Add tests for drivers

Add ePhotosynthesis function for running different drivers
Add control parameters to allow drivers to be called with global input variables (not calling Condition) and without graphs
Added .gitignore file
Added function InitRatios for initializing Ratios vectors that can be used by the drivers

.gitattributes

@@ -0,0 +1,28 @@
+* text=auto
+
+*.fig binary
+*.mat binary
+*.mdl binary diff merge=mlAutoMerge
+*.mdlp binary
+*.mex* binary
+*.mlapp binary
+*.mldatx binary
+*.mlproj binary
+*.mlx binary
+*.p binary
+*.sfx binary
+*.sldd binary
+*.slreqx binary merge=mlAutoMerge
+*.slmx binary merge=mlAutoMerge
+*.sltx binary
+*.slxc binary
+*.slx binary merge=mlAutoMerge
+*.slxp binary
+
+## Other common binary file types
+*.docx binary
+*.exe binary
+*.jpg binary
+*.pdf binary
+*.png binary
+*.xlsx binary

.github/workflows/test-suite.yml

@@ -0,0 +1,29 @@
+name: Verify that MATLAB & C++ versions return the same answers
+'on':
+  push:
+    branches-ignore:
+     - gh-pages
+    tags:
+     - '*'
+  schedule:
+  - cron: 0 10 * * 1
+jobs:
+  build_cxx:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v2
+      - name: Run tests command
+        matlab-actions/run-command@v2
+        with:
+          command: runtests('tests'); exit;
+          startup-options: -nodisplay -nosplash -nodesktop -nojvm -logfile matlab_log.txt
+      - name: Display MATLAB log
+        run: cat matlab_log.txt
+      - name: Run tests
+        matlab-actions/run-tests@v2
+        select-by-folder: tests

.gitignore

@@ -0,0 +1,2 @@
+*~
+*.asv

CM_Drive.m

@@ -23,8 +23,11 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
-
-clear all; 
+global dontClear;
+if (~dontClear)
+    clear all;
+end
+InitRatios(1, 1);
 
 Begin = 1;
 fin = SYSInitial(Begin);
@@ -93,8 +96,13 @@
 %   output  step      %
 %%%%%%%%%%%%%%%%%%%%%%%%
 
+global dontGraph;
+if (~dontGraph)
 success = CM_OUT(Tt, d);
+else
+success = 1;
+end
 
 % Reinitialize some values of global variables. 
 PSPR_SUCS_com = 0;
-IniModelCom;
+IniModelCom;

CM_Drive2.m

@@ -25,6 +25,8 @@
 
 function CO2AR = CM_Drive2(pop, currentPop)
 
+InitRatios(1, 1);
+
 Begin = 1;
 fin = SysInitial(Begin);
 global options1;
@@ -107,4 +109,4 @@
 PSPR_SUCS_com = 0;
 IniModelCom;
 
-CO2AR = TargetFunVal
+CO2AR = TargetFunVal

CM_OUT.m

@@ -33,7 +33,7 @@
 
 PSPR(:,24) = d(:,36);
 
-out1 = PSPR_OUT(Tt,PSPR);
+out1 = PSPR_Out(Tt,PSPR);
 out2 = SUCS_Graph(Tt,SUCS);
 
-OUTSUC = 1;
+OUTSUC = 1;

Condition.m

@@ -30,6 +30,15 @@
 % second part contains the detailed conditions for different time period.
 
 function fini = Condition (t)
+% Allow early abort if environmental inputs handled via ePhotosynthesis
+% function
+global dontCondition;
+if (dontCondition)
+    global NumInter_draw;
+    NumInter_draw = 10;
+    fini = 1;
+    return;
+end
 global TestCa;
 global TestLi;
 global RUBISCOMETHOD;         % The method for calculation of Rubisco catalyzed reaction
@@ -142,4 +151,4 @@
 % end
 
 GLight   = light;
-fini = 1;   
+fini = 1;   

DynaPS_Drive.m

@@ -26,46 +26,7 @@
 % This part include the function to begin the simulation.
 
 % The time information is set in a global variable called tglobal in SYSInitial. 
-global PSRatio;
-PSRatio=ones(103,1); 
-if ParaNum <= 103
-PSRatio(ParaNum)=Ratio;
-end
-global SUCRatio;
-SUCRatio=ones(66,1);
-if ParaNum > 103&&ParaNum<=169
-SUCRatio(ParaNum-103)=Ratio;
-end
-global PRRatio;
-PRRatio=ones(48,1);
-if ParaNum > 169&&ParaNum<=217
-PRRatio(ParaNum-169)=Ratio;
-end
-
-global RacRatio;
-RacRatio=ones(16,1);
-if ParaNum > 217&&ParaNum<=233
-RacRatio(ParaNum-217)=Ratio;
-end
-
-global FIRatio;
-FIRatio=ones(23,1);
-if ParaNum > 233&&ParaNum<=256
-FIRatio(ParaNum-233)=Ratio;
-end
-
-global BFRatio;
-BFRatio=ones(49,1);
-if ParaNum > 256&&ParaNum<=305
-BFRatio(ParaNum-256)=Ratio;
-end    
-
-
-global XanRatio;
-XanRatio=ones(4,1);
-if ParaNum > 305&&ParaNum<=309
-XanRatio(ParaNum-305)=Ratio;
-end 
+InitRatios(ParaNum, Ratio);
 
 % DynaPS_Drive.m
 % This part include the function to begin the simulation.

EPS_Drive.m

@@ -23,8 +23,11 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
-
-clear; 
+global dontClear;
+if (~dontClear)
+clear;
+end
+InitRatios(1, 1);
 
 Begin = 1;
 fin = SYSInitial(Begin);
@@ -91,7 +94,10 @@
 [Tt,d] = ode15s(@EPS_mb,[0,time],EPS_Con,options1,BF_Param, FI_Param, PS_PR_Param, Sucs_Param);
 
 %   The following section deals with the data output of the program.
-GraphSuc = EPS_Graph(Tt,d);    
+global dontGraph;
+if (~dontGraph)
+GraphSuc = EPS_Graph(Tt,d);
+end
 % Here is the place to recover the status of the regulatory variables. 
 
 %     ATPActive = 0;
@@ -107,4 +113,4 @@
     global FI_VEL; 
     global FI_CON; 
     global BF_VEL; 
-    global BF_CON; 
+    global BF_CON; 

InitRatios.m

@@ -0,0 +1,48 @@
+function InitRatios(ParaNum, Ratio)
+if ParaNum <= 0
+  return;
+end
+
+global PSRatio;
+PSRatio=ones(103,1); 
+if ParaNum <= 103
+PSRatio(ParaNum)=Ratio;
+end
+
+global SUCRatio;
+SUCRatio=ones(66,1);
+if ParaNum > 103&&ParaNum<=169
+SUCRatio(ParaNum-103)=Ratio;
+end
+
+global PRRatio;
+PRRatio=ones(48,1);
+if ParaNum > 169&&ParaNum<=217
+PRRatio(ParaNum-169)=Ratio;
+end
+
+global RacRatio;
+RacRatio=ones(16,1);
+if ParaNum > 217&&ParaNum<=233
+RacRatio(ParaNum-217)=Ratio;
+end
+
+global FIRatio;
+FIRatio=ones(23,1);
+if ParaNum > 233&&ParaNum<=256
+FIRatio(ParaNum-233)=Ratio;
+end
+
+global BFRatio;
+BFRatio=ones(49,1);
+if ParaNum > 256&&ParaNum<=305
+BFRatio(ParaNum-256)=Ratio;
+end    
+
+global XanRatio;
+XanRatio=ones(4,1);
+if ParaNum > 305&&ParaNum<=309
+XanRatio(ParaNum-305)=Ratio;
+end
+
+end