Updates for new SOILWAT2 project structure

- switch to SOILWAT2 branch feature_restructure - paths renamed in submodule SOILWAT2 * *.c -> src/ * *.h -> include * pcg/ -> external/pcg/ * googletest/ -> external/googletest/ - makefile gained ability to create required paths at obj/ -> remove obj/ and fixed nested folder structure -> remove nested `.gitignore` for each subfolder of obj/ -> add obj to global `.gitignore`
DrylandEcology · Dec 22, 2022 · 5505457 · 5505457
1 parent eb67f2c
commit 5505457
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Showing 33 changed files with 175 additions and 172 deletions.
diff --git a/.gitignore b/.gitignore
@@ -16,6 +16,7 @@
 *.exe
 *.o
 *.so
+obj
 
 # Packages #
 ############

diff --git a/.gitmodules b/.gitmodules
@@ -1,5 +1,5 @@
 [submodule "sw_src"]
 	path = sw_src
 	url = https://github.com/DrylandEcology/SOILWAT2.git
-	branch = release/devel_v7.0.0
+	branch = feature_restructure
         ignore = dirty
diff --git a/ST_colonization.c b/ST_colonization.c
@@ -9,8 +9,8 @@
  */
 
 #include "ST_colonization.h"
-#include "sw_src/myMemory.h"
-#include "sw_src/filefuncs.h"
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/filefuncs.h"
 #include "ST_functions.h"
 #include "ST_globals.h"
 

diff --git a/ST_defines.h b/ST_defines.h
@@ -17,7 +17,7 @@
 #ifndef STEPPE_DEF_H
 #define STEPPE_DEF_H
 
-#include "sw_src/generic.h"
+#include "sw_src/include/generic.h"
 
 /* see #include "ST_structs.h" below */
 

diff --git a/ST_grid.c b/ST_grid.c
@@ -33,13 +33,13 @@
 #include <string.h>
 #include <ctype.h>
 #include <dirent.h>
-#include "sw_src/generic.h"
-#include "sw_src/filefuncs.h"
-#include "sw_src/myMemory.h"
-#include "sw_src/rands.h"
-#include "sw_src/SW_SoilWater.h" // externs SW_Soilwat
-#include "sw_src/SW_Weather.h" // externs SW_Weather
-#include "sw_src/SW_Markov.h"// externs `markov_rng`
+#include "sw_src/include/generic.h"
+#include "sw_src/include/filefuncs.h"
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/rands.h"
+#include "sw_src/include/SW_SoilWater.h" // externs SW_Soilwat
+#include "sw_src/include/SW_Weather.h" // externs SW_Weather
+#include "sw_src/include/SW_Markov.h"// externs `markov_rng`
 #include "ST_grid.h"
 #include "ST_steppe.h"
 #include "ST_globals.h" // externs `UseProgressBar`
@@ -51,12 +51,12 @@
 #include "ST_colonization.h"
 #include "ST_seedDispersal.h" // externs `UseSeedDispersal`
 #include "ST_mortality.h" // externs `mortality_rng`, `*_SomeKillage`, `UseCheatgrassWildfire`
-#include "sw_src/SW_Output.h"
-#include "sw_src/SW_Output_outtext.h"
-#include "sw_src/SW_Output_outarray.h"
+#include "sw_src/include/SW_Output.h"
+#include "sw_src/include/SW_Output_outtext.h"
+#include "sw_src/include/SW_Output_outarray.h"
 
-#include "sw_src/SW_Flow.h" // for `SW_FLW_init_run()`
-#include "sw_src/SW_Flow_lib.h" // for `SW_ST_init_run()`
+#include "sw_src/include/SW_Flow.h" // for `SW_FLW_init_run()`
+#include "sw_src/include/SW_Flow_lib.h" // for `SW_ST_init_run()`
 
 
 

diff --git a/ST_grid.h b/ST_grid.h
@@ -17,23 +17,23 @@
 /******** These modules are necessary to compile ST_grid.c ********/
 #include "ST_stats.h"
 #include "ST_defines.h"
-#include "sw_src/pcg/pcg_basic.h"
+#include "sw_src/external/pcg/pcg_basic.h"
 #include "sxw_vars.h"
-#include "sw_src/SW_Site.h"
-#include "sw_src/SW_SoilWater.h"
-#include "sw_src/SW_VegProd.h"
-#include "sw_src/SW_Model.h"
-#include "sw_src/SW_Weather.h"
+#include "sw_src/include/SW_Site.h"
+#include "sw_src/include/SW_SoilWater.h"
+#include "sw_src/include/SW_VegProd.h"
+#include "sw_src/include/SW_Model.h"
+#include "sw_src/include/SW_Weather.h"
 #include "ST_seedDispersal.h"
 
 /*********************** Grid Structures ****************************/
 
-/** 
+/**
  * \brief Soil layer information for a single [cell](\ref CellType)
- * 
+ *
  * This struct requires dynamic memory allocation, so be carefull when
  * instanciating it.
- * 
+ *
  * \ingroup GRID
  */
 typedef struct Soil_st

diff --git a/ST_indivs.c b/ST_indivs.c
@@ -21,8 +21,8 @@
 #include <stdlib.h>
 #include "ST_steppe.h"
 #include "ST_globals.h"
-#include "sw_src/filefuncs.h"
-#include "sw_src/myMemory.h"
+#include "sw_src/include/filefuncs.h"
+#include "sw_src/include/myMemory.h"
 
 
 /******** Modular External Function Declarations ***********/

diff --git a/ST_main.c b/ST_main.c
@@ -23,21 +23,21 @@
 #include <string.h>
 #include <stdlib.h>
 #include "ST_steppe.h"
-#include "sw_src/generic.h" // externs `*logfp`, `errstr`, `EchoInits`, `QuietMode`, `logged`
-#include "sw_src/filefuncs.h" // externs `inbuf`
-#include "sw_src/myMemory.h"
-#include "sw_src/SW_VegProd.h"
-#include "sw_src/SW_Control.h"
-#include "sw_src/pcg/pcg_basic.h"
-#include "sw_src/SW_Markov.h"// externs `markov_rng`
+#include "sw_src/include/generic.h" // externs `*logfp`, `errstr`, `EchoInits`, `QuietMode`, `logged`
+#include "sw_src/include/filefuncs.h" // externs `inbuf`
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/SW_VegProd.h"
+#include "sw_src/include/SW_Control.h"
+#include "sw_src/external/pcg/pcg_basic.h"
+#include "sw_src/include/SW_Markov.h"// externs `markov_rng`
 
 #include "sxw_funcs.h"
 #include "sxw.h"
 // externs `prepare_IterationSummary`, `storeAllIterations`
-#include "sw_src/SW_Output.h"
-#include "sw_src/SW_Output_outtext.h" // externs `print_IterationSummary`
-#include "sw_src/SW_Output_outarray.h"
-#include "sw_src/rands.h"
+#include "sw_src/include/SW_Output.h"
+#include "sw_src/include/SW_Output_outtext.h" // externs `print_IterationSummary`
+#include "sw_src/include/SW_Output_outarray.h"
+#include "sw_src/include/rands.h"
 #include "ST_functions.h" // externs `environs_rng`, `resgroups_rng`, `species_rng`
 #include "ST_spinup.h"
 #include "ST_stats.h"

diff --git a/ST_mortality.c b/ST_mortality.c
@@ -23,12 +23,12 @@
 #include <string.h>
 
 #include "ST_mortality.h"
-#include "sw_src/filefuncs.h"
-#include "sw_src/rands.h"
-#include "sw_src/myMemory.h"
+#include "sw_src/include/filefuncs.h"
+#include "sw_src/include/rands.h"
+#include "sw_src/include/myMemory.h"
 #include "ST_steppe.h"
 #include "ST_globals.h"
-#include "sw_src/pcg/pcg_basic.h"
+#include "sw_src/external/pcg/pcg_basic.h"
 #include "sxw_vars.h"
 
 

diff --git a/ST_mortality.h b/ST_mortality.h
@@ -10,22 +10,22 @@
 #ifndef MORTALITY_H
 #define MORTALITY_H
 
-#include "sw_src/generic.h"
-#include "sw_src/pcg/pcg_basic.h"
+#include "sw_src/include/generic.h"
+#include "sw_src/external/pcg/pcg_basic.h"
 
 /* --------------------------- Exported Structs ---------------------------- */
 
 /**
  * \brief Information used when simulating the cheatgrass-wildfire loop.
- * 
+ *
  * The biggest determinant in cheatgrass driven wildfire is precipitation,
- * specifically precipitation in Spring and Winter. This struct stores the 
+ * specifically precipitation in Spring and Winter. This struct stores the
  * values from previous Spring and Winter precipitation as well as the running
  * averages of both.
- * 
+ *
  * Note that "year" in this context refers to the water year, which runs from
  * October to September.
- * 
+ *
  * \sa _updateCheatgrassPrecip, where this struct is updated each year.
  * \author Chandler Haukap
  * \date 13 January 2020

diff --git a/ST_output.c b/ST_output.c
@@ -15,14 +15,14 @@
 #include <string.h>
 #include "ST_steppe.h"
 #include "ST_globals.h"
-#include "sw_src/filefuncs.h"
-#include "sw_src/myMemory.h"
+#include "sw_src/include/filefuncs.h"
+#include "sw_src/include/myMemory.h"
 
 
 /******** Modular External Function Declarations ***********/
 /* -- truly global functions are declared in functions.h --*/
 /***********************************************************/
-#include "sw_src/SW_Model.h" // externs `SW_Model`
+#include "sw_src/include/SW_Model.h" // externs `SW_Model`
 
 
 /*------------------------------------------------------*/

diff --git a/ST_params.c b/ST_params.c
@@ -23,9 +23,9 @@
 #include <ctype.h>
 #include <errno.h>
 #include "ST_steppe.h"
-#include "sw_src/filefuncs.h"
-#include "sw_src/myMemory.h"
-#include "sw_src/rands.h"
+#include "sw_src/include/filefuncs.h"
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/rands.h"
 #include "sxw_funcs.h"
 #include "ST_globals.h"
 #include "sxw_vars.h"

diff --git a/ST_resgroups.c b/ST_resgroups.c
@@ -29,9 +29,9 @@
 #include <string.h>
 #include "ST_steppe.h"
 #include "ST_globals.h"
-#include "sw_src/myMemory.h"
-#include "sw_src/rands.h"
-#include "sw_src/filefuncs.h"
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/rands.h"
+#include "sw_src/include/filefuncs.h"
 #include "sxw_funcs.h"
 
 

diff --git a/ST_seedDispersal.c b/ST_seedDispersal.c
@@ -14,9 +14,9 @@
 #include "ST_defines.h"
 #include "ST_grid.h"
 #include "ST_seedDispersal.h"
-#include "sw_src/rands.h"
-#include "sw_src/myMemory.h"
-#include "sw_src/rands.h"
+#include "sw_src/include/rands.h"
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/rands.h"
 
 float _distance(int x1, int y1, int x2, int y2, float cellWidth);
 Bool _shouldProduceSeeds(SppIndex sp);

diff --git a/ST_species.c b/ST_species.c
@@ -22,9 +22,9 @@
 #include <string.h>
 #include "ST_steppe.h"
 #include "ST_globals.h"
-#include "sw_src/filefuncs.h"
-#include "sw_src/myMemory.h"
-#include "sw_src/rands.h"
+#include "sw_src/include/filefuncs.h"
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/rands.h"
 #include "ST_spinup.h"
 #include "ST_seedDispersal.h" // externs `UseSeedDispersal`
 

diff --git a/ST_spinup.c b/ST_spinup.c
@@ -17,21 +17,21 @@
 #include "ST_stats.h"
 #include "ST_globals.h" // externs UseProgressBar
 #include "ST_mortality.h"
-#include "sw_src/rands.h"
-#include "sw_src/SW_SoilWater.h" // externs SW_Soilwat
-#include "sw_src/SW_Weather.h" // externs SW_Weather
-#include "sw_src/SW_Site.h" // externs SW_Site
-#include "sw_src/SW_VegProd.h" // externs SW_VegProd
-#include "sw_src/SW_Markov.h"// externs `markov_rng`
+#include "sw_src/include/rands.h"
+#include "sw_src/include/SW_SoilWater.h" // externs SW_Soilwat
+#include "sw_src/include/SW_Weather.h" // externs SW_Weather
+#include "sw_src/include/SW_Site.h" // externs SW_Site
+#include "sw_src/include/SW_VegProd.h" // externs SW_VegProd
+#include "sw_src/include/SW_Markov.h"// externs `markov_rng`
 #include "sxw_funcs.h"
-#include "sw_src/myMemory.h"
-#include "sw_src/filefuncs.h"
+#include "sw_src/include/myMemory.h"
+#include "sw_src/include/filefuncs.h"
 #include "ST_progressBar.h"
 #include "ST_grid.h" // externs grid_rng
 // externs `prepare_IterationSummary`, `storeAllIterations`
-#include "sw_src/SW_Output.h"
-#include "sw_src/SW_Output_outtext.h" // externs `print_IterationSummary`
-#include "sw_src/SW_Output_outarray.h"
+#include "sw_src/include/SW_Output.h"
+#include "sw_src/include/SW_Output_outtext.h" // externs `print_IterationSummary`
+#include "sw_src/include/SW_Output_outarray.h"
 #include "ST_functions.h" // externs `environs_rng`, `resgroups_rng`, `species_rng`
 
 

diff --git a/ST_stats.c b/ST_stats.c
@@ -40,8 +40,8 @@
 
 #include <string.h>
 #include "ST_steppe.h"
-#include "sw_src/filefuncs.h"
-#include "sw_src/myMemory.h"
+#include "sw_src/include/filefuncs.h"
+#include "sw_src/include/myMemory.h"
 #include "ST_stats.h" // Contains most of the function declarations.
 #include "ST_seedDispersal.h" // externs `UseSeedDispersal`
 #include "ST_globals.h"

diff --git a/ST_structs.h b/ST_structs.h
@@ -23,7 +23,7 @@
 #ifndef STEPPE_STRUCT_DEF
 #define STEPPE_STRUCT_DEF
 
-#include "sw_src/generic.h"
+#include "sw_src/include/generic.h"
 #include "ST_mortality.h"
 
 /**