Merge branch 'C3-metabolic-and-leaf-model-tests' into C3-metabolic-an…

…d-leaf-model-compare

Update tests for this branch
Fix bug in export_mod_dict where empty export_mod_enabled was interpreted incorrectly
Added test for exported variables
Move export functions into utils
Generalize the export functions to allow for use with other 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 +1,23 @@
+name: Run tests
+'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
+        uses: matlab-actions/run-tests@v2
+        with:
+          select-by-folder: tests

BF_Rate.m

@@ -433,4 +433,7 @@
 global BF2TrDynaPSMB_vcet; 
 BF2TrDynaPSMB_vcet = vcet; 
 
-export_mod_dict("BF", BF_con, "");
+global export_mod_enabled;
+if export_mod_enabled == 1
+    export_mod_dict(t, "BF", BF_con, "");
+end

CM_Drive2.m

@@ -100,6 +100,11 @@
 
 suc = AssignVelocity(pop, currentPop);
 
+global export_mod;
+global export_mod_enabled;
+export_mod = 'CM';
+reenable_export_mod = export_mod_enabled;
+
 [Tt,d] = ode15s(@CM_mb,[0,time],CMs, options1,PS_PR_Param, SUCS_Param);
 
 global d_plot;
@@ -116,3 +121,9 @@
 IModelCom;
 
 CO2AR = TargetFunVal
+
+if reenable_export_mod == 1
+    export_mod_enabled = 1;
+    [row,col]=size(d);
+    CM_mb(time, d(row, :), PS_PR_Param, Sucs_Param);
+end

CM_Rate.m

@@ -1003,6 +1003,10 @@
 CMr(40)=	vpga_use	;%	PGA utilisation in cytosol
 CMr(41)=	vatpf	;%	ATP synthesis rate
 
-export_mod_dict("PS", CM_Con, "Ps");
-export_mod_dict("PR", CM_Con, "Pr");
-export_mod_dict("SUCS", CM_Con, "");
+global export_mod_enabled;
+if export_mod_enabled == 1
+    export_mod_dict(t, "PS", CM_Con, "Ps", "", 1);
+    export_mod_dict(t, "PR", CM_Con, "Pr", "", 15);
+    export_mod_dict(t, "SUCS", CM_Con, "", "", 24);
+    export_mod_dict(t, "CM", CM_Con, "");
+end

CM_mb.m

@@ -27,7 +27,7 @@
 
 % SUCS_Param(1) is unused
 % global GLight;
-% fini = cdn (t);
+% fini = Condition(t);
 % light = GLight;
 
 % SUCS_Param(1) = light; 

Condition.m

@@ -0,0 +1,164 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%   Copyright   Xin-Guang Zhu, Yu Wang, Donald R. ORT and Stephen P. LONG
+%CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031 
+%China Institute of Genomic Biology and Department of Plant Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031 
+%University of Illinois at Urbana Champaign
+%Global Change and Photosynthesis Research Unit, USDA/ARS, 1406 Institute of Genomic Biology, Urbana, IL 61801, USA.
+
+%   This file is part of e-photosynthesis.
+
+%    e-photosynthesis is free software; you can redistribute it and/or modify
+%    it under the terms of the GNU General Public License as published by
+%    the Free Software Foundation; 
+
+%    e-photosynthesis is distributed in the hope that it will be useful,
+%    but WITHOUT ANY WARRANTY; without even the implied warranty of
+%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%    GNU General Public License for more details.
+
+%    You should have received a copy of the GNU General Public License (GPL)
+%    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+% Function [light] = condition; This function is used to store all the required 
+% environmental variables, such as light, CO2, O2, humidity as such. This function 
+% contains two parts. Part a includes the generic (default) conditions and the 
+% 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 RUBISCOTOTAL;
+global RUBISCOMETHOD;         % The method for calculation of Rubisco catalyzed reaction
+RUBISCOTOTAL = 3;           
+RUBISCOMETHOD = 2;          % 1: Use enzyme concentration for calculation
+                            % 2: Use the michaelis menton and enzyme together for calculation
+global VolRatioStCyto
+VolRatioStCyto =1; 
+
+global GP;
+global gp2condition_RuCon;
+
+if GP ==1
+    RUBISCOTOTAL = gp2condition_RuCon;
+end
+
+
+% First get the generic conditions
+
+global CO2_cond;
+global O2_cond;
+global GLight;
+global V16;
+global Temp_cond;
+
+global Cond_V16;        % This variable is transfered from PSInitial for modificatin of V16, the rate of ATP synthesis. 
+% CO2Temp = TestCa*0.7;%280;          % CO2 concentation  % ppm
+O2Temp = 0.21;          % O2 concentration  %default is 0.21, i.e. 21%. 
+
+% CO2_cond = CO2Temp /(3 * 10^4);
+O2_cond = O2Temp*1.26;
+% Temp_cond = 25;
+
+light = 1000;
+% light =  TestLi*0.85*0.85;  % light umol m-2 s-1      
+
+% Here the time dependent variable is regulated. 
+global tglobal;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%   Here define how many interval needed for the experiments  %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+NumberInterval = 10;
+
+global NumInter_draw; 
+NumInter_draw = NumberInterval;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% This is an experimental protocol for doing repeatative experiment
+
+Tinter = tglobal/NumberInterval;
+
+FirstMet = 0;
+
+%     for index = 1:NumberInterval 
+%             b = index * Tinter;
+%         if t <= b & FirstMet == 0
+%             
+%             modifier = 1 * index; 
+%             
+%             global BF2XanCycle_pHl;
+% 
+%             global Xan2Stom_ABA;
+% 
+%                 
+%             % Light regulation
+%             light =  100 * index; 
+%             light = 2000; 
+%             
+%             % CO2 regulation
+%             temp = 280;
+%             %temp = 1000-100 * (index-1); 
+%             
+%             % O2 regualtion
+%             O2Temp = 0.21 ;   
+%             
+%             CO2_cond = temp /(3 * 10 ^ 4);   
+%             O2_cond = O2Temp*1.26;
+%             
+%             % Regulation of Vmax
+%             % Global RuACT_RC;
+%             % RuACT_RC(9) = 25 + 25  * index/2;
+%             
+%             FirstMet = 1;                
+%             
+%         end
+%     end
+
+
+
+% % % PAM MEASUREMENT
+% if t < 20
+%     light = 7;
+% else
+%     light=500;
+% end
+% % % PAM MEASUREMENT
+%   StepL = 20; 
+%     if t<1
+%         light = 8000;
+%     elseif t>1 & t < 20
+%         light = 1;
+%     else 
+%         index = floor(t/StepL);
+%         if t > (StepL*index) & t < (StepL*index+1)
+%             light = 8000; 
+%         else 
+%             light = 500; 
+%         end
+%     end   
+
+
+% if t<200
+%     light = 1000;
+% elseif t>200 & t<400
+%     light = 100;
+% else
+%     light = 1000;
+% end
+
+GLight   = light;
+fini = 1;   

EPS_Drive.m

@@ -114,7 +114,9 @@
 CO2A = zeros(5,1);
 
 
+global export_mod;
 global export_mod_enabled;
+export_mod = 'EPS';
 reenable_export_mod = export_mod_enabled;
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -148,7 +150,7 @@
     PhotosynthesisRate=Arate;
 
     % Run again to output variables
-    if reenable_export_mod
+    if reenable_export_mod == 1
         export_mod_enabled = 1;
         EPS_mb(time, d(row, :), BF_Param, FI_Param, PS_PR_Param, Sucs_Param);
     end

EPS_mb.m

@@ -48,25 +48,6 @@
 CM_DYDT = CM_mb(t,CMs,PS_PR_Param, Sucs_Param);
 FIBF_DYDT = FIBF_MB(t, FIBF_Con, BF_Param, FI_Param);
 
-% Dump a copy of the model parameters if export_mod_enabled is set
-global export_mod_enabled;
-if (export_mod_enabled)
-    global export_mod_file_base;
-    if (t == 0)
-        dump_vars(export_mod_file_base + "init.txt", EPS_Dict(EPS_Con));
-    else
-        EPS_Con_dump = zeros(87,1);
-        for m = 1:52
-            EPS_Con_dump(m) = FIBF_Con(m);
-        end
-        for m = 1:35
-            EPS_Con_dump(m+52) = CMs(m);
-        end
-        dump_vars(export_mod_file_base + "last.txt", EPS_Dict(EPS_Con_dump));
-    end
-    export_mod_enabled = 0;
-end
-
 % Step III: Calculate the mass balanec equation for the EPS model. This basically need to make sure that the variables 
 % used in the mass balance equation should be in exact sequence with the sequence used in the inialization.
 
@@ -95,3 +76,18 @@
 %EPS_DYDT(62) = BF2EPS_vbfn2 - PS2EPS_v3 - 1 * PS2EPS_NADPH/(PS2EPS_NADPH + 0.5) ;
 EPS_DYDT(62) = BF2EPS_vbfn2/2 - PS2EPS_v3;% - 1 * PS2EPS_NADPH/(PS2EPS_NADPH + 0.5) ;  %QF changed /2 and ;% - 1 * PS2EPS_NADPH/(PS2EPS_NADPH + 0.5)
 EPS_DYDT(29) = EPS_DYDT(62);           
+
+global export_mod_enabled;
+if export_mod_enabled == 1
+    EPS_Con_dump = EPS_Con;
+    if t ~= 0
+        EPS_Con_dump = zeros(87,1);
+        for m = 1:52
+            EPS_Con_dump(m) = FIBF_Con(m);
+        end
+        for m = 1:35
+            EPS_Con_dump(m+52) = CMs(m);
+        end
+    end
+    export_mod_dict(t, "EPS", EPS_Con_dump, "");
+end

FIBF_MB.m

@@ -181,4 +181,7 @@
 FIBF_mb	(	12	)	=	GPQH2_t;	%	QH2	The PQH2 concentration; the coefficient 2 represent the fact that 2 protons were taken up by one Q2-.
 FIBF_mb	(	51	)	=	GPQH2_t;	%	QH2	The PQH2 concentration; the coefficient 2 represent the fact that 2 protons were taken up by one Q2-.
 
-export_mod_dict("FIBF", FIBF_Con, "");
+global export_mod_enabled;
+if export_mod_enabled == 1
+    export_mod_dict(t, "FIBF", FIBF_Con);
+end

FI_Rate.m

@@ -375,5 +375,7 @@
 FI_Vel  (   57  )   =   vP680_d;
 FI_Vel  (   58  )   =   vP680_f;
 
-
-export_mod_dict("FI", FI_Con, "");
+global export_mod_enabled;
+if export_mod_enabled == 1
+    export_mod_dict(t, "FI", FI_Con, "");
+end