Merge pull request #83 from Burke-Lauenroth-Lab/feature_AddDocumentat…

…ionAndTesting

- cleaner code
- defined swprintf to be used both by rSOILWAT and SOILWAT2-standalone code
- improved makefile
- eliminated (almost all) compiler warnings
- improved handling of unit tests (i.e., don't include any more source files in the unit test files as we did initially)

.travis.yml

@@ -3,7 +3,6 @@ compiler:
   - clang
   - gcc
 script:
-  - make compilel
-  - make gtest
-  - ./sw_test
+  - make bin
+  - make test test_run
   - make cleaner

Doxyfile

@@ -713,7 +713,7 @@ LAYOUT_FILE            =
 # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
 # search path. See also \cite for info how to create references.
 
-CITE_BIB_FILES         =
+CITE_BIB_FILES         = SOILWAT2.bib
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages

SOILWAT2.bib

@@ -0,0 +1,9 @@
+
+@Article{Cheng1978,
+  author = "R. Cheng",
+  title = "Generating Beta Variates with Nonintegral Shape Parameters",
+  journal = "Communications of the ACM",
+  volume = 21,
+  year = 1978,
+  pages = {317--322},
+  }

SW_Control.c

@@ -43,15 +43,18 @@
 /* --------------------------------------------------- */
 extern SW_MODEL SW_Model;
 extern SW_VEGESTAB SW_VegEstab;
+extern SW_SITE SW_Site;
+extern SW_VEGPROD SW_VegProd;
 #ifdef RSOILWAT
 	extern Bool useFiles;
 	extern SEXP InputData;
 	void SW_FLW_construct(void);
 #endif
+
+
 /* =================================================== */
 /*                Module-Level Declarations            */
 /* --------------------------------------------------- */
-static void _read_inputs(void);
 static void _begin_year(void);
 static void _begin_day(void);
 static void _end_day(void);
@@ -69,7 +72,7 @@ void SW_CTL_main(void) {
 
 	for (*cur_yr = SW_Model.startyr; *cur_yr <= SW_Model.endyr; (*cur_yr)++) {
 		SW_CTL_run_current_year();
-	}
+	}
 
 #ifndef RSOILWAT
 	SW_OUT_close_files();
@@ -90,9 +93,6 @@ void SW_CTL_init_model(const char *firstfile) {
 	SW_OUT_construct();
 	SW_SWC_construct();
 	SW_FLW_construct();
-
-	_read_inputs();
-
 }
 
 void SW_CTL_run_current_year(void) {
@@ -154,44 +154,78 @@ static void _collect_values(void) {
 
 }
 
-static void _read_inputs(void) {
+void SW_CTL_read_inputs_from_disk(void) {
+  int debug = 0;
+
+  if (debug) swprintf("'SW_CTL_read_inputs_from_disk': Read input from disk:");
+  SW_F_read(NULL);
+  if (debug) swprintf(" 'files'");
+
+  SW_MDL_read();
+  if (debug) swprintf(" > 'model'");
+
+  SW_WTH_read();
+  if (debug) swprintf(" > 'weather'");
+
+  SW_VPD_read();
+  if (debug) swprintf(" > 'veg'");
+
+  SW_SIT_read();
+  if (debug) swprintf(" > 'site'");
+
+  SW_VES_read();
+  if (debug) swprintf(" > 'establishment'");
+
+  SW_OUT_read();
+  if (debug) swprintf(" > 'ouput'");
+
+  SW_SWC_read();
+  if (debug) swprintf(" > 'swc'");
+  if (debug) swprintf(" completed.\n");
+}
+
+
+void SW_CTL_obtain_inputs(void) {
 	/*=======================================================*/
+
 #ifndef RSOILWAT
-	SW_F_read(NULL );
-	SW_MDL_read();
-	SW_WTH_read();
-	SW_VPD_read();
-	SW_SIT_read();
-	SW_VES_read();
-	SW_OUT_read();
-	SW_SWC_read();
+  SW_CTL_read_inputs_from_disk();
+
 #else
-	if (useFiles) { //Read in the data and set it
-		SW_F_read(NULL );
-		SW_MDL_read();
-		SW_WTH_read();
-		SW_VPD_read();
-		SW_SIT_read();
-		SW_VES_read();
-		SW_OUT_read();
-		SW_SWC_read();
+	if (useFiles) {
+    SW_CTL_read_inputs_from_disk();
+
 	} else { //Use R data to set the data
-		onSet_SW_F(GET_SLOT(InputData,install("files")));
-		//Rprintf("swFiles\n");
-		onSet_SW_MDL(GET_SLOT(InputData,install("years")));
-		//Rprintf("swYears\n");
-		onSet_SW_WTH(GET_SLOT(InputData,install("weather")));
-		//Rprintf("swWeather\n");
-		onSet_SW_VPD(GET_SLOT(InputData,install("prod")));
-		//Rprintf("swProd\n");
-		onSet_SW_SIT(GET_SLOT(InputData,install("site")));
-		//Rprintf("swSite\n");
-		onSet_SW_VES(GET_SLOT(InputData,install("estab")));
-		//Rprintf("swEstab\n");
-		onSet_SW_OUT(GET_SLOT(InputData,install("output")));
-		//Rprintf("swOutput\n");
-		onSet_SW_SWC(GET_SLOT(InputData,install("swc")));
-		//Rprintf("swSWC\n");
+	  int debug = 0;
+
+    if (debug) swprintf("'SW_CTL_obtain_inputs': Copy input from 'InputData':");
+
+		onSet_SW_F(GET_SLOT(InputData, install("files")));
+    if (debug) swprintf(" 'files'");
+
+		onSet_SW_MDL(GET_SLOT(InputData, install("years")));
+    if (debug) swprintf(" > 'model'");
+
+		onSet_SW_WTH(GET_SLOT(InputData, install("weather")));
+    if (debug) swprintf(" > 'weather'");
+
+		onSet_SW_VPD(GET_SLOT(InputData, install("prod")));
+    if (debug) swprintf(" > 'veg'");
+
+		onSet_SW_SIT(GET_SLOT(InputData, install("site")));
+    if (debug) swprintf(" > 'site'");
+
+		onSet_SW_VES(GET_SLOT(InputData, install("estab")));
+    if (debug) swprintf(" > 'establishment'");
+
+		onSet_SW_OUT(GET_SLOT(InputData, install("output")));
+    if (debug) swprintf(" > 'ouput'");
+
+
+
+		onSet_SW_SWC(GET_SLOT(InputData, install("swc")));
+    if (debug) swprintf(" > 'swc'");
+    if (debug) swprintf(" completed.\n");
 	}
 #endif
 }

SW_Control.h

@@ -19,6 +19,8 @@
 #define SW_CONTROL_H
 
 void SW_CTL_init_model(const char *firstfile);
+void SW_CTL_obtain_inputs(void);
+void SW_CTL_read_inputs_from_disk(void);
 void SW_CTL_main(void); /* main controlling loop for SOILWAT  */
 void SW_CTL_run_current_year(void);
 

SW_Files.c

@@ -121,7 +121,7 @@ void SW_F_read(const char *s) {
 
 	if (fileno < eEndFile - 1) {
 		CloseFile(&f);
-		LogError(stdout, LOGFATAL, "Too few files (%d) in %s", fileno, MyFileName);
+		LogError(logfp, LOGFATAL, "Too few files (%d) in %s", fileno, MyFileName);
 	}
 
 	CloseFile(&f);