frac; for two-pool version
+} FertilizationParams;
+
+typedef struct PlantingParams {
+  int emergenceLag;
+  double addedC;
+  double addedN;
+} PlantingParams;
+
+typedef struct TillageParams {
+  double fractionLitterTransferred;
+  double somDecompModifier;
+  double litterDecompModifier;
+} TillageParams;
+
+typedef struct EventNode EventNode;
+struct EventNode {
+  enum EventType type;
+  int loc, year, day;
+  void *eventParams;
+  EventNode *nextEvent;
+};
+
+/* Read event data from <FILENAME>.event
+ *
+ * Format: returned data is structured as an array of EventNode pointers, indexed by
+ * location. Each element of the array is the first event for that location (or null
+ * if there are no events). It is assumed that the events are in chrono order.
+ */
+EventNode** readEventData(char *eventFile, int numLocs);
+
+
+#endif //EVENTS_H
diff --git a/frontend.c b/frontend.c
index 018039d7..c79633fe 100755
--- a/frontend.c
+++ b/frontend.c
@@ -13,6 +13,7 @@
 #include "spatialParams.h"
 #include "namelistInput.h"
 #include "outputItems.h"
+#include "modelStructures.h"
 
 // important constants - default values:
 
@@ -81,6 +82,10 @@ int main(int argc, char *argv[]) {
   double **standarddevs;
   int dataTypeIndices[MAX_DATA_TYPES];
 
+#ifdef EVENT_HANDLER
+	// Extra filename if we are handing events
+	char eventFile[FILE_MAXNAME+24];
+#endif
 
   // get command-line arguments:
   while ((option = getopt(argc, argv, "hi:")) != -1) {
@@ -151,6 +156,12 @@ int main(int argc, char *argv[]) {
   strcat(climFile, ".clim");
   numLocs = initModel(&spatialParams, &steps, paramFile, climFile);
 
+#ifdef EVENT_HANDLER
+	strcpy(eventFile, fileName);
+	strcat(eventFile, ".event");
+	initEvents(eventFile, numLocs);
+#endif
+
   if (doSingleOutputs)  {
     outputItems = newOutputItems(fileName, ' ');
     setupOutputItems(outputItems);
diff --git a/modelStructures.h b/modelStructures.h
new file mode 100644
index 00000000..5a591bb0
--- /dev/null
+++ b/modelStructures.h
@@ -0,0 +1,17 @@
+//
+// This file is inteneded to hold settings for different model structure options,
+// implemented as compile-time flags. The options are here (with nothing else) to
+// improve testability.
+//
+
+#ifndef MODEL_STRUCTURES_H
+#define MODEL_STRUCTURES_H
+
+// Begin definitions for choosing different model structures
+// See also sipnet.c for other options (that should be moved here if/when testing is added)
+
+#define EVENT_HANDLER 1
+// Read in and process agronomic events. Expects a file named <FILENAME>.event to exist.
+
+
+#endif //MODEL_STRUCTURES_H
diff --git a/sipnet.c b/sipnet.c
index 08751453..ee6f717a 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -18,6 +18,8 @@
 #include "util.h"
 #include "spatialParams.h"
 #include "outputItems.h"
+#include "modelStructures.h"
+#include "events.h"
 
 // begin definitions for choosing different model structures
 // (1 -> true, 0 -> false)
@@ -26,14 +28,14 @@
 
 //alternative transpiration methods modified by Dave Moore
 #define ALTERNATIVE_TRANS 0
-// do we want to impliment alternative transpiration?
+// do we want to implement alternative transpiration?
 
 #define BALL_BERRY 0
-//impliment a Ball Berry submodel to calculate gs from RH, CO2 and A
+//implement a Ball Berry submodel to calculate gs from RH, CO2 and A
 //MUST BE OFF for PENMAN MONTEITH TO RUN
 
 #define PENMAN_MONTEITH_TRANS 0
-//impliment a transpiration calculation based on the Penman-Monteith Equation.
+//implement a transpiration calculation based on the Penman-Monteith Equation.
 //March 1st 2007 PM equation not really working.
 
 //#define G 0
@@ -487,7 +489,9 @@ static ClimateNode *climate; // current climate
 static Fluxes fluxes;
 static double *outputPtrs[MAX_DATA_TYPES]; // pointers to different possible outputs
 
-
+#ifdef EVENT_HANDLER
+static EventNode **events; // MJL: event structs
+#endif
 
 /* Read climate file into linked lists,
    make firstClimates be a vector where each element is a pointer to the head of a list corresponding to one spatial location
@@ -934,8 +938,8 @@ void calcLightEff3 (double *lightEff, double lai, double par) {
     coeff = 1;
     int err;
     double fAPAR;		// Calculation of fAPAR according to 1 - exp(attenuation*LAI)
-    double APAR;		// Absorbed PAR by the canopy
-    double lightIntensityTop, lightIntensityBottom;	// PAR absorbed by the canopy
+    //double APAR;		// Absorbed PAR by the canopy
+    //double lightIntensityTop, lightIntensityBottom;	// PAR absorbed by the canopy
     cumfAPAR = 0.0;
 
 
@@ -966,11 +970,11 @@ void calcLightEff3 (double *lightEff, double lai, double par) {
     fAPAR = cumfAPAR/(3.0*NUM_LAYERS);  // the average value, multiplying by h/3 in Simpson's rule, and dividing by the number of steps
 
 
-    lightIntensityTop = par;  // Energy at the top of the canopy
-    lightIntensityBottom = par * exp(-1.0 * params.attenuation * lai); // LAI at the bottom of the canopy
+    //lightIntensityTop = par;  // Energy at the top of the canopy
+    //lightIntensityBottom = par * exp(-1.0 * params.attenuation * lai); // LAI at the bottom of the canopy
 																		// between 0 and par
         // this is the amount of incident par
-    APAR = params.m_ballBerry * (lightIntensityTop - lightIntensityBottom);		// APAR at this layer
+    //APAR = params.m_ballBerry * (lightIntensityTop - lightIntensityBottom);		// APAR at this layer
               // is a fraction of the difference between incoming par and transmitted par
 
 
@@ -1932,8 +1936,8 @@ void calculateFluxes() {
   	double potGrossPsn; // potential photosynthesis, without water stress
   	double dWater;
   	double lai; // m^2 leaf/m^2 ground (calculated from plantLeafC)
-  	double litterBreakdown; /* total litter breakdown (i.e. litterToSoil + rLitter)
-							 (g C/m^2 ground/day) */
+  	//double litterBreakdown; /* total litter breakdown (i.e. litterToSoil + rLitter)
+		//					 (g C/m^2 ground/day) */
   	double folResp, woodResp; // maintenance respiration terms, g C * m^-2 ground area * day^-1
   	double litterWater, soilWater; /* amount of water in litter and soil (cm)
 				    taken from either environment or climate drivers, depending on value of MODEL_WATER */
@@ -2005,7 +2009,7 @@ void calculateFluxes() {
 		fluxes.litterToSoil = litterBreakdown * (1.0 - params.fracLitterRespired);
   	// NOTE: right now, we don't have capability to use separate cold soil params for litter
 	#else
-  		litterBreakdown = 0;
+  	//	litterBreakdown = 0;
 		fluxes.rLitter = 0;
 		fluxes.litterToSoil = 0;
 	#endif
@@ -2479,6 +2483,12 @@ void setupModel(SpatialParams *spatialParams, int loc) {
 }
 
 
+// Setup events at given location
+void setupEvents(int currLoc) {
+
+}
+
+
 /* Do one run of the model using parameter values in spatialParams
    If out != NULL, output results to out
     If printHeader = 1, print a header for the output file, if 0 don't
@@ -2504,6 +2514,9 @@ void runModelOutput(FILE *out, OutputItems *outputItems, int printHeader, Spatia
 
   for (currLoc = firstLoc; currLoc <= lastLoc; currLoc++) {
     setupModel(spatialParams, currLoc);
+#ifdef EVENT_HANDLER
+  	setupEvents(currLoc);
+#endif
     if ((loc == -1) && (outputItems != NULL))  {  // print the current location at the start of the line
       sprintf(label, "%d", currLoc);
       writeOutputItemLabels(outputItems, label);
@@ -2511,10 +2524,12 @@ void runModelOutput(FILE *out, OutputItems *outputItems, int printHeader, Spatia
 
     while (climate != NULL) {
       updateState();
-      if (out != NULL)
-	outputState(out, currLoc, climate->year, climate->day, climate->time);
-      if (outputItems != NULL)
-	writeOutputItemValues(outputItems);
+      if (out != NULL) {
+	      outputState(out, currLoc, climate->year, climate->day, climate->time);
+      }
+      if (outputItems != NULL) {
+	      writeOutputItemValues(outputItems);
+      }
       climate = climate->nextClim;
     }
     if (outputItems != NULL)
@@ -2775,8 +2790,14 @@ int initModel(SpatialParams **spatialParams, int **steps, char *paramFile, char
   return numLocs;
 }
 
-
-
+/* Do initialization of event data if event handling is turned on.
+ * Populates static event structs
+ */
+void initEvents(char *eventFile, int numLocs) {
+#ifdef EVENT_HANDLER
+	events = readEventData(eventFile, numLocs);
+#endif
+}
 // call this when done running model:
 // de-allocates space for climate linked list
 // (needs to know number of locations)
diff --git a/sipnet.h b/sipnet.h
index 3378d40d..6c8278b8 100755
--- a/sipnet.h
+++ b/sipnet.h
@@ -51,6 +51,10 @@ char **getDataTypeNames();
 */
 int initModel(SpatialParams **spatialParams, int **steps, char *paramFile, char *climFile);
 
+/*
+ * TBD
+ */
+void initEvents(char *eventFile, int numLocs);
 
 // call this when done running model:
 // de-allocates space for climate linked list
diff --git a/tests/sipnet/test_events/Makefile b/tests/sipnet/test_events/Makefile
new file mode 100644
index 00000000..261cb8a6
--- /dev/null
+++ b/tests/sipnet/test_events/Makefile
@@ -0,0 +1,27 @@
+CC=gcc
+LD=gcc
+CFLAGS=-Wall -g
+LDFLAGS=-L../../..
+LDLIBS=-lsipnet
+#INCLUDE=../../../.
+
+# List test files in this directory here
+TEST_CFILES=testEventInfra.c
+TEST_OBJ_FILES=$(TEST_CFILES:%.c=%.o)
+TEST_EXECUTABLES:=$(basename $(TEST_CFILES))
+
+all: tests
+
+tests: $(TEST_EXECUTABLES)
+
+$(TEST_EXECUTABLES): %: %.o
+	$(CC) $(LDFLAGS) $< $(LDLIBS) -o $@
+
+$(TEST_OBJ_FILES): ../utils.h ../../../libsipnet.a
+$(TEST_OBJ_FILES): %.o: %.c
+	$(CC) $(CFLAGS) -c -o $@ $<
+
+clean:
+	rm -f $(TEST_OBJ_FILES) $(TEST_EXECUTABLES) events.in
+
+.PHONY: all tests clean
diff --git a/tests/sipnet/test_events/infra_events.in b/tests/sipnet/test_events/infra_events.in
new file mode 100644
index 00000000..ef0169f8
--- /dev/null
+++ b/tests/sipnet/test_events/infra_events.in
@@ -0,0 +1,5 @@
+0  2022  40 irrig   5   0           # 5cm canopy irrigation on day 40
+0  2022  40  fert   15 5 10         # fertilized with 15 g/m2 organic N, 5 g/m2 organic C, and 10 g/m2 mineral N on day 40
+0  2022  45  till   0.1 0.2 0.3     # tilled on day 45, 10% of surface litter transferred to soil pool, soil organic matter pool decomposition rate increases by 20% and soil litter pool decomposition rate increases by 30%
+0  2022  46  plant  10 10 1         # planting - planting occurs on day 40, after 10 days the plants have emerged with a size of 10 g C/m2 and 1 g N / m2
+0  2022  250 harv   0.4 0.1 0.2 0.3 # harvest 10% of aboveground plant biomass on day 250
diff --git a/tests/sipnet/test_events/modelStructures.h b/tests/sipnet/test_events/modelStructures.h
new file mode 100644
index 00000000..5a591bb0
--- /dev/null
+++ b/tests/sipnet/test_events/modelStructures.h
@@ -0,0 +1,17 @@
+//
+// This file is inteneded to hold settings for different model structure options,
+// implemented as compile-time flags. The options are here (with nothing else) to
+// improve testability.
+//
+
+#ifndef MODEL_STRUCTURES_H
+#define MODEL_STRUCTURES_H
+
+// Begin definitions for choosing different model structures
+// See also sipnet.c for other options (that should be moved here if/when testing is added)
+
+#define EVENT_HANDLER 1
+// Read in and process agronomic events. Expects a file named <FILENAME>.event to exist.
+
+
+#endif //MODEL_STRUCTURES_H
diff --git a/tests/sipnet/test_events/testEventInfra.c b/tests/sipnet/test_events/testEventInfra.c
new file mode 100644
index 00000000..8081baed
--- /dev/null
+++ b/tests/sipnet/test_events/testEventInfra.c
@@ -0,0 +1,152 @@
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#include "../utils.h"
+#include "../../../events.c"
+
+int checkEvent(EventNode* event, int loc, int year, int day, enum EventType type) {
+  int success =
+    event->loc == loc &&
+    event->year == year &&
+    event->day == day &&
+    event->type == type;
+  if (!success) {
+    printf("Error checking event\n");
+    printEvent(event);
+    return 1;
+  }
+  return 0;
+}
+
+int checkHarvestParams(
+  HarvestParams *params, double fracRemAbove,
+  double fracRemBelow,
+  double fracTransAbove,
+  double fracTransBelow
+) {
+  return !(
+    compareDoubles(params->fractionRemovedAbove, fracRemAbove) &&
+    compareDoubles(params->fractionRemovedBelow, fracRemBelow) &&
+    compareDoubles(params->fractionTransferredAbove, fracTransAbove) &&
+    compareDoubles(params->fractionTransferredBelow, fracTransBelow)
+    );
+}
+
+int checkIrrigationParams(
+  IrrigationParams *params,
+  double amountAdded,
+  int location
+  ) {
+  return !(
+    compareDoubles(params->amountAdded, amountAdded) &&
+    params->location == location
+    );
+}
+
+int checkFertilizationParams(
+  FertilizationParams *params,
+  double orgN,
+  double orgC,
+  double minN
+) {
+  return !(
+    compareDoubles(params->orgN, orgN) &&
+    compareDoubles(params->orgC, orgC) &&
+    compareDoubles(params->minN, minN)
+    );
+}
+
+int checkPlantingParams(
+  PlantingParams *params, int emergenceLag, double addedC, double addedN
+  ) {
+  return !(
+    params->emergenceLag == emergenceLag &&
+    compareDoubles(params->addedC, addedC) &&
+    compareDoubles(params->addedN, addedN)
+    );
+}
+
+int checkTillageParams(
+  TillageParams *params,
+  double fracLitterTransferred,
+  double somDecompModifier,
+  double litterDecompModifier
+  ) {
+  return !(
+    compareDoubles(params->fractionLitterTransferred, fracLitterTransferred) &&
+    compareDoubles(params->somDecompModifier, somDecompModifier) &&
+    compareDoubles(params->litterDecompModifier, litterDecompModifier)
+    );
+}
+
+int init() {
+  // char * filename = "infra_events.in";
+  // if (access(filename, F_OK) == -1) {
+  //   return 1;
+  // }
+  //
+  // return copyFile(filename, "events.in");
+  return 0;
+}
+
+int run() {
+  int numLocs = 1;
+  EventNode** output = readEventData("infra_events.in", numLocs);
+
+  if (!output) {
+    return 1;
+  }
+
+  // check output is correct
+  int status = 0;
+  EventNode *event = output[0];
+  status |= checkEvent(event, 0, 2022, 40, IRRIGATION);
+  status |= checkIrrigationParams((IrrigationParams*)event->eventParams, 5, 0);
+  event = event->nextEvent;
+  status |= checkEvent(event, 0, 2022, 40, FERTILIZATION);
+  status |= checkFertilizationParams((FertilizationParams*)event->eventParams, 15, 5,10);
+  event = event->nextEvent;
+  status |= checkEvent(event, 0, 2022, 45, TILLAGE);
+  status |= checkTillageParams((TillageParams*)event->eventParams, 0.1, 0.2, 0.3);
+  event = event->nextEvent;
+  status |= checkEvent(event, 0, 2022, 46, PLANTING);
+  status |= checkPlantingParams((PlantingParams*)event->eventParams, 10, 10, 1);
+  event = event->nextEvent;
+  status |= checkEvent(event, 0, 2022, 250, HARVEST);
+  status |= checkHarvestParams((HarvestParams*)event->eventParams, 0.4, 0.1, 0.2, 0.3);
+
+  if (status) {
+    return 1;
+  }
+
+  return 0;
+}
+
+void cleanup() {
+  // Perform any cleanup as needed
+  // None needed here, we can leave the copied file
+}
+
+int main() {
+  int status;
+  status = init();
+  if (status) {
+    printf("Test initialization failed with status %d\n", status);
+    exit(status);
+  } else {
+    printf("Test initialized\n");
+  }
+
+  printf("Starting run()\n");
+  status = run();
+  if (status) {
+    printf("Test run failed with status %d\n", status);
+    exit(status);
+  }
+
+  printf("testEventInfra PASSED\n");
+
+  cleanup();
+}
\ No newline at end of file
diff --git a/tests/sipnet/utils.h b/tests/sipnet/utils.h
new file mode 100644
index 00000000..54f3429c
--- /dev/null
+++ b/tests/sipnet/utils.h
@@ -0,0 +1,37 @@
+#ifndef UTILS_H
+#define UTILS_H
+
+#include <math.h>
+#include <stdio.h>
+
+extern inline int copyFile(char* src, char* dest) {
+  FILE *source = fopen(src, "rb"); // Binary mode for compatibility
+  if (source == NULL) {
+    printf("Error opening source file %s", src);
+    return 1;
+  }
+
+  FILE *destination = fopen(dest, "wb");
+  if (destination == NULL) {
+    printf("Error opening destination file %s", dest);
+    fclose(source);
+    return 1;
+  }
+
+  char buffer[4096]; // 4KB buffer
+  size_t bytesRead;
+
+  while ((bytesRead = fread(buffer, 1, sizeof(buffer), source)) > 0) {
+    fwrite(buffer, 1, bytesRead, destination);
+  }
+
+  fclose(source);
+  fclose(destination);
+  return 0;
+}
+
+extern inline int compareDoubles(double a, double b) {
+  return fabs(a-b) < 1e-6;
+}
+
+#endif //UTILS_H
diff --git a/tests/test.template b/tests/test.template
new file mode 100644
index 00000000..4ec9aec2
--- /dev/null
+++ b/tests/test.template
@@ -0,0 +1,37 @@
+// Unit test template file
+//
+// Copy and modify as needed (and remove these comments!)
+
+#include <stdio.h>
+#include <stdlib.h>
+
+int init() {
+  // Initialization steps for the test; eg copying files, allocating mem, etc
+
+  // Return a status code, 0 = success
+}
+
+int run() {
+  // Run the tests, of course
+
+  // Return a status code, 0 = success
+}
+
+void cleanup() {
+  // Perform any cleanup as needed
+}
+
+int main() {
+  int status;
+  status = init();
+  if (status) {
+    printf("Test initialization failed with status %d\b", status);
+  }
+
+  status = run();
+  if (status) {
+    printf("Test run failed with status %d\b", status);
+  }
+
+  cleanup();
+}
\ No newline at end of file

From 7418af62aba94ab6407f4fa58ddae40be795b5f7 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 19 Dec 2024 12:15:25 -0500
Subject: [PATCH 02/34] Sets event handler off by default

---
 modelStructures.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modelStructures.h b/modelStructures.h
index 5a591bb0..e0c8014d 100644
--- a/modelStructures.h
+++ b/modelStructures.h
@@ -10,7 +10,7 @@
 // Begin definitions for choosing different model structures
 // See also sipnet.c for other options (that should be moved here if/when testing is added)
 
-#define EVENT_HANDLER 1
+#define EVENT_HANDLER 0
 // Read in and process agronomic events. Expects a file named <FILENAME>.event to exist.
 
 

From 1e9b7e62246327115f7328914ff5caaeeb890e83 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 19 Dec 2024 12:19:48 -0500
Subject: [PATCH 03/34] Sets event handler off by default for realz, I hope

---
 frontend.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend.c b/frontend.c
index c79633fe..96333f76 100755
--- a/frontend.c
+++ b/frontend.c
@@ -156,9 +156,9 @@ int main(int argc, char *argv[]) {
   strcat(climFile, ".clim");
   numLocs = initModel(&spatialParams, &steps, paramFile, climFile);
 
-#ifdef EVENT_HANDLER
 	strcpy(eventFile, fileName);
 	strcat(eventFile, ".event");
+#if EVENT_HANDLER
 	initEvents(eventFile, numLocs);
 #endif
 

From 86175afc7cfe5d3f48ba2b1fdbde3a343ae5edb3 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 19 Dec 2024 12:32:49 -0500
Subject: [PATCH 04/34] Adds ci steps to run unit tests

---
 .github/workflows/ci.yml          | 24 ++++++++++++++++++++++++
 Makefile                          |  8 +++++++-
 tests/sipnet/test_events/Makefile |  9 +++++++--
 3 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0c2880ac..1da462f8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -9,6 +9,30 @@ on:
 
 jobs:
 
+  # Build and run unit tests
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        OS:
+          - macos-latest
+          - ubuntu-latest
+          - ubuntu-20.04
+
+    runs-on: ${{ matrix.OS }}
+
+    steps:
+      # checkout source code
+      - uses: actions/checkout@v2
+
+      # compile tests
+      - name: compile tests
+        run: make test
+
+      # run tests
+      - name: run tests
+        run: make testrun
+
   # try to build SIPNET on Ubuntu & MacOS
   build:
     strategy:
diff --git a/Makefile b/Makefile
index 9b2a37c3..6adbfe3b 100755
--- a/Makefile
+++ b/Makefile
@@ -46,6 +46,7 @@ clean:
 #
 # UNIT TESTS
 SIPNET_TEST_DIRS:=$(shell find tests/sipnet -type d -mindepth 1 -maxdepth 1)
+SIPNET_TEST_DIRS_RUN:= $(addsuffix .run, $(SIPNET_TEST_DIRS))
 SIPNET_TEST_DIRS_CLEAN:= $(addsuffix .clean, $(SIPNET_TEST_DIRS))
 SIPNET_LIB=libsipnet.a
 
@@ -67,13 +68,18 @@ $(SIPNET_TEST_DIRS): pretest $(SIPNET_LIB)
 posttest: $(SIPNET_TEST_DIRS)
 	mv modelStructures.orig.h modelStructures.h
 
+testrun: $(SIPNET_TEST_DIRS_RUN)
+
+$(SIPNET_TEST_DIRS_RUN):
+	$(MAKE) -C $(basename $@) run
+
 testclean: $(SIPNET_TEST_DIRS_CLEAN)
 	rm -f $(SIPNET_LIB)
 
 $(SIPNET_TEST_DIRS_CLEAN):
 	$(MAKE) -C $(basename $@) clean
 
-.PHONY: all test $(SIPNET_TEST_DIRS) pretest posttest $(SIPNET_LIB) testclean $(SIPNET_TEST_DIRS_CLEAN)
+.PHONY: all test $(SIPNET_TEST_DIRS) pretest posttest $(SIPNET_LIB) testrun $(SIPNET_TEST_DIRS_RUN) testclean $(SIPNET_TEST_DIRS_CLEAN)
 
 
 #This target automatically builds dependencies.
diff --git a/tests/sipnet/test_events/Makefile b/tests/sipnet/test_events/Makefile
index 261cb8a6..dbf1d024 100644
--- a/tests/sipnet/test_events/Makefile
+++ b/tests/sipnet/test_events/Makefile
@@ -3,12 +3,12 @@ LD=gcc
 CFLAGS=-Wall -g
 LDFLAGS=-L../../..
 LDLIBS=-lsipnet
-#INCLUDE=../../../.
 
 # List test files in this directory here
 TEST_CFILES=testEventInfra.c
 TEST_OBJ_FILES=$(TEST_CFILES:%.c=%.o)
 TEST_EXECUTABLES:=$(basename $(TEST_CFILES))
+RUN_EXECUTABLES:= $(addsuffix .run, $(TEST_EXECUTABLES))
 
 all: tests
 
@@ -21,7 +21,12 @@ $(TEST_OBJ_FILES): ../utils.h ../../../libsipnet.a
 $(TEST_OBJ_FILES): %.o: %.c
 	$(CC) $(CFLAGS) -c -o $@ $<
 
+run: $(RUN_EXECUTABLES)
+
+$(RUN_EXECUTABLES):
+	./$(basename $@)
+
 clean:
 	rm -f $(TEST_OBJ_FILES) $(TEST_EXECUTABLES) events.in
 
-.PHONY: all tests clean
+.PHONY: all tests clean run $(RUN_EXECUTABLES)

From f9690e3a6be3b6b4633cc4c774cdae4248df5649 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 19 Dec 2024 13:57:25 -0500
Subject: [PATCH 05/34] Adds math lib to linux build linking

---
 tests/sipnet/test_events/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/sipnet/test_events/Makefile b/tests/sipnet/test_events/Makefile
index dbf1d024..0da516a2 100644
--- a/tests/sipnet/test_events/Makefile
+++ b/tests/sipnet/test_events/Makefile
@@ -2,7 +2,7 @@ CC=gcc
 LD=gcc
 CFLAGS=-Wall -g
 LDFLAGS=-L../../..
-LDLIBS=-lsipnet
+LDLIBS=-lsipnet -lm
 
 # List test files in this directory here
 TEST_CFILES=testEventInfra.c

From a10988b28bfeca9c2f764f9c0aac9906d5198695 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 19 Dec 2024 17:04:06 -0500
Subject: [PATCH 06/34] Adds negative tests and an exit function handler

---
 events.c                                      |  7 +-
 tests/sipnet/exitHandler.c                    | 47 ++++++++++
 tests/sipnet/test_events/Makefile             |  6 +-
 .../test_events/infra_events_date_ooo.in      |  2 +
 .../test_events/infra_events_loc_ooo.in       |  3 +
 .../sipnet/test_events/infra_events_multi.in  | 15 ++++
 ...infra_events.in => infra_events_simple.in} |  2 +-
 .../test_events/infra_events_unknown.in       |  1 +
 tests/sipnet/test_events/testEventInfra.c     | 86 ++++++++++++++++++-
 tests/sipnet/test_events/testEventInfraNeg.c  | 68 +++++++++++++++
 10 files changed, 226 insertions(+), 11 deletions(-)
 create mode 100644 tests/sipnet/exitHandler.c
 create mode 100644 tests/sipnet/test_events/infra_events_date_ooo.in
 create mode 100644 tests/sipnet/test_events/infra_events_loc_ooo.in
 create mode 100644 tests/sipnet/test_events/infra_events_multi.in
 rename tests/sipnet/test_events/{infra_events.in => infra_events_simple.in} (90%)
 create mode 100644 tests/sipnet/test_events/infra_events_unknown.in
 create mode 100644 tests/sipnet/test_events/testEventInfraNeg.c

diff --git a/events.c b/events.c
index b8c48cc7..a1526736 100644
--- a/events.c
+++ b/events.c
@@ -135,7 +135,6 @@ EventNode** readEventData(char *eventFile, int numLocs) {
     printf("Error: unknown event type %s\n", eventTypeStr);
     exit(1);
   }
-  printf("Found event type %d (%s)\n", eventType, eventTypeStr);
 
   next = createEventNode(loc, year, day, eventType, eventParamsStr);
   events[loc] = next;
@@ -143,8 +142,8 @@ EventNode** readEventData(char *eventFile, int numLocs) {
   currYear = year;
   currDay = day;
 
-  printf("Found events:\n");
-  printEvent(next);
+  //printf("Found events:\n");
+  //printEvent(next);
 
   while (fgets(line, EVENT_LINE_SIZE, in) != NULL) {
     // We have another event
@@ -172,7 +171,7 @@ EventNode** readEventData(char *eventFile, int numLocs) {
     }
 
     next = createEventNode(loc, year, day, eventType, eventParamsStr);
-    printEvent(next);
+    //printEvent(next);
     if (currLoc == loc) {
       // Same location, add the new event to this location's list
       curr->nextEvent = next;
diff --git a/tests/sipnet/exitHandler.c b/tests/sipnet/exitHandler.c
new file mode 100644
index 00000000..acda85e6
--- /dev/null
+++ b/tests/sipnet/exitHandler.c
@@ -0,0 +1,47 @@
+#include <setjmp.h>
+#include <unistd.h>
+
+static int expected_code = 1;  // the expected value a tested function passes to exit
+static int should_exit = 1;    // 1 if exit should have been called
+static int really_exit = 0;           // set to 1 to prevent stubbing behavior and actually exit
+
+static jmp_buf jump_env;
+
+static int exit_result = 1;
+#define test_assert(x) (exit_result = exit_result && (x))
+
+// set should_exit=0 when code SHOULDN'T exit(), e.g.:
+//
+// should_exit = 0;
+// if (!(jmp_rval=setjmp(jump_env)))
+// {
+//   call_to_non_exiting_code();
+// }
+// test_assert(jmp_rval==0);
+//
+// set should_exit=1 when exit(0 is expected:
+//
+// should_exit = 1;
+// expected_code = 1; // or whatever the exit code should be
+// if (!(jmp_rval=setjmp(jump_env)))
+// {
+//   call_to_exiting_code();
+// }
+//
+// test_assert(jmp_rval==1);
+
+// stub function
+void exit(int code)
+{
+  if (!really_exit)
+  {
+    printf("Mocking the exit call\n");
+    test_assert(should_exit==1);
+    test_assert(expected_code==code);
+    longjmp(jump_env, 1);
+  }
+  else
+  {
+    _exit(code);
+  }
+}
diff --git a/tests/sipnet/test_events/Makefile b/tests/sipnet/test_events/Makefile
index 0da516a2..d224b95c 100644
--- a/tests/sipnet/test_events/Makefile
+++ b/tests/sipnet/test_events/Makefile
@@ -5,7 +5,9 @@ LDFLAGS=-L../../..
 LDLIBS=-lsipnet -lm
 
 # List test files in this directory here
-TEST_CFILES=testEventInfra.c
+TEST_CFILES=testEventInfra.c testEventInfraNeg.c
+
+# The rest is boilerplate, likely copyable as is to a new test directory
 TEST_OBJ_FILES=$(TEST_CFILES:%.c=%.o)
 TEST_EXECUTABLES:=$(basename $(TEST_CFILES))
 RUN_EXECUTABLES:= $(addsuffix .run, $(TEST_EXECUTABLES))
@@ -17,7 +19,7 @@ tests: $(TEST_EXECUTABLES)
 $(TEST_EXECUTABLES): %: %.o
 	$(CC) $(LDFLAGS) $< $(LDLIBS) -o $@
 
-$(TEST_OBJ_FILES): ../utils.h ../../../libsipnet.a
+$(TEST_OBJ_FILES): ../utils.h ../../../libsipnet.a ../exitHandler.c
 $(TEST_OBJ_FILES): %.o: %.c
 	$(CC) $(CFLAGS) -c -o $@ $<
 
diff --git a/tests/sipnet/test_events/infra_events_date_ooo.in b/tests/sipnet/test_events/infra_events_date_ooo.in
new file mode 100644
index 00000000..a39aa789
--- /dev/null
+++ b/tests/sipnet/test_events/infra_events_date_ooo.in
@@ -0,0 +1,2 @@
+0  2024  60  till   0.1 0.2 0.3
+0  2024  55  plant  15 20 5
diff --git a/tests/sipnet/test_events/infra_events_loc_ooo.in b/tests/sipnet/test_events/infra_events_loc_ooo.in
new file mode 100644
index 00000000..26786210
--- /dev/null
+++ b/tests/sipnet/test_events/infra_events_loc_ooo.in
@@ -0,0 +1,3 @@
+0  2024  60  till   0.1 0.2 0.3
+1  2024  65  plant  15 20 5
+0  2024  70  irrig  5 1
diff --git a/tests/sipnet/test_events/infra_events_multi.in b/tests/sipnet/test_events/infra_events_multi.in
new file mode 100644
index 00000000..9013e358
--- /dev/null
+++ b/tests/sipnet/test_events/infra_events_multi.in
@@ -0,0 +1,15 @@
+0  2024  60  till   0.1 0.2 0.3
+0  2024  65  plant  15 20 5
+0  2024  70  irrig  5 1
+0  2024  75  fert   15 10 5
+0  2024  250 harv   0.1 0.2 0.3 0.4
+1  2024  59  till   0.2 0.3 0.1
+1  2024  64  plant  15 20 5
+1  2024  69  irrig  5 0
+1  2024  74  fert   5 15 10
+1  2024  249 harv   0.2 0.3 0.4 0.1
+2  2024  58  till   0.3 0.1 0.2
+2  2024  63  plant  15 20 5
+2  2024  68  irrig  6 1
+2  2024  73  fert   5 10 15
+2  2024  248 harv   0.3 0.4 0.1 0.2
diff --git a/tests/sipnet/test_events/infra_events.in b/tests/sipnet/test_events/infra_events_simple.in
similarity index 90%
rename from tests/sipnet/test_events/infra_events.in
rename to tests/sipnet/test_events/infra_events_simple.in
index ef0169f8..506cf141 100644
--- a/tests/sipnet/test_events/infra_events.in
+++ b/tests/sipnet/test_events/infra_events_simple.in
@@ -1,4 +1,4 @@
-0  2022  40 irrig   5   0           # 5cm canopy irrigation on day 40
+0  2022  40  irrig  5   0           # 5cm canopy irrigation on day 40
 0  2022  40  fert   15 5 10         # fertilized with 15 g/m2 organic N, 5 g/m2 organic C, and 10 g/m2 mineral N on day 40
 0  2022  45  till   0.1 0.2 0.3     # tilled on day 45, 10% of surface litter transferred to soil pool, soil organic matter pool decomposition rate increases by 20% and soil litter pool decomposition rate increases by 30%
 0  2022  46  plant  10 10 1         # planting - planting occurs on day 40, after 10 days the plants have emerged with a size of 10 g C/m2 and 1 g N / m2
diff --git a/tests/sipnet/test_events/infra_events_unknown.in b/tests/sipnet/test_events/infra_events_unknown.in
new file mode 100644
index 00000000..2e7b0971
--- /dev/null
+++ b/tests/sipnet/test_events/infra_events_unknown.in
@@ -0,0 +1 @@
+0  2022  40  blarg  5   0
diff --git a/tests/sipnet/test_events/testEventInfra.c b/tests/sipnet/test_events/testEventInfra.c
index 8081baed..6538b491 100644
--- a/tests/sipnet/test_events/testEventInfra.c
+++ b/tests/sipnet/test_events/testEventInfra.c
@@ -1,7 +1,6 @@
 
 #include <stdio.h>
 #include <stdlib.h>
-#include <unistd.h>
 
 #include "../utils.h"
 #include "../../../events.c"
@@ -82,7 +81,7 @@ int checkTillageParams(
 }
 
 int init() {
-  // char * filename = "infra_events.in";
+  // char * filename = "infra_events_simple.in";
   // if (access(filename, F_OK) == -1) {
   //   return 1;
   // }
@@ -91,9 +90,10 @@ int init() {
   return 0;
 }
 
-int run() {
+int runTestSimple() {
+  // Simple test with one loc, one event per type
   int numLocs = 1;
-  EventNode** output = readEventData("infra_events.in", numLocs);
+  EventNode** output = readEventData("infra_events_simple.in", numLocs);
 
   if (!output) {
     return 1;
@@ -117,6 +117,84 @@ int run() {
   status |= checkEvent(event, 0, 2022, 250, HARVEST);
   status |= checkHarvestParams((HarvestParams*)event->eventParams, 0.4, 0.1, 0.2, 0.3);
 
+  return status;
+}
+
+int runTestMulti() {
+  // More complex test; multiple locations
+  int numLocs = 1;
+  EventNode** output = readEventData("infra_events_multi.in", numLocs);
+
+  if (!output) {
+    return 1;
+  }
+
+  // check output is correct
+  int status = 0;
+  int loc = 0;
+  EventNode *event = output[loc];
+  status |= checkEvent(event, loc, 2024, 60, TILLAGE);
+  status |= checkTillageParams((TillageParams*)event->eventParams, 0.1, 0.2, 0.3);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 65, PLANTING);
+  status |= checkPlantingParams((PlantingParams*)event->eventParams, 15, 20, 5);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 70, IRRIGATION);
+  status |= checkIrrigationParams((IrrigationParams*)event->eventParams, 5, 1);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 75, FERTILIZATION);
+  status |= checkFertilizationParams((FertilizationParams*)event->eventParams, 15, 10,5);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 250, HARVEST);
+  status |= checkHarvestParams((HarvestParams*)event->eventParams, 0.1, 0.2, 0.3, 0.4);
+
+  loc++;
+  event = output[loc];
+  status |= checkEvent(event, loc, 2024, 59, TILLAGE);
+  status |= checkTillageParams((TillageParams*)event->eventParams, 0.2, 0.3, 0.1);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 64, PLANTING);
+  status |= checkPlantingParams((PlantingParams*)event->eventParams, 15, 20, 5);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 69, IRRIGATION);
+  status |= checkIrrigationParams((IrrigationParams*)event->eventParams, 5, 0);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 74, FERTILIZATION);
+  status |= checkFertilizationParams((FertilizationParams*)event->eventParams, 5, 15,10);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 249, HARVEST);
+  status |= checkHarvestParams((HarvestParams*)event->eventParams, 0.2, 0.3, 0.4, 0.1);
+
+  loc++;
+  event = output[loc];
+  status |= checkEvent(event, loc, 2024, 58, TILLAGE);
+  status |= checkTillageParams((TillageParams*)event->eventParams, 0.3, 0.1, 0.2);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 63, PLANTING);
+  status |= checkPlantingParams((PlantingParams*)event->eventParams, 15, 20, 5);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 68, IRRIGATION);
+  status |= checkIrrigationParams((IrrigationParams*)event->eventParams, 6, 1);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 73, FERTILIZATION);
+  status |= checkFertilizationParams((FertilizationParams*)event->eventParams, 5, 10,15);
+  event = event->nextEvent;
+  status |= checkEvent(event, loc, 2024, 248, HARVEST);
+  status |= checkHarvestParams((HarvestParams*)event->eventParams, 0.3, 0.4, 0.1, 0.2);
+
+  return status;
+}
+
+int run() {
+
+  int status;
+
+  status = runTestSimple();
+  if (status) {
+    return 1;
+  }
+
+  status = runTestMulti();
   if (status) {
     return 1;
   }
diff --git a/tests/sipnet/test_events/testEventInfraNeg.c b/tests/sipnet/test_events/testEventInfraNeg.c
new file mode 100644
index 00000000..eb7d06a1
--- /dev/null
+++ b/tests/sipnet/test_events/testEventInfraNeg.c
@@ -0,0 +1,68 @@
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "../../../events.c"
+#include "../exitHandler.c"
+
+int run() {
+  int status = 0;
+
+  // exit() handling params
+  int jmp_rval;
+  expected_code = 1;
+  exit_result = 1;
+
+  // Step 0: make sure that we don't have a false positive on good data
+  should_exit = 0;
+  jmp_rval = setjmp(jump_env);
+  if (!jmp_rval) {
+    readEventData("infra_events_simple.in", 1);
+  }
+  test_assert(jmp_rval==0);
+  status |= !exit_result;
+
+  // First test
+  should_exit = 1;
+  jmp_rval = setjmp(jump_env);
+  if (!jmp_rval) {
+    readEventData("infra_events_unknown.in", 1);
+  }
+  printf("status %d exit_res %d jmp_rval %d\n", status, exit_result, jmp_rval);
+  test_assert(jmp_rval==1);
+  status |= !exit_result;
+
+  // Second test
+  jmp_rval = setjmp(jump_env);
+  if (!jmp_rval) {
+    readEventData("infra_events_loc_ooo.in", 1);
+  }
+  test_assert(jmp_rval==1);
+  status |= !exit_result;
+
+  // Third test
+  jmp_rval = setjmp(jump_env);
+  if (!jmp_rval) {
+    readEventData("infra_events_date_ooo.in", 1);
+  }
+  test_assert(jmp_rval==1);
+  status |= !exit_result;
+
+  // Allow a real exit, not that this is really needed
+  really_exit = 1;
+
+  return status;
+}
+
+int main() {
+  int status;
+
+  printf("Starting testEventInfraNeg:run()\n");
+  status = run();
+  if (status) {
+    printf("Test run failed with status %d\n", status);
+    exit(status);
+  }
+
+  printf("testEventInfra PASSED\n");
+}
\ No newline at end of file

From 682e25c7f3c65843e99aa5d95bb94986d068a636 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 19 Dec 2024 23:52:56 -0700
Subject: [PATCH 07/34] Update CONTRIBUTING.md

---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index f15c9c4d..7806eda2 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -3,7 +3,7 @@
 
 ## Compiling
 
-SIPNET uses `make` build the model and documentation. There are also miscellaneous targets for running analysis workflows:
+SIPNET uses `make` to build the model and documentation. There are also miscellaneous targets for running analysis workflows:
 
 ```sh
 # build SIPNET executable

From 8108736968eb9ca6ae7edcca702711103058b305 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 19 Dec 2024 23:53:03 -0700
Subject: [PATCH 08/34] Update Makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index caeeaea1..e47457e2 100755
--- a/Makefile
+++ b/Makefile
@@ -68,7 +68,7 @@ help:
 	@echo "  all         - Builds all components."
 	@echo "  document    - Generate documentation."
 	@echo "  sipnet      - Builds the 'sipnet' executable."
-	@echo "  clean       - Removes compiled files and executables."
+	@echo "  clean       - Removes compiled files, executables, and documentation."
 	@echo "  depend      - Automatically generates dependency information for source files."
 	@echo "  === additional tools ==="
 	@echo "  estimate    - Builds 'estimate' executable to estimate parameters using MCMC."

From 8e89d94c029209ca67bd7eb4eb2f26889f31957c Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 19 Dec 2024 23:54:30 -0700
Subject: [PATCH 09/34] Update .gitignore

Remove duplicate lines
---
 .gitignore | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/.gitignore b/.gitignore
index 5c662284..757dc24a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,20 +14,6 @@ docs/latex
 .Rproj.user
 .Rhistory
 
-
-# build artifacts and executables
-*.o
-estimate
-sipnet
-subsetData
-transpose
-.doxygen.stamp
-
-# documentation
-docs/html/
-docs/latex/
-
-
 # System-specific files
 .DS_Store
 .Rproj.user

From e9ed8b0f51ad5d90cc9c3ca666f1510072573196 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Tue, 7 Jan 2025 16:21:27 -0500
Subject: [PATCH 10/34] Code cleanup 1 for PR

---
 events.c                   |  4 ----
 events.h                   |  5 +++--
 frontend.c                 |  2 +-
 modelStructures.h          |  3 ++-
 sipnet.c                   | 23 ++++++++++++-----------
 sipnet.h                   |  9 ++++++++-
 tests/sipnet/exitHandler.c | 14 +++++++-------
 tests/test.template        |  2 +-
 8 files changed, 34 insertions(+), 28 deletions(-)

diff --git a/events.c b/events.c
index a1526736..b4f30279 100644
--- a/events.c
+++ b/events.c
@@ -142,9 +142,6 @@ EventNode** readEventData(char *eventFile, int numLocs) {
   currYear = year;
   currDay = day;
 
-  //printf("Found events:\n");
-  //printEvent(next);
-
   while (fgets(line, EVENT_LINE_SIZE, in) != NULL) {
     // We have another event
     curr = next;
@@ -171,7 +168,6 @@ EventNode** readEventData(char *eventFile, int numLocs) {
     }
 
     next = createEventNode(loc, year, day, eventType, eventParamsStr);
-    //printEvent(next);
     if (currLoc == loc) {
       // Same location, add the new event to this location's list
       curr->nextEvent = next;
diff --git a/events.h b/events.h
index de027a64..f96f27a8 100644
--- a/events.h
+++ b/events.h
@@ -55,11 +55,12 @@ struct EventNode {
   EventNode *nextEvent;
 };
 
-/* Read event data from <FILENAME>.event
+/* Read event data from input filename (canonically events.in)
  *
  * Format: returned data is structured as an array of EventNode pointers, indexed by
  * location. Each element of the array is the first event for that location (or null
- * if there are no events). It is assumed that the events are in chrono order.
+ * if there are no events). It is assumed that the events are ordered first by location
+ * and then by year and day.
  */
 EventNode** readEventData(char *eventFile, int numLocs);
 
diff --git a/frontend.c b/frontend.c
index 96333f76..302929c8 100755
--- a/frontend.c
+++ b/frontend.c
@@ -82,7 +82,7 @@ int main(int argc, char *argv[]) {
   double **standarddevs;
   int dataTypeIndices[MAX_DATA_TYPES];
 
-#ifdef EVENT_HANDLER
+#if EVENT_HANDLER
 	// Extra filename if we are handing events
 	char eventFile[FILE_MAXNAME+24];
 #endif
diff --git a/modelStructures.h b/modelStructures.h
index e0c8014d..207287a6 100644
--- a/modelStructures.h
+++ b/modelStructures.h
@@ -11,7 +11,8 @@
 // See also sipnet.c for other options (that should be moved here if/when testing is added)
 
 #define EVENT_HANDLER 0
-// Read in and process agronomic events. Expects a file named <FILENAME>.event to exist.
+// Read in and process agronomic events. SIPNET expects a file named events.in to exist, though
+// unit tests may use other names.
 
 
 #endif //MODEL_STRUCTURES_H
diff --git a/sipnet.c b/sipnet.c
index ee6f717a..ddcdd0ff 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -489,8 +489,8 @@ static ClimateNode *climate; // current climate
 static Fluxes fluxes;
 static double *outputPtrs[MAX_DATA_TYPES]; // pointers to different possible outputs
 
-#ifdef EVENT_HANDLER
-static EventNode **events; // MJL: event structs
+#if EVENT_HANDLER
+static EventNode **events;
 #endif
 
 /* Read climate file into linked lists,
@@ -1936,8 +1936,8 @@ void calculateFluxes() {
   	double potGrossPsn; // potential photosynthesis, without water stress
   	double dWater;
   	double lai; // m^2 leaf/m^2 ground (calculated from plantLeafC)
-  	//double litterBreakdown; /* total litter breakdown (i.e. litterToSoil + rLitter)
-		//					 (g C/m^2 ground/day) */
+    //double litterBreakdown; /* total litter breakdown (i.e. litterToSoil + rLitter)
+    //(g C/m^2 ground/day) */
   	double folResp, woodResp; // maintenance respiration terms, g C * m^-2 ground area * day^-1
   	double litterWater, soilWater; /* amount of water in litter and soil (cm)
 				    taken from either environment or climate drivers, depending on value of MODEL_WATER */
@@ -2485,7 +2485,7 @@ void setupModel(SpatialParams *spatialParams, int loc) {
 
 // Setup events at given location
 void setupEvents(int currLoc) {
-
+  // Implementation TBD
 }
 
 
@@ -2514,8 +2514,8 @@ void runModelOutput(FILE *out, OutputItems *outputItems, int printHeader, Spatia
 
   for (currLoc = firstLoc; currLoc <= lastLoc; currLoc++) {
     setupModel(spatialParams, currLoc);
-#ifdef EVENT_HANDLER
-  	setupEvents(currLoc);
+#if EVENT_HANDLER
+    setupEvents(currLoc);
 #endif
     if ((loc == -1) && (outputItems != NULL))  {  // print the current location at the start of the line
       sprintf(label, "%d", currLoc);
@@ -2525,15 +2525,16 @@ void runModelOutput(FILE *out, OutputItems *outputItems, int printHeader, Spatia
     while (climate != NULL) {
       updateState();
       if (out != NULL) {
-	      outputState(out, currLoc, climate->year, climate->day, climate->time);
+        outputState(out, currLoc, climate->year, climate->day, climate->time);
       }
       if (outputItems != NULL) {
-	      writeOutputItemValues(outputItems);
+        writeOutputItemValues(outputItems);
       }
       climate = climate->nextClim;
     }
-    if (outputItems != NULL)
+    if (outputItems != NULL) {
       terminateOutputItemLines(outputItems);
+    }
   }
 }
 
@@ -2794,7 +2795,7 @@ int initModel(SpatialParams **spatialParams, int **steps, char *paramFile, char
  * Populates static event structs
  */
 void initEvents(char *eventFile, int numLocs) {
-#ifdef EVENT_HANDLER
+#if EVENT_HANDLER
 	events = readEventData(eventFile, numLocs);
 #endif
 }
diff --git a/sipnet.h b/sipnet.h
index 6c8278b8..5ce33499 100755
--- a/sipnet.h
+++ b/sipnet.h
@@ -52,7 +52,14 @@ char **getDataTypeNames();
 int initModel(SpatialParams **spatialParams, int **steps, char *paramFile, char *climFile);
 
 /*
- * TBD
+ * Read in event data for all the model runs
+ *
+ * Read in event data from a file with the following specification:
+ * - one line per event
+ * - all events are ordered first by location (ascending) and then by year/day (ascending)
+ *
+ * @param eventFile Name of file containing event data
+ * @param numLocs Number of locations in the event file.
  */
 void initEvents(char *eventFile, int numLocs);
 
diff --git a/tests/sipnet/exitHandler.c b/tests/sipnet/exitHandler.c
index acda85e6..8fc56a77 100644
--- a/tests/sipnet/exitHandler.c
+++ b/tests/sipnet/exitHandler.c
@@ -1,9 +1,11 @@
 #include <setjmp.h>
 #include <unistd.h>
 
+//
+
 static int expected_code = 1;  // the expected value a tested function passes to exit
-static int should_exit = 1;    // 1 if exit should have been called
-static int really_exit = 0;           // set to 1 to prevent stubbing behavior and actually exit
+static int should_exit = 1;    // set in test code; 1 if exit should have been called
+static int really_exit = 0;    // set to 1 to prevent stubbing behavior and actually exit
 
 static jmp_buf jump_env;
 
@@ -19,7 +21,7 @@ static int exit_result = 1;
 // }
 // test_assert(jmp_rval==0);
 //
-// set should_exit=1 when exit(0 is expected:
+// set should_exit=1 when exit is expected:
 //
 // should_exit = 1;
 // expected_code = 1; // or whatever the exit code should be
@@ -40,8 +42,6 @@ void exit(int code)
     test_assert(expected_code==code);
     longjmp(jump_env, 1);
   }
-  else
-  {
-    _exit(code);
-  }
+
+  _exit(code);
 }
diff --git a/tests/test.template b/tests/test.template
index 4ec9aec2..53aac2d1 100644
--- a/tests/test.template
+++ b/tests/test.template
@@ -34,4 +34,4 @@ int main() {
   }
 
   cleanup();
-}
\ No newline at end of file
+}

From 0d8d16c3624ecc258f4f68b9d5cd4fedb2df77fb Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 9 Jan 2025 11:44:47 -0500
Subject: [PATCH 11/34] Adds fix for frontend.c and test Makefile template

---
 frontend.c              |  2 +-
 tests/Makefile.template | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+), 1 deletion(-)
 create mode 100644 tests/Makefile.template

diff --git a/frontend.c b/frontend.c
index 302929c8..9fc48e7c 100755
--- a/frontend.c
+++ b/frontend.c
@@ -156,9 +156,9 @@ int main(int argc, char *argv[]) {
   strcat(climFile, ".clim");
   numLocs = initModel(&spatialParams, &steps, paramFile, climFile);
 
+#if EVENT_HANDLER
 	strcpy(eventFile, fileName);
 	strcat(eventFile, ".event");
-#if EVENT_HANDLER
 	initEvents(eventFile, numLocs);
 #endif
 
diff --git a/tests/Makefile.template b/tests/Makefile.template
new file mode 100644
index 00000000..e26a64d5
--- /dev/null
+++ b/tests/Makefile.template
@@ -0,0 +1,34 @@
+CC=gcc
+LD=gcc
+CFLAGS=-Wall -g
+LDFLAGS=-L../../..
+LDLIBS=-lsipnet -lm
+
+# List test files in this directory here
+TEST_CFILES=<c files in this directory containing tests> <<== CHANGE THIS
+
+# The rest is boilerplate, likely copyable as is to a new test directory
+TEST_OBJ_FILES=$(TEST_CFILES:%.c=%.o)
+TEST_EXECUTABLES:=$(basename $(TEST_CFILES))
+RUN_EXECUTABLES:= $(addsuffix .run, $(TEST_EXECUTABLES))
+
+all: tests
+
+tests: $(TEST_EXECUTABLES)
+
+$(TEST_EXECUTABLES): %: %.o
+	$(CC) $(LDFLAGS) $< $(LDLIBS) -o $@
+
+$(TEST_OBJ_FILES): ../utils.h ../../../libsipnet.a ../exitHandler.c
+$(TEST_OBJ_FILES): %.o: %.c
+	$(CC) $(CFLAGS) -c -o $@ $<
+
+run: $(RUN_EXECUTABLES)
+
+$(RUN_EXECUTABLES):
+	./$(basename $@)
+
+clean:
+	rm -f $(TEST_OBJ_FILES) $(TEST_EXECUTABLES) events.in
+
+.PHONY: all tests clean run $(RUN_EXECUTABLES)

From 72e92de6d08ca0e1641809b4e2ed62995b82db69 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 14:39:24 -0700
Subject: [PATCH 12/34] Add Doxygen install to CI.yml

---
 .github/workflows/ci.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0c2880ac..8798b2ba 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -25,7 +25,16 @@ jobs:
     # checkout source code
     - uses: actions/checkout@v2
 
-    # compile sipnet
+    # install doxygen
+    - name: Install Doxygen
+      run:  |
+        if [[ "$RUNNER_OS" == "Linux" ]]; then
+          sudo apt-get install doxygen -y
+        elif [[ "$RUNNER_OS" == "macOS" ]]; then
+          brew install doxygen
+        fi
+        
+    # compile SIPNET
     - name: compile sipnet
       run: make
 

From 573a76c7397b704c3b5cd606ef756903633c480f Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 14:42:04 -0700
Subject: [PATCH 13/34] fix brew install doxygen warning

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8798b2ba..20106891 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
         if [[ "$RUNNER_OS" == "Linux" ]]; then
           sudo apt-get install doxygen -y
         elif [[ "$RUNNER_OS" == "macOS" ]]; then
-          brew install doxygen
+          brew install --formula doxygen
         fi
         
     # compile SIPNET

From 94730e57d0c0971a8a82078a782a8da897540c42 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 15:13:24 -0700
Subject: [PATCH 14/34] replace spaces with tab

---
 Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 77a9925f..fa78dd38 100755
--- a/Makefile
+++ b/Makefile
@@ -92,8 +92,8 @@ $(SIPNET_TEST_DIRS_CLEAN):
 	$(MAKE) -C $(basename $@) clean
 
 .PHONY: all clean document estimate sipnet transpose subsetData doxygen
-        test $(SIPNET_TEST_DIRS) pretest posttest $(SIPNET_LIB) testrun 
-        $(SIPNET_TEST_DIRS_RUN) testclean $(SIPNET_TEST_DIRS_CLEAN)
+	test $(SIPNET_TEST_DIRS) pretest posttest $(SIPNET_LIB) testrun 
+	$(SIPNET_TEST_DIRS_RUN) testclean $(SIPNET_TEST_DIRS_CLEAN)
 
 help:
 	@echo "Available targets:"

From f379cb9a95f5790a465aa15bac7d7ce26170c190 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 15:36:05 -0700
Subject: [PATCH 15/34] Update ci.yml

change order of build and unit tests
update names and error messages for clarity
---
 .github/workflows/ci.yml | 104 +++++++++++++++++++--------------------
 1 file changed, 51 insertions(+), 53 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 131f49e6..25efadfc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -4,85 +4,83 @@ on:
   push:
     branches:
       - master
-
   pull_request:
 
 jobs:
-
-  # Build and run unit tests
-  test:
+  # Build and Integration Test
+  build_integration_test:
     strategy:
       fail-fast: false
       matrix:
-        OS:
+        OS: 
           - macos-latest
           - ubuntu-latest
           - ubuntu-20.04
-
     runs-on: ${{ matrix.OS }}
 
     steps:
       # checkout source code
       - uses: actions/checkout@v2
 
-      # compile tests
-      - name: compile tests
-        run: make test
+      # install doxygen
+      - name: Install Doxygen
+        run:  |
+          if [[ "$RUNNER_OS" == "Linux" ]]; then
+            sudo apt-get install doxygen -y
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            brew install --formula doxygen
+          fi
+        
+      # compile SIPNET
+      - name: compile sipnet
+        run: make
 
-      # run tests
-      - name: run tests
-        run: make testrun
+      # remove existing test output file
+      - name: Remove Niwout Output File
+        run: rm Sites/Niwot/niwot.out
+
+      # run single sipnet run
+      - name: Run SIPNET on Sites/Niwot/niwot
+        run: ./sipnet
+
+      # check for correct output of Niwot run
+      - name: Check if niwot.out is generated
+        if: ${{ !files.exists('Sites/Niwot/niwot.out') }}
+        run: |
+          echo "::error title={No Output}::Test run for Niwot site failed to produce output"
+          exit 1
+      # Check if niwot.out has changed 
+      - name: Check whether niwot.out has changed 
+        shell: bash
+        run: |
+          if git diff --exit-code Sites/Niwot/niwot.out; then
+            echo "Success: Niwot.out created and has not changed"
+          else
+            echo "::error title={Output Changed}::The test file niwot.out has changed. This is expected to fail with some changes to SIPNET. When this happens, assess correctness and then update the reference niwot.out."
+            exit 1
+          fi
 
-  # try to build SIPNET on Ubuntu & MacOS
-  build:
+  # Run Unit Tests
+  test:
+    needs: build_integration_test
     strategy:
       fail-fast: false
       matrix:
-        OS:
+        OS: 
           - macos-latest
           - ubuntu-latest
           - ubuntu-20.04
-
     runs-on: ${{ matrix.OS }}
 
     steps:
-    # checkout source code
-    - uses: actions/checkout@v2
-
-    # install doxygen
-    - name: Install Doxygen
-      run:  |
-        if [[ "$RUNNER_OS" == "Linux" ]]; then
-          sudo apt-get install doxygen -y
-        elif [[ "$RUNNER_OS" == "macOS" ]]; then
-          brew install --formula doxygen
-        fi
-        
-    # compile SIPNET
-    - name: compile sipnet
-      run: make
+      # checkout source code
+      - uses: actions/checkout@v2
 
-    # remove existing test output file
-    - name: Remove Niwout Output File
-      run: rm Sites/Niwot/niwot.out
+      # compile unit tests
+      - name: compile tests
+        run: make test
 
-    # run single sipnet run
-    - name: sipnet on Sites/Niwot/niwot
-      run: ./sipnet
+      # run tests
+      - name: Run Unit Tests
+        run: make testrun
 
-    # check output of test
-    - name: fail if no niwot output exists
-      if: ${{ hashFiles('Sites/Niwot/niwot.out') == '' }}
-      run: |
-        echo "::error title={No Output}::Test run for Niwot site failed to produce output"
-        exit 1
-    # check whether niwot.out has changed
-    - name: Check whether niwot.out has changed 
-      shell: bash
-      run: |
-         if git diff --exit-code Sites/Niwot/niwot.out; then
-           echo "Success: Niwot.out created and has not changed"
-           else
-             echo "::error title={Output Changed}::The test file niwot.out has changed"
-           exit 1
-           fi

From 1b5123a5b5c295abde74ac82b82535b72acd72bf Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 15:46:31 -0700
Subject: [PATCH 16/34] Update ci.yml

---
 .github/workflows/ci.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 25efadfc..de333916 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,10 +45,13 @@ jobs:
 
       # check for correct output of Niwot run
       - name: Check if niwot.out is generated
-        if: ${{ !files.exists('Sites/Niwot/niwot.out') }}
+        shell: bash
         run: |
-          echo "::error title={No Output}::Test run for Niwot site failed to produce output"
-          exit 1
+          if: ${{ !files.exists('Sites/Niwot/niwot.out') }}
+            echo "::error title={No Output}::Test run for Niwot site failed to produce output"
+            exit 1
+          fi
+        
       # Check if niwot.out has changed 
       - name: Check whether niwot.out has changed 
         shell: bash

From ad10b3dcc360db03dc616fe93d7a92a1734b2074 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 15:48:24 -0700
Subject: [PATCH 17/34] Update ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index de333916..8238260d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -47,7 +47,7 @@ jobs:
       - name: Check if niwot.out is generated
         shell: bash
         run: |
-          if: ${{ !files.exists('Sites/Niwot/niwot.out') }}
+          if [ ! -f Sites/Niwot/niwot.out ]; then
             echo "::error title={No Output}::Test run for Niwot site failed to produce output"
             exit 1
           fi

From 6fc965f6af5b8d5c7121fa24d26636f94149a89a Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 15:49:13 -0700
Subject: [PATCH 18/34] Update ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8238260d..4708e41c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -8,7 +8,7 @@ on:
 
 jobs:
   # Build and Integration Test
-  build_integration_test:
+  build:
     strategy:
       fail-fast: false
       matrix:

From 93adfd1328e7c924351f07fb4a137549e5bba85a Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Thu, 9 Jan 2025 15:49:55 -0700
Subject: [PATCH 19/34] Update ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4708e41c..fe0c452e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -65,7 +65,7 @@ jobs:
 
   # Run Unit Tests
   test:
-    needs: build_integration_test
+    needs: build
     strategy:
       fail-fast: false
       matrix:

From e5774f3784f0b5bd1c2d078de2f7f7f438caf92a Mon Sep 17 00:00:00 2001
From: Mike Longfritz <Mike.Longfritz@gmail.com>
Date: Fri, 10 Jan 2025 12:22:28 -0500
Subject: [PATCH 20/34] Updates events.c to add doc comments at top

Co-authored-by: David LeBauer <dlebauer@gmail.com>
---
 events.c | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/events.c b/events.c
index b4f30279..15259afb 100644
--- a/events.c
+++ b/events.c
@@ -1,5 +1,27 @@
 //
 // events.c
+/**
+ * @file events.c
+ * @brief Handles reading, parsing, and storing agronomic events for SIPNET simulations.
+ *
+ * The `events.in` file specifies agronomic events with the following columns:
+ * | col | parameter   | description                                | units            |
+ * |-----|-------------|--------------------------------------------|------------------|
+ * | 1   | loc         | spatial location index                     |                  |
+ * | 2   | year        | year of start of this timestep             |                  |
+ * | 3   | day         | day of start of this timestep              | Day of year      |
+ * | 4   | event_type  | type of event                              | (e.g., "irrig")  |
+ * | 5...n| event_param| parameters specific to the event type      | (varies)         |
+ *
+ *
+ * Event types include:
+ * - "irrig": Parameters = [amount added (cm/d), type (0=canopy, 1=soil, 2=flood)]
+ * - "fert": Parameters = [Org-N (g/m²), Org-C (g/ha), Min-N (g/m²), Min-N2 (g/m²)]
+ * - "till": Parameters = [SOM decomposition modifier, litter decomposition modifier]
+ * - "plant": Parameters = [emergence lag (days), C (g/m²), N (g/m²)]]
+ * - "harv": Parameters = [fraction aboveground removed, fraction belowground removed, ...]
+ * See test examples in `tests/sipnet/test_events/`.
+ */
 //
 
 #include "events.h"

From 394c4ab8d3ce5d76e2bc782e9964482cc06085e5 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Fri, 10 Jan 2025 12:32:43 -0500
Subject: [PATCH 21/34] Adds docs for building and running unit tests to
 CONTRIBUTING.md

---
 CONTRIBUTING.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7806eda2..2d1d609d 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -15,3 +15,14 @@ make clean
 # list all make commands
 make help
 ```
+## Testing
+
+SIPNET also uses `make` to build and run its unit tests. This can be done with the following commands:
+```shell
+# Compile tests
+make test
+# Run tests
+make testrun
+# Clean after tests are run
+make testclean
+```

From e94682a6fbca211a7d664d746f0c75fc439389f6 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Wed, 15 Jan 2025 13:24:34 -0500
Subject: [PATCH 22/34] Moves two switches to modelStructures.h, adds test
 update script

---
 modelStructures.h                          |  9 ++-
 sipnet.c                                   |  4 +-
 tests/sipnet/test_events/modelStructures.h | 15 ++++-
 tests/update_model_structures.sh           | 70 ++++++++++++++++++++++
 4 files changed, 93 insertions(+), 5 deletions(-)
 create mode 100755 tests/update_model_structures.sh

diff --git a/modelStructures.h b/modelStructures.h
index 207287a6..73783143 100644
--- a/modelStructures.h
+++ b/modelStructures.h
@@ -1,8 +1,10 @@
 //
-// This file is inteneded to hold settings for different model structure options,
+// This file is intended to hold settings for different model structure options,
 // implemented as compile-time flags. The options are here (with nothing else) to
 // improve testability.
 //
+// If this file is changed, consider running tests/update_model_structures.sh to update
+// the corresponding unit test versions of this file.
 
 #ifndef MODEL_STRUCTURES_H
 #define MODEL_STRUCTURES_H
@@ -14,5 +16,10 @@
 // Read in and process agronomic events. SIPNET expects a file named events.in to exist, though
 // unit tests may use other names.
 
+// have extra litter pool, in addition to soil c pool
+#define LITTER_POOL 0
+
+// Whether we model root dynamics
+#define ROOTS 1
 
 #endif //MODEL_STRUCTURES_H
diff --git a/sipnet.c b/sipnet.c
index ddcdd0ff..7e0e056e 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -96,7 +96,7 @@
 #define SOIL_PHENOL 0 && !GDD
 // use soil temp. to determine leaf growth? (note: mutually exclusive with GDD)
 
-#define LITTER_POOL 0
+// LITTER_POOL moved to modelStructures.h
 // have extra litter pool, in addition to soil c pool
 
 #define SOIL_MULTIPOOL 0 && !LITTER_POOL
@@ -120,7 +120,7 @@
 #define STOICHIOMETRY 0 && MICROBES
 // do we utilize stoichometric considerations for the microbial pool?
 
-#define ROOTS 1
+// ROOTS moved to modelStructures.h
 // do we model root dynamics?
 
 
diff --git a/tests/sipnet/test_events/modelStructures.h b/tests/sipnet/test_events/modelStructures.h
index 5a591bb0..d0307d36 100644
--- a/tests/sipnet/test_events/modelStructures.h
+++ b/tests/sipnet/test_events/modelStructures.h
@@ -1,8 +1,13 @@
 //
-// This file is inteneded to hold settings for different model structure options,
+// DO NOT ADD CUSTOM CODE TO THIS FILE (other than #define overrides for unit tests)
+// IT MAY BE OVERWRITTEN BY update_model_structures.sh
+//
+// This file is intended to hold settings for different model structure options,
 // implemented as compile-time flags. The options are here (with nothing else) to
 // improve testability.
 //
+// If this file is changed, consider running tests/update_model_structures.sh to update
+// the corresponding unit test versions of this file.
 
 #ifndef MODEL_STRUCTURES_H
 #define MODEL_STRUCTURES_H
@@ -11,7 +16,13 @@
 // See also sipnet.c for other options (that should be moved here if/when testing is added)
 
 #define EVENT_HANDLER 1
-// Read in and process agronomic events. Expects a file named <FILENAME>.event to exist.
+// Read in and process agronomic events. SIPNET expects a file named events.in to exist, though
+// unit tests may use other names.
+
+// have extra litter pool, in addition to soil c pool
+#define LITTER_POOL 0
 
+// Whether we model root dynamics
+#define ROOTS 1
 
 #endif //MODEL_STRUCTURES_H
diff --git a/tests/update_model_structures.sh b/tests/update_model_structures.sh
new file mode 100755
index 00000000..0656b64c
--- /dev/null
+++ b/tests/update_model_structures.sh
@@ -0,0 +1,70 @@
+#!/bin/bash
+# Run this script from the root SIPNET directory with the command:
+# > tests/update_model_structures.sh
+
+# Name of the file containing #define compiler switches
+STRUCTURES_FILE="modelStructures.h"
+
+# Get the path to the current directory's STRUCTURES_FILE - that is,
+# the production version
+PROD_MODEL_STRUCTURES="./${STRUCTURES_FILE}"
+
+# Check if the current directory has the base model_structures.h
+if [[ ! -f $PROD_MODEL_STRUCTURES ]]; then
+    echo "Error: ${STRUCTURES_FILE} not found in the current directory."
+    exit 1
+fi
+
+# Define the awk script to update #define values; this will be called on each test
+# version of STRUCTURES_FILE
+read -r -d '' AWK_SCRIPT << 'EOF'
+BEGIN {
+    FS = "[ \t]+";  # Set field separator to handle spaces or tabs
+    define_regex = "^#define";
+    skip_regex = "MODEL_STRUCTURES_H";
+}
+
+# Process the test structures file and store the #define values in an associative array
+FNR == NR {
+    if ($1 ~ define_regex && $2 !~ skip_regex) {
+        name = $2;   # The second field is the name of the #define
+        value = $3;  # The third field is the value of the #define
+        defines[name] = value;
+    }
+    next;
+}
+
+# Update the new file with the old #define values
+{
+    if ($1 ~ define_regex && $2 !~ skip_regex) {
+        name = $2;
+        if (name in defines) {
+            printf "#define %s %s\n", name, defines[name];
+            next;
+        }
+    }
+    # Print the line as-is if no overwrite is needed
+    print $0;
+}
+EOF
+
+# Find and process all target files in subdirectories
+find . -type f -name "$STRUCTURES_FILE" -mindepth 2 | while read -r file; do
+    echo "Processing: $file"
+
+    # Create a backup of the original file
+    cp "$file" "${file}.bak"
+
+    # Add a warning at the top, then update defines
+    {
+        echo "//"
+        echo "// DO NOT ADD CUSTOM CODE TO THIS FILE (other than #define overrides for unit tests)"
+        echo "// IT MAY BE OVERWRITTEN BY update_model_structures.sh"
+        cat "$PROD_MODEL_STRUCTURES"
+    } | awk "$AWK_SCRIPT" "$file" - > "${file}.tmp"
+
+    # Overwrite the target file with the updated content
+    mv "${file}.tmp" "$file"
+
+    echo "Updated: $file"
+done

From dadb7e99ce7dfcedd05bd44bcd2d8e96a5dce85c Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Wed, 15 Jan 2025 13:37:40 -0500
Subject: [PATCH 23/34] Updates CONTRIBUTING.md with test update script command

---
 CONTRIBUTING.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 2d1d609d..fa5d2e1a 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -26,3 +26,9 @@ make testrun
 # Clean after tests are run
 make testclean
 ```
+
+If changes are made to the `modelStructure.h` file and unit tests are failing, try running the update script as shown below. Consider running this script even if unit tests _are not_ failing.
+```shell
+# Run this command from the root directory to update unit test versions of modelStructures.h
+tests/update_model_structures.sh
+```

From 84fdae8de9f045d04b741d12b200721e5562adc2 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Fri, 31 Jan 2025 11:31:03 -0500
Subject: [PATCH 24/34] Adds event fetch and stubbed processing in sipnet.c

---
 sipnet.c | 92 +++++++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 77 insertions(+), 15 deletions(-)

diff --git a/sipnet.c b/sipnet.c
index ddcdd0ff..59eaebac 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -489,8 +489,12 @@ static ClimateNode *climate; // current climate
 static Fluxes fluxes;
 static double *outputPtrs[MAX_DATA_TYPES]; // pointers to different possible outputs
 
+// MJL REMOVE THIS BEFORE CHECKIN
+#define EVENT_HANDLER 1
+
 #if EVENT_HANDLER
 static EventNode **events;
+static EventNode *locEvent; // current location event list
 #endif
 
 /* Read climate file into linked lists,
@@ -2275,33 +2279,76 @@ void updateTrackers(double oldSoilWater) {
   // mean of soil wetness at start of time step at soil wetness at end of time step - assume linear
 }
 
+// This should be in events.h/c, but with all the global state defined in this file,
+// let's leave it here for now. Maybe someday we will factor that out.
+//
+// Process events for current location/year/day
+void processEvents() {
+#if EVENT_HANDLER
+	// If locEvent starts off NULL, this function will just fall through, as it should.
+	const int year = climate->year;
+	const int day = climate->day;
+
+	// The events file has been tested on read, so we know this event list should be in chrono
+	// order. However, we need to check to make sure the current event is not in the past, as
+	// that would indicate an event that did not have a corresponding climate file record.
+	while (locEvent != NULL && locEvent->year <= year && locEvent->day <= day) {
+		if (locEvent->year < year || locEvent->day < day) {
+			printf("Agronomic event found for loc: %d year: %d day: %d that does not have a corresponding record in the climate file\n", locEvent->year, locEvent->year, locEvent->day);
+			exit(1);
+		}
+		switch (locEvent->type) {
+			// Implementation TBD, as we enable the various event types
+			case IRRIGATION:
+				// TBD
+					printf("Irrigation events not yet implemented\n");
+					break;
+			case PLANTING:
+				// TBD
+					printf("Planting events not yet implemented\n");
+					break;
+			case HARVEST:
+				// TBD
+					printf("Harvest events not yet implemented\n");
+					break;
+			case TILLAGE:
+				// TBD
+					printf("Tillage events not yet implemented\n");
+					break;
+			case FERTILIZATION:
+				// TBD
+					printf("Fertilization events not yet implemented\n");
+					break;
+			default:
+				printf("Unknown event type (%d) in processEvents()\n", locEvent->type);
+				exit(1);
+		}
 
-// !!! main runner function !!!
+		locEvent = locEvent->nextEvent;
+	}
+#endif
+}
 
 
+// !!! main runner function !!!
 
 // calculate all fluxes and update state for this time step
 // we calculate all fluxes before updating state in case flux calculations depend on the old state
 void updateState() {
 	double npp; // net primary productivity, g C * m^-2 ground area * day^-1
-  	double oldSoilWater; // how much soil water was there before we updated it? Used in trackers
-    int err;
-  	oldSoilWater = envi.soilWater;
-
-  	calculateFluxes();
-
-  	// update the stocks, with fluxes adjusted for length of time step:
-  	envi.plantWoodC += (fluxes.photosynthesis + fluxes.woodCreation - fluxes.leafCreation - fluxes.woodLitter
-  				- fluxes.rVeg-fluxes.coarseRootCreation-fluxes.fineRootCreation)* climate->length;
-  	envi.plantLeafC += (fluxes.leafCreation - fluxes.leafLitter) * climate->length;
-
+  double oldSoilWater; // how much soil water was there before we updated it? Used in trackers
+  int err;
+  oldSoilWater = envi.soilWater;
 
+  calculateFluxes();
 
+  // update the stocks, with fluxes adjusted for length of time step:
+  envi.plantWoodC += (fluxes.photosynthesis + fluxes.woodCreation - fluxes.leafCreation - fluxes.woodLitter
+  			- fluxes.rVeg-fluxes.coarseRootCreation-fluxes.fineRootCreation)* climate->length;
+  envi.plantLeafC += (fluxes.leafCreation - fluxes.leafLitter) * climate->length;
 
 	soilDegradation();		// This updates all the soil functions
 
-
-
 	#if MODEL_WATER // water pool updating happens here:
 
 		#if LITTER_WATER // (2 soil water layers; litter water will only be on if complex water is also on)
@@ -2323,6 +2370,13 @@ void updateState() {
 
   ensureNonNegativeStocks();
 
+#if EVENT_HANDLER
+	// Process events for this location/year/day, AFTER updates are made to fluxes and state
+	// variables above. Events are (currently, Jan 25) handled as instantaneous deltas to
+	// relevant state (envi and fluxes fields),
+	processEvents();
+#endif
+
 
   npp = fluxes.photosynthesis - fluxes.rVeg-fluxes.rCoarseRoot-fluxes.rFineRoot;
 
@@ -2485,7 +2539,9 @@ void setupModel(SpatialParams *spatialParams, int loc) {
 
 // Setup events at given location
 void setupEvents(int currLoc) {
-  // Implementation TBD
+#if EVENT_HANDLER
+	locEvent = events[currLoc];
+#endif
 }
 
 
@@ -2554,6 +2610,12 @@ void runModelNoOut(double **outArray, int numDataTypes, int dataTypeIndices[], S
 
   setupModel(spatialParams, loc);
 
+#if EVENT_HANDLER
+	// Implementation TBD
+	printf("Event handler not yet implemented for running model with no output\n");
+	exit(1);
+#endif
+
   // loop through every step of the model:
   while (climate != NULL) {
     updateState();

From 8b03f77bfdc5b0f2e57dc30e95369a7b4723af9c Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Fri, 31 Jan 2025 11:34:49 -0500
Subject: [PATCH 25/34] Removes EVENT_HANDLER override used in dev

---
 sipnet.c | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/sipnet.c b/sipnet.c
index 27559343..83790e1e 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -489,9 +489,6 @@ static ClimateNode *climate; // current climate
 static Fluxes fluxes;
 static double *outputPtrs[MAX_DATA_TYPES]; // pointers to different possible outputs
 
-// MJL REMOVE THIS BEFORE CHECKIN
-#define EVENT_HANDLER 1
-
 #if EVENT_HANDLER
 static EventNode **events;
 static EventNode *locEvent; // current location event list

From a0a57a6fb481f51b2fa2faa0832be3ce668ae5c0 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Fri, 31 Jan 2025 12:42:43 -0500
Subject: [PATCH 26/34] Fixes (some) formatting issues

---
 sipnet.c | 124 +++++++++++++++++++++++++++----------------------------
 1 file changed, 61 insertions(+), 63 deletions(-)

diff --git a/sipnet.c b/sipnet.c
index 83790e1e..0e2433c7 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -2282,47 +2282,47 @@ void updateTrackers(double oldSoilWater) {
 // Process events for current location/year/day
 void processEvents() {
 #if EVENT_HANDLER
-	// If locEvent starts off NULL, this function will just fall through, as it should.
-	const int year = climate->year;
-	const int day = climate->day;
-
-	// The events file has been tested on read, so we know this event list should be in chrono
-	// order. However, we need to check to make sure the current event is not in the past, as
-	// that would indicate an event that did not have a corresponding climate file record.
-	while (locEvent != NULL && locEvent->year <= year && locEvent->day <= day) {
-		if (locEvent->year < year || locEvent->day < day) {
-			printf("Agronomic event found for loc: %d year: %d day: %d that does not have a corresponding record in the climate file\n", locEvent->year, locEvent->year, locEvent->day);
-			exit(1);
-		}
-		switch (locEvent->type) {
-			// Implementation TBD, as we enable the various event types
-			case IRRIGATION:
-				// TBD
-					printf("Irrigation events not yet implemented\n");
-					break;
-			case PLANTING:
-				// TBD
-					printf("Planting events not yet implemented\n");
-					break;
-			case HARVEST:
-				// TBD
-					printf("Harvest events not yet implemented\n");
-					break;
-			case TILLAGE:
-				// TBD
-					printf("Tillage events not yet implemented\n");
-					break;
-			case FERTILIZATION:
-				// TBD
-					printf("Fertilization events not yet implemented\n");
-					break;
-			default:
-				printf("Unknown event type (%d) in processEvents()\n", locEvent->type);
-				exit(1);
-		}
+  // If locEvent starts off NULL, this function will just fall through, as it should.
+  const int year = climate->year;
+  const int day = climate->day;
+
+  // The events file has been tested on read, so we know this event list should be in chrono
+  // order. However, we need to check to make sure the current event is not in the past, as
+  // that would indicate an event that did not have a corresponding climate file record.
+  while (locEvent != NULL && locEvent->year <= year && locEvent->day <= day) {
+    if (locEvent->year < year || locEvent->day < day) {
+      printf("Agronomic event found for loc: %d year: %d day: %d that does not have a corresponding record in the climate file\n", locEvent->year, locEvent->year, locEvent->day);
+      exit(1);
+    }
+    switch (locEvent->type) {
+      // Implementation TBD, as we enable the various event types
+      case IRRIGATION:
+        // TBD
+          printf("Irrigation events not yet implemented\n");
+          break;
+      case PLANTING:
+        // TBD
+          printf("Planting events not yet implemented\n");
+          break;
+      case HARVEST:
+        // TBD
+          printf("Harvest events not yet implemented\n");
+          break;
+      case TILLAGE:
+        // TBD
+          printf("Tillage events not yet implemented\n");
+          break;
+      case FERTILIZATION:
+        // TBD
+          printf("Fertilization events not yet implemented\n");
+          break;
+      default:
+        printf("Unknown event type (%d) in processEvents()\n", locEvent->type);
+        exit(1);
+    }
 
-		locEvent = locEvent->nextEvent;
-	}
+    locEvent = locEvent->nextEvent;
+  }
 #endif
 }
 
@@ -2332,7 +2332,7 @@ void processEvents() {
 // calculate all fluxes and update state for this time step
 // we calculate all fluxes before updating state in case flux calculations depend on the old state
 void updateState() {
-	double npp; // net primary productivity, g C * m^-2 ground area * day^-1
+  double npp; // net primary productivity, g C * m^-2 ground area * day^-1
   double oldSoilWater; // how much soil water was there before we updated it? Used in trackers
   int err;
   oldSoilWater = envi.soilWater;
@@ -2341,40 +2341,39 @@ void updateState() {
 
   // update the stocks, with fluxes adjusted for length of time step:
   envi.plantWoodC += (fluxes.photosynthesis + fluxes.woodCreation - fluxes.leafCreation - fluxes.woodLitter
-  			- fluxes.rVeg-fluxes.coarseRootCreation-fluxes.fineRootCreation)* climate->length;
+        - fluxes.rVeg-fluxes.coarseRootCreation-fluxes.fineRootCreation)* climate->length;
   envi.plantLeafC += (fluxes.leafCreation - fluxes.leafLitter) * climate->length;
 
-	soilDegradation();		// This updates all the soil functions
+  soilDegradation();    // This updates all the soil functions
 
-	#if MODEL_WATER // water pool updating happens here:
+  #if MODEL_WATER // water pool updating happens here:
 
-		#if LITTER_WATER // (2 soil water layers; litter water will only be on if complex water is also on)
-  			envi.litterWater += (fluxes.rain + fluxes.snowMelt - fluxes.immedEvap - fluxes.fastFlow
-		    	   - fluxes.evaporation - fluxes.topDrainage) * climate->length;
-  			envi.soilWater += (fluxes.topDrainage - fluxes.transpiration - fluxes.bottomDrainage)
-    		* climate->length;
+    #if LITTER_WATER // (2 soil water layers; litter water will only be on if complex water is also on)
+        envi.litterWater += (fluxes.rain + fluxes.snowMelt - fluxes.immedEvap - fluxes.fastFlow
+             - fluxes.evaporation - fluxes.topDrainage) * climate->length;
+        envi.soilWater += (fluxes.topDrainage - fluxes.transpiration - fluxes.bottomDrainage)
+        * climate->length;
 
-		#else // LITTER_WATER = 0 (only one soil water layer)
-  		// note: some of these fluxes will always be 0 if complex water is off
-  			envi.soilWater += (fluxes.rain + fluxes.snowMelt - fluxes.immedEvap - fluxes.fastFlow
-		     	- fluxes.evaporation - fluxes.transpiration - fluxes.bottomDrainage) * climate->length;
-		#endif // LITTER_WATER
+    #else // LITTER_WATER = 0 (only one soil water layer)
+      // note: some of these fluxes will always be 0 if complex water is off
+        envi.soilWater += (fluxes.rain + fluxes.snowMelt - fluxes.immedEvap - fluxes.fastFlow
+          - fluxes.evaporation - fluxes.transpiration - fluxes.bottomDrainage) * climate->length;
+    #endif // LITTER_WATER
 
-  		// if COMPLEX_WATER = 0 or SNOW = 0, some or all of these fluxes will always be 0
-  		envi.snow += (fluxes.snowFall - fluxes.snowMelt - fluxes.sublimation) * climate->length;
+      // if COMPLEX_WATER = 0 or SNOW = 0, some or all of these fluxes will always be 0
+      envi.snow += (fluxes.snowFall - fluxes.snowMelt - fluxes.sublimation) * climate->length;
 
-	#endif // MODEL_WATER
+  #endif // MODEL_WATER
 
   ensureNonNegativeStocks();
 
 #if EVENT_HANDLER
-	// Process events for this location/year/day, AFTER updates are made to fluxes and state
-	// variables above. Events are (currently, Jan 25) handled as instantaneous deltas to
-	// relevant state (envi and fluxes fields),
-	processEvents();
+  // Process events for this location/year/day, AFTER updates are made to fluxes and state
+  // variables above. Events are (currently, Jan 25) handled as instantaneous deltas to
+  // relevant state (envi and fluxes fields),
+  processEvents();
 #endif
 
-
   npp = fluxes.photosynthesis - fluxes.rVeg-fluxes.rCoarseRoot-fluxes.rFineRoot;
 
   err = addValueToMeanTracker(meanNPP, npp, climate->length); // update running mean of NPP
@@ -2394,7 +2393,6 @@ void updateState() {
   }
 
   updateTrackers(oldSoilWater);
-
 }
 
 

From 7b7bab15b59b6b8e482b5becc0fbe7f5fa95a849 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@gmail.com>
Date: Fri, 31 Jan 2025 17:36:45 -0700
Subject: [PATCH 27/34] clarify comment

---
 sipnet.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sipnet.c b/sipnet.c
index 0e2433c7..369e0288 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -2369,7 +2369,7 @@ void updateState() {
 
 #if EVENT_HANDLER
   // Process events for this location/year/day, AFTER updates are made to fluxes and state
-  // variables above. Events are (currently, Jan 25) handled as instantaneous deltas to
+  // variables above. Events are (currently, Jan 25, 2025) handled as instantaneous deltas to
   // relevant state (envi and fluxes fields),
   processEvents();
 #endif

From 88aa5a95f4b6845cb1da9423e5175ff3d5141497 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Mon, 3 Feb 2025 14:22:18 -0500
Subject: [PATCH 28/34] Fixes some indentation issues

---
 sipnet.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sipnet.c b/sipnet.c
index 369e0288..0cef7af3 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -2535,7 +2535,7 @@ void setupModel(SpatialParams *spatialParams, int loc) {
 // Setup events at given location
 void setupEvents(int currLoc) {
 #if EVENT_HANDLER
-	locEvent = events[currLoc];
+  locEvent = events[currLoc];
 #endif
 }
 
@@ -2606,9 +2606,9 @@ void runModelNoOut(double **outArray, int numDataTypes, int dataTypeIndices[], S
   setupModel(spatialParams, loc);
 
 #if EVENT_HANDLER
-	// Implementation TBD
-	printf("Event handler not yet implemented for running model with no output\n");
-	exit(1);
+  // Implementation TBD
+  printf("Event handler not yet implemented for running model with no output\n");
+  exit(1);
 #endif
 
   // loop through every step of the model:

From 4207e80038d4042f736d4f88adcb60b22fb5193b Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Mon, 3 Feb 2025 15:05:15 -0500
Subject: [PATCH 29/34] Adds exit code defs and minor fixes from PR feedback

---
 exitCodes.h | 12 ++++++++++++
 sipnet.c    |  7 ++++---
 2 files changed, 16 insertions(+), 3 deletions(-)
 create mode 100644 exitCodes.h

diff --git a/exitCodes.h b/exitCodes.h
new file mode 100644
index 00000000..58b6982a
--- /dev/null
+++ b/exitCodes.h
@@ -0,0 +1,12 @@
+#ifndef EXITCODES_H
+#define EXITCODES_H
+
+// Exit codes for SIPNET; most of the current uses of exit(1) should
+// get better codes, which will appear here
+typedef enum {
+  EXIT_SUCCESS = 0,
+  EXIT_FAILURE = 1,
+  EXIT_UNKNOWN_EVENT = 2
+} ExitCode;
+
+#endif
diff --git a/sipnet.c b/sipnet.c
index 0cef7af3..5e7d7a7d 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -20,6 +20,7 @@
 #include "outputItems.h"
 #include "modelStructures.h"
 #include "events.h"
+#include "exitCodes.h"
 
 // begin definitions for choosing different model structures
 // (1 -> true, 0 -> false)
@@ -2280,8 +2281,8 @@ void updateTrackers(double oldSoilWater) {
 // let's leave it here for now. Maybe someday we will factor that out.
 //
 // Process events for current location/year/day
-void processEvents() {
 #if EVENT_HANDLER
+void processEvents() {
   // If locEvent starts off NULL, this function will just fall through, as it should.
   const int year = climate->year;
   const int day = climate->day;
@@ -2318,13 +2319,13 @@ void processEvents() {
           break;
       default:
         printf("Unknown event type (%d) in processEvents()\n", locEvent->type);
-        exit(1);
+        exit(EXIT_UNKNOWN_EVENT);
     }
 
     locEvent = locEvent->nextEvent;
   }
-#endif
 }
+#endif
 
 
 // !!! main runner function !!!

From f22f0cdb5f3319324f00d48eded430dd01f53d47 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Tue, 4 Feb 2025 13:31:24 -0500
Subject: [PATCH 30/34] Fixes exit code success and failure naming

---
 exitCodes.h | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/exitCodes.h b/exitCodes.h
index 58b6982a..d7a760ab 100644
--- a/exitCodes.h
+++ b/exitCodes.h
@@ -4,9 +4,9 @@
 // Exit codes for SIPNET; most of the current uses of exit(1) should
 // get better codes, which will appear here
 typedef enum {
-  EXIT_SUCCESS = 0,
-  EXIT_FAILURE = 1,
-  EXIT_UNKNOWN_EVENT = 2
-} ExitCode;
+  EXIT_CODE_SUCCESS = 0,
+  EXIT_CODE_FAILURE = 1,
+  EXIT_CODE_UNKNOWN_EVENT = 2
+} exit_code_t;
 
 #endif

From 55a77e4a99e4160e84978a94dcd3726b9a9b97c0 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Tue, 4 Feb 2025 13:50:05 -0500
Subject: [PATCH 31/34] Updates exit code defs

---
 exitCodes.h | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/exitCodes.h b/exitCodes.h
index d7a760ab..5d2308c1 100644
--- a/exitCodes.h
+++ b/exitCodes.h
@@ -5,8 +5,14 @@
 // get better codes, which will appear here
 typedef enum {
   EXIT_CODE_SUCCESS = 0,
-  EXIT_CODE_FAILURE = 1,
-  EXIT_CODE_UNKNOWN_EVENT = 2
+  EXIT_CODE_FAILURE = 1, // generic failure
+  // code 2 typically has a special meaning, see below
+  EXIT_CODE_UNKNOWN_EVENT = 3
 } exit_code_t;
 
+// Note for future: these codes typically have other meanings and should not be
+// used here (except for 0 and 1, for which our meaning is the special meaning)
+// 0-2, 126-165, and 255
+// See, e.g., https://tldp.org/LDP/abs/html/exitcodes.html
+
 #endif

From 364615629d85bc24cb6981f2cbf69c601f5e2b82 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 6 Feb 2025 11:57:56 -0500
Subject: [PATCH 32/34] Minor updates for PR feedback

---
 exitCodes.h | 15 +++++++++------
 sipnet.c    |  4 ++--
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/exitCodes.h b/exitCodes.h
index 5d2308c1..63ec780f 100644
--- a/exitCodes.h
+++ b/exitCodes.h
@@ -2,7 +2,15 @@
 #define EXITCODES_H
 
 // Exit codes for SIPNET; most of the current uses of exit(1) should
-// get better codes, which will appear here
+// get better codes, which will appear here.
+//
+// Note for future: some codes typically have other meanings and should not be
+// used here (except for 0 and 1, for which our meaning is the usual meaning).
+// Some somewhat-standard codes in use:
+// - 0-2, 126-165, and 255; see, e.g., https://tldp.org/LDP/abs/html/exitcodes.html
+// - 64-78, see https://man7.org/linux/man-pages/man3/sysexits.h.3head.html
+//
+// The upshot here is that we should be a little sparing in our list of error codes.
 typedef enum {
   EXIT_CODE_SUCCESS = 0,
   EXIT_CODE_FAILURE = 1, // generic failure
@@ -10,9 +18,4 @@ typedef enum {
   EXIT_CODE_UNKNOWN_EVENT = 3
 } exit_code_t;
 
-// Note for future: these codes typically have other meanings and should not be
-// used here (except for 0 and 1, for which our meaning is the special meaning)
-// 0-2, 126-165, and 255
-// See, e.g., https://tldp.org/LDP/abs/html/exitcodes.html
-
 #endif
diff --git a/sipnet.c b/sipnet.c
index 5e7d7a7d..169160b6 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -2534,11 +2534,11 @@ void setupModel(SpatialParams *spatialParams, int loc) {
 
 
 // Setup events at given location
-void setupEvents(int currLoc) {
 #if EVENT_HANDLER
+void setupEvents(int currLoc) {
   locEvent = events[currLoc];
-#endif
 }
+#endif
 
 
 /* Do one run of the model using parameter values in spatialParams

From e1d0aa610b9488f8e93466264ae5bc310da52497 Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 6 Feb 2025 12:05:18 -0500
Subject: [PATCH 33/34] Fixes comment typo

---
 exitCodes.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/exitCodes.h b/exitCodes.h
index 63ec780f..25eb79d8 100644
--- a/exitCodes.h
+++ b/exitCodes.h
@@ -14,7 +14,7 @@
 typedef enum {
   EXIT_CODE_SUCCESS = 0,
   EXIT_CODE_FAILURE = 1, // generic failure
-  // code 2 typically has a special meaning, see below
+  // code 2 typically has a special meaning, see above
   EXIT_CODE_UNKNOWN_EVENT = 3
 } exit_code_t;
 

From 20cf9b117b0ed5617dd3a3a2827357d28f3ea5ab Mon Sep 17 00:00:00 2001
From: Alomir <mike.longfritz@gmail.com>
Date: Thu, 6 Feb 2025 12:15:24 -0500
Subject: [PATCH 34/34] Fixes exit code typo in processEvents

---
 sipnet.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sipnet.c b/sipnet.c
index 169160b6..0c517acb 100644
--- a/sipnet.c
+++ b/sipnet.c
@@ -2319,7 +2319,7 @@ void processEvents() {
           break;
       default:
         printf("Unknown event type (%d) in processEvents()\n", locEvent->type);
-        exit(EXIT_UNKNOWN_EVENT);
+        exit(EXIT_CODE_UNKNOWN_EVENT);
     }
 
     locEvent = locEvent->nextEvent;