Merge pull request #166 from DrylandEcology/resource_partitioning_ove…

…rhaul

All desired functionality has been added and @kpalmqui has created figures demonstrating the new functionality.

.gitignore

@@ -16,7 +16,7 @@
 *.exe
 *.o
 *.so
- 
+
 # Packages #
 ############
 # it's better to unpack these files and commit the raw source
@@ -29,13 +29,13 @@
 *.rar
 *.tar
 *.zip
- 
+
 # Logs and databases #
 ######################
 *.log
 *.sql
 *.sqlite
- 
+
 # OS generated files #
 ######################
 .DS_Store
@@ -53,13 +53,24 @@ Thumbs.db
 *outsetup_v30.in
 testing_shortegrass/
 stepwat
+stepwat.dSYM/
 testing/stepwat
 testing/valgrind.out
 testing/stepwat.dSYM/
-testing/Output
 
-testing.sagebrush.MT_drs/Output
-testing.sagebrush.MT_drs/Stepwat_Inputs/Output
 testing.sagebrush.MT_drs/Stepwat_Inputs/Input/sxw/Input/outsetup_v30.in
 *.out
 *.log
+
+*/Output
+*/Stepwat_Inputs/Output
+
+# Netbeans project files
+#######################
+nbproject/configurations.xml
+nbproject/private/CodeAssistancePathMapper.properties
+nbproject/private/configurations.xml
+nbproject/private/Default.properties
+nbproject/private/launcher.properties
+nbproject/private/private.xml
+nbproject/project.xml

.gitmodules

@@ -1,5 +1,5 @@
 [submodule "sw_src"]
 	path = sw_src
-	url = https://github.com/Burke-Lauenroth-Lab/SOILWAT2.git
+	url = https://github.com/DrylandEcology/SOILWAT2.git
 	branch = master
         ignore = dirty

.travis.yml

@@ -0,0 +1,10 @@
+language: c
+compiler:
+  - clang
+  - gcc
+
+script:
+  # check that we can cleanly compile STEPWAT2 and run the `default`, non-gridded example project
+  - make clean bint_testing_nongridded CPPFLAGS=-DSWDEBUG
+  # remove created files including (possibly) large output
+  - make cleanall

README.md

@@ -1,3 +1,22 @@
+| Unix | Windows | Release | License | Coverage | Downloads |
+| :---- | :---- | :---- | :---- | :---- | :---- |
+[ ![Travis build status][1]][2] | [![Appveyor build status][3]][4] | [ ![github release][5]][6] | [![license][7]][8] | [![codecov status][9]][10] | [![github downloads][11]][12] |
+
+[1]: https://travis-ci.org/DrylandEcology/STEPWAT2.svg?branch=master
+[2]: https://travis-ci.org/DrylandEcology/STEPWAT2
+[3]: https://ci.appveyor.com/api/projects/status/qx2o3j4jpp0ej0on/branch/master?svg=true
+[4]: https://ci.appveyor.com/project/DrylandEcologyGit/stepwat2/branch/master
+[5]: https://img.shields.io/github/release/DrylandEcology/STEPWAT2.svg?label=current+release
+[6]: https://github.com/DrylandEcology/STEPWAT2/releases
+[7]: https://img.shields.io/github/license/DrylandEcology/STEPWAT2.svg
+[8]: https://www.gnu.org/licenses/gpl.html
+[9]: https://codecov.io/gh/DrylandEcology/STEPWAT2/branch/master/graph/badge.svg
+[10]: https://codecov.io/gh/DrylandEcology/STEPWAT2
+[11]: https://img.shields.io/github/downloads/DrylandEcology/STEPWAT2/total.svg
+[12]: https://github.com/DrylandEcology/STEPWAT2
+
+<br>
+
 # STEPWAT2
 
 <br>
@@ -62,6 +81,15 @@ cd testing.sagebrush.master/Stepwat_Inputs/
 ```
 
 
+* Run non-gridded version of STEPWAT using SOILWAT and output all variables passed between
+  Stepwat and SOILWAT:
+
+```
+cd testing.sagebrush.master/Stepwat_Inputs/
+./stepwat -s -f files.in -ssxwdebug.in
+```
+
+
 * Run STEPPE (no SOILWAT2)
 
 ```
@@ -76,6 +104,31 @@ cd testing.sagebrush.master/Stepwat_Inputs/
 ./stepwat -f files.in -o -i -s
 ```
 
+* Alternatively, use `makefile` targets (compile, copy, and execute in one command)
+  - Non-gridded version, with SOILWAT2 water cycle, and with iteration and aggregated SOILWAT2-output:
+    ```
+    make bint_testing_nongridded
+    ```
+  - Gridded version with SOILWAT2 water cycle
+    ```
+    make bint_testing_gridded
+    ```
+  - If you need to clean up first, then run, e.g.,
+    ```
+    make cleanall bint_testing_nongridded
+    ```
+
+
+
+<br>
+
+## If switching to resource_partitioning_overhaul from another branch:
+
+* run 
+  ```
+  git submodule update --init --recursive
+  ```
+  To ensure all submodules are updated correctly.
 
 <br>
 

ST_defines.h

@@ -1,13 +1,12 @@
 /********************************************************/
 /********************************************************/
 /*  Source file: ST_defines.h
-/*  Type: header
-/*  Application: STEPPE - plant community dynamics simulator
-/*  Purpose: Generic model definitions such as constants,
- *           enums, and looping contructs.
-/*  History:
-/*     (6/15/2000) -- INITIAL CODING - cwb
-/*
+ *  Type: header
+ *  Application: STEPPE - plant community dynamics simulator
+ *  Purpose: Generic model definitions such as constants,
+ *           enums, and looping contructs. */
+/*  History */
+/*     (6/15/2000) -- INITIAL CODING - cwb */
 /********************************************************/
 /********************************************************/