Merge pull request #1 from cropsinsilico/add_tests

Add tests & CI

.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 +1,30 @@
+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
+      #   uses: 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
+        uses: matlab-actions/run-tests@v2
+        with:
+          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