Re-organize repository (part 2)

- addressing #89 - update file paths (see previous commit 90b1741 "Re-organize repository (part 1)" - note: additional commits to complete #89 will need to update makefile and scripts
DrylandEcology · Dec 21, 2022 · dc521a4 · dc521a4
1 parent 90b1741
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diff --git a/.gitignore b/.gitignore
@@ -38,7 +38,9 @@ doc/html/*
 doc/log_doxygen.log
 doc/Doxyfile.bak
 
-# Binary files
+# Build and binary directories and files
+bin/*
+build/*
 SOILWAT2
 tests/example/SOILWAT2
 libSOILWAT2*

diff --git a/README.md b/README.md
@@ -239,15 +239,15 @@ __Integration tests__
 We use integration tests to check that the entire simulation model works
 as expected when used in a real-world application setting.
 
-The folder `testing/` contains all necessary inputs to run `SOILWAT2`
+The folder `tests/example/` contains all necessary inputs to run `SOILWAT2`
 for one generic location
 (it is a relatively wet and cool site in the sagebrush steppe).
 
 ```{.sh}
       make bin bint_run
 ```
 
-The simulated output is stored at `testing/Output/`.
+The simulated output is stored at `tests/example/Output/`.
 
 
 Another use case is to compare output of a new (development) branch to output
@@ -263,15 +263,15 @@ The following steps provide a starting point for such comparisons:
       # Simulate on refernce branch and copy output to "Output_ref"
       git checkout master
       make bin bint_run
-      cp -r testing/Output testing/Output_ref
+      cp -r tests/example/Output tests/example/Output_ref
 
       # Switch to development branch <branch_xxx> and run the same simulation
       git checkout <branch_xxx>
       make bin bint_run
 
       # Compare the two sets of outputs
       #   * Lists all output files and determine if they are exactly they same
-      diff testing/Output/ testing/Output_ref/ -qs
+      diff tests/example/Output/ tests/example/Output_ref/ -qs
 ```
 
 

diff --git a/doc/Doxyfile b/doc/Doxyfile
@@ -876,8 +876,8 @@ WARN_LOGFILE           =
 
 INPUT                  = . \
                          doc/additional_pages/ \
-                         testing/ \
-                         testing/Input
+                         tests/example/ \
+                         tests/example/Input
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -925,7 +925,7 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = testing/README.md
+EXCLUDE                = tests/example/README.md
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -958,8 +958,8 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = testing \
-                         testing/Input
+EXAMPLE_PATH           = tests/example \
+                         tests/example/Input
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and

diff --git a/doc/additional_pages/A_SOILWAT2_user_guide.md b/doc/additional_pages/A_SOILWAT2_user_guide.md
@@ -133,18 +133,16 @@ on your side.
 
 
 ### Example
-  * The source code contains a complete example simulation project in `testing/`
-  * Copy the executable to the testing path, modify inputs as desired,
-    and run a simulation, e.g.,
+  * The source code contains a complete example simulation project in
+    `tests/example/`
+  * Modify inputs as desired and run a simulation, e.g.,
 ```{.sh}
-    make bint bint_run
+    make bin_run
 ```
     or, equivalently,
 ```{.sh}
     make bin
-    cp SOILWAT2 testing/
-    cd testing/
-    ./SOILWAT2
+    bin/SOILWAT2 -d ./tests/example -f files.in
 ```
 
   * The inputs comprise the master file `files.in` and the content of the
@@ -154,7 +152,7 @@ on your side.
     warnings and errors. The output files are in `.csv` format and can be
     opened by a spreadsheet program (e.g., `LibreOffice` or `Excel`) or
     imported into `R`
-    (e.g., `data <- read.csv("testing/Output/sw2_yearly.csv")`).
+    (e.g., `data <- read.csv("tests/example/sw2_yearly.csv")`).
     Outputs are explained in detail
     [here](doc/additional_pages/SOILWAT2_Inputs.md).
 

diff --git a/doc/additional_pages/SOILWAT2_Inputs.md b/doc/additional_pages/SOILWAT2_Inputs.md
@@ -8,20 +8,19 @@ Note: this document is best viewed as part of the doxygen-built documentation
 <br>
 
 ### Example
-  * The source code contains a complete example simulation project in `testing/`
-  * Copy the executable to the testing path, modify inputs as desired,
-    and run a simulation, e.g.,
+  * The source code contains a complete example simulation project in
+    `tests/example/`
+  * Modify inputs as desired and run a simulation, e.g.,
 ```{.sh}
-    make bint bint_run
+    make bin_run
 ```
     or, equivalently,
 ```{.sh}
     make bin
-    cp SOILWAT2 testing/
-    cd testing/
-    ./SOILWAT2
+    bin/SOILWAT2 -d ./tests/example -f files.in
 ```
 
+
   * The inputs comprise the master file `files.in` and the content of the
     `Input/` folder. They are explained in detail
     \ref explain_inputs "below".
@@ -64,78 +63,78 @@ Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section yearsin years.in
-\verbinclude testing/Input/years.in
+\verbinclude tests/example/Input/years.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section siteparamin siteparam.in
-\verbinclude testing/Input/siteparam.in
+\verbinclude tests/example/Input/siteparam.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section soilsin soils.in
-\verbinclude testing/Input/soils.in
+\verbinclude tests/example/Input/soils.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section swrcpin swrc_params.in
-\verbinclude testing/Input/swrc_params.in
+\verbinclude tests/example/Input/swrc_params.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section weathsetupin weathsetup.in
-\verbinclude testing/Input/weathsetup.in
+\verbinclude tests/example/Input/weathsetup.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section mkvprobin mkv_prob.in
-\verbinclude testing/Input/mkv_prob.in
+\verbinclude tests/example/Input/mkv_prob.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section mkvcovarin mkv_covar.in
-\verbinclude testing/Input/mkv_covar.in
+\verbinclude tests/example/Input/mkv_covar.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section climatein climate.in
-\verbinclude testing/Input/climate.in
+\verbinclude tests/example/Input/climate.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section vegin veg.in
-\verbinclude testing/Input/veg.in
+\verbinclude tests/example/Input/veg.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section estabin estab.in
-\verbinclude testing/Input/estab.in
+\verbinclude tests/example/Input/estab.in
 <hr>
 Go back to the \ref explain_inputs "list of input files"
 
 \section carbonin carbon.in
-\verbinclude testing/Input/carbon.in
+\verbinclude tests/example/Input/carbon.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section swcsetupin swcsetup.in
-\verbinclude testing/Input/swcsetup.in
+\verbinclude tests/example/Input/swcsetup.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>
 
 \section outsetupin outsetup.in
-\verbinclude testing/Input/outsetup.in
+\verbinclude tests/example/Input/outsetup.in
 
 Go back to the \ref explain_inputs "list of input files"
 <hr>

diff --git a/doc/additional_pages/SOILWAT2_Outputs.md b/doc/additional_pages/SOILWAT2_Outputs.md
@@ -8,18 +8,16 @@ Note: this document is best viewed as part of the doxygen-built documentation
 <br>
 
 ### Example
-  * The source code contains a complete example simulation project in `testing/`
-  * Copy the executable to the testing path, modify inputs as desired,
-    and run a simulation, e.g.,
+  * The source code contains a complete example simulation project in
+    `tests/example/`
+  * Modify inputs as desired and run a simulation, e.g.,
 ```{.sh}
-    make bint bint_run
+    make bin_run
 ```
     or, equivalently,
 ```{.sh}
     make bin
-    cp SOILWAT2 testing/
-    cd testing/
-    ./SOILWAT2
+    bin/SOILWAT2 -d ./tests/example -f files.in
 ```
 
   * The inputs comprise the master file `files.in` and the content of the

diff --git a/include/SW_Carbon.h b/include/SW_Carbon.h
@@ -7,7 +7,7 @@
 #ifndef CARBON
 #define CARBON
 
-#include "SW_Defines.h"
+#include "include/SW_Defines.h"
 
 
 #ifdef __cplusplus

diff --git a/include/SW_Defines.h b/include/SW_Defines.h
@@ -20,7 +20,7 @@
 #define SOILW_DEF_H
 
 #include <math.h>  /* >= C99; for: atan(), isfinite() */
-#include "generic.h"
+#include "include/generic.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/include/SW_Markov.h b/include/SW_Markov.h
@@ -13,7 +13,7 @@
 #ifndef SW_MARKOV_H
 #define SW_MARKOV_H
 
-#include "pcg/pcg_basic.h"
+#include "external/pcg/pcg_basic.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/include/SW_Model.h b/include/SW_Model.h
@@ -20,8 +20,8 @@
 #ifndef SW_MODEL_H
 #define SW_MODEL_H
 
-#include "Times.h"
-#include "SW_Defines.h"
+#include "include/Times.h"
+#include "include/SW_Defines.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/include/SW_Output.h b/include/SW_Output.h
@@ -56,10 +56,10 @@
 #ifndef SW_OUTPUT_H
 #define SW_OUTPUT_H
 
-#include "Times.h"
-#include "SW_Defines.h"
-#include "SW_SoilWater.h"
-#include "SW_VegProd.h"
+#include "include/Times.h"
+#include "include/SW_Defines.h"
+#include "include/SW_SoilWater.h"
+#include "include/SW_VegProd.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/include/SW_Site.h b/include/SW_Site.h
@@ -47,7 +47,7 @@
 #ifndef SW_SITE_H
 #define SW_SITE_H
 
-#include "SW_Defines.h"
+#include "include/SW_Defines.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/include/SW_Sky.h b/include/SW_Sky.h
@@ -18,7 +18,7 @@
 #ifndef SW_SKY_H
 #define SW_SKY_H
 
-#include "SW_Times.h"
+#include "include/SW_Times.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/include/SW_SoilWater.h b/include/SW_SoilWater.h
@@ -45,10 +45,10 @@
 extern "C" {
 #endif
 
-#include "generic.h"
-#include "SW_Defines.h"
-#include "SW_Times.h"
-#include "SW_Site.h"
+#include "include/generic.h"
+#include "include/SW_Defines.h"
+#include "include/SW_Times.h"
+#include "include/SW_Site.h"
 
 typedef enum {
 	SW_Adjust_Avg = 1, SW_Adjust_StdErr

diff --git a/include/SW_Times.h b/include/SW_Times.h
@@ -31,7 +31,7 @@
 #ifndef SW_TIMES_H
 #define SW_TIMES_H
 
-#include "Times.h"
+#include "include/Times.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/include/SW_VegEstab.h b/include/SW_VegEstab.h
@@ -15,8 +15,8 @@
 #ifndef SW_VEGESTAB_H
 #define SW_VEGESTAB_H
 
-#include "SW_Defines.h"
-#include "SW_Times.h"
+#include "include/SW_Defines.h"
+#include "include/SW_Times.h"
 
 
 #ifdef __cplusplus

diff --git a/include/SW_VegProd.h b/include/SW_VegProd.h
@@ -34,8 +34,8 @@
 #ifndef SW_VEGPROD_H
 #define SW_VEGPROD_H
 
-#include "SW_Defines.h"    /* for tanfunc_t*/
-#include "Times.h" 				// for MAX_MONTHS
+#include "include/SW_Defines.h"    /* for tanfunc_t*/
+#include "include/Times.h" 				// for MAX_MONTHS
 
 #ifdef __cplusplus
 extern "C" {