Add tests for EPS driver

.gitattributes

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+* 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

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+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

InitRatios.m

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+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

ePhotosynthesis.m

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+function values = ePhotosynthesis(driver, EnvFile, GRNFile, EnzymeFile, ATPCostFile, ...
+                                 OutputFile, OutputParamBase, WeatherTemp, ...
+                                 PARi, CO2i, O2i, ...
+                                 ProteinTotalRatio, GRNCin, GRNTin, ...
+                                 RUBISCOMETHODin, RUBISCOTOTALin, ...
+                                 PAR_in_Wpm2)
+arguments
+    driver (1,1) string
+    EnvFile (1,1) string = ""
+    GRNFile (1,1) string = ""
+    EnzymeFile (1,1) string = ""
+    ATPCostFile (1,1) string = ""
+    OutputFile (1,1) string = "output.data"
+    OutputParamBase (1,1) string = ""
+    WeatherTemp (1,1) double = 25
+    PARi (1,1) double = 470
+    CO2i (1,1) double = 400
+    O2i (1,1) double = 0.21  % i.e. 21%
+    ProteinTotalRatio (1,1) double = 0.973
+    GRNCin (1,1) double = 0
+    GRNTin (1,1) double = 0
+    RUBISCOMETHODin (1,1) double = 2
+    RUBISCOTOTALin (1,1) double = 3
+    PAR_in_Wpm2 (1, 1) double = 0
+end
+driver = str2double(driver);
+
+global GRNC;
+global GRNT;
+global pcfactor;
+global cATPsyn;
+global CPSi;
+global cNADPHsyn;
+global cpsii;
+global VfactorC;
+global CO2_Env;
+global CO2_cond;
+global O2_cond;
+global Temp_cond;
+global TestLi;
+global TestCa;
+global TestATPCost;
+global TestSucPath;
+global LI;
+global Tp;
+global RUBISCOMETHOD;
+global RUBISCOTOTAL;
+global GLight;
+global VolRatioStCyto;
+global dontCondition;
+global dontGraph;
+global dontClear;
+% dontCondition = 1;
+dontGraph = 1;
+% dontClear = 1;
+
+SucPath = 0;
+ATPCost = 0.0;
+GRNC = GRNCin;
+GRNT = GRNTin;
+RUBISCOMETHOD = RUBISCOMETHODin;
+RUBISCOTOTAL = RUBISCOTOTALin;
+pcfactor = 1.0 / 0.973;
+
+if (strlength(EnvFile) > 0)
+    fprintf("EVN FILE PROVIDED: %s\n", EnvFile);
+    Env_data = ReadParam(EnvFile);
+    if isKey(Env_data, "WeatherTemp")
+        WeatherTemp = Env_data("WeatherTemp");
+    end
+    if isKey(Env_data, "PAR")
+        PARi = Env_data("PAR");
+    end
+    % TODO: Propery unit parsing?
+    if isKey(Env_data, "PAR_in_Wpm2")
+        PAR_in_Wpm2 = Env_data("PAR_in_Wpm2");
+    end
+    if isKey(Env_data, "CO2")
+        CO2i = Env_data("CO2");
+    end
+    if isKey(Env_data, "ProteinTotalRatio")
+        ProteinTotalRatio = Env_data("ProteinTotalRatio");
+    end
+    if isKey(Env_data, "GRNC")
+        GRNC = Env_data("GRNC");
+    end
+    if isKey(Env_data, "GRNT")
+        GRNT = Env_data("GRNT");
+    end
+    if isKey(Env_data, "SucPath")
+        SucPath = Env_data("SucPath");
+    end
+end
+if (strlength(ATPCostFile) > 0)
+    fprintf("ATPCOST FILE PROVIDED: %s\n", ATPCostFile);
+    ATPCost_data = ReadParam(ATPCostFile);
+    if isKey(ATPCost_data, "ATPCost")
+        ATPCost = ATPCost_data("ATPCost");
+    end
+end
+
+TestCa = CO2i;
+TestLi = PARi;
+if (PAR_in_Wpm2)
+    TestLi = TestLi * 1E6/(2.35E5); % Convert W m^{-2} to u moles m^{-2} s^{-1}
+end
+TestATPCost = ATPCost;
+TestSucPath = SucPath;
+
+if dontCondition
+    CO2_Env = 0.7 * TestCa; % intercellular CO2
+    CO2_cond = CO2_Env/(3 * 10^4);
+    % TestLi = TestLi / 30;
+    O2_cond = O2i * 1.26;
+    Tp = WeatherTemp;
+    pcfactor = 1/ProteinTotalRatio;
+    Temp_cond = Tp;
+    GLight = TestLi*0.85*0.85;  % light umol m-2 s-1
+    VolRatioStCyto = 1;
+end
+
+if (strlength(GRNFile) > 0)
+    fprintf("GRN FILE PROVIDED: %s\n", GRNFile);
+    GRN_data = pcfactor * ReadGRN(GRNFile);
+    VfactorC = GRN_data(1:33);
+    if GRNC == 1
+        cATPsyn = GRN_data(34);
+        CPSi = GRN_data(35);
+        cNADPHsyn = GRN_data(37);
+        cpsii = GRN_data(36);
+    else
+        cATPsyn = 1;
+        CPSi = 1;
+        cNADPHsyn = 1;
+        cpsii = 1;
+    end
+else
+    GRN_data = ones(36, 1);
+end
+if (strlength(EnzymeFile) > 0)
+    fprintf("ENZYME FILE PROVIDED: %s\n", EnzymeFile);
+    Enzyme_data = ReadEnzymes(EnzymeFile);
+    global EnzymeAct;
+    EnzymeAct = Enzyme_data(1:27) / 30; % unit change
+    global Jmax;
+    Jmax = EnzymeAct(27);
+    global BFVmax;
+    BFVmax = Enzyme_data(28:45);
+    global FIVmax;
+    FIVmax = Enzyme_data(46:66);
+else
+    Enzyme_data = ones(66, 1);
+end
+
+if (strlength(OutputParamBase) > 0)
+    global export_mod_file_base;
+    global export_mod_enabled;
+    export_mod_enabled = 1;
+    export_mod_file_base = OutputParamBase;
+end
+
+if (driver == 1)
+    error("trDynaPS driver is disabled on this branch");
+    % ResultRate = trDynaPS_Drive(TestCa, TestLi, TestATPCost, TestSucPath, 1, 1);
+    % Arate = TargetFunVal;
+    % names = ["Light intensity", "Vc", "Vo", "VPGA", "VT3P", ...
+    %          "Vstarch", "Vt_glycerate", "Vt_glycolate", "CO2AR"];
+    % nres = size(ResultRate, 1);
+    % values = zeros(nres+2, 1);
+    % values(1, 1) = TestLi;
+    % for i=1:nres
+    %     values(i+1, 1) = ResultRate(i);
+    % end
+    % values(nres+2, 1) = Arate;
+elseif (driver == 2)
+    error("DynaPS driver is disabled on this branch");
+    % ResultRate = DynaPS_Drive(1, 1);
+    % Arate = TargetFunVal;
+    % names = ["Light intensity", "PSIIabs", "PSIabs", "Vc", "Vo", ...
+    %          "VPGA", "Vstarch", "Vsucrose", "CO2AR"];
+    % nres = size(ResultRate, 1);
+    % values = zeros(nres+2, 1);
+    % values(1, 1) = TestLi;
+    % for i=1:nres
+    %     values(i+1, 1) = ResultRate(i);
+    % end
+    % values(nres+2, 1) = Arate;
+elseif (driver == 3)
+    error("CM driver is disabled on this branch");
+    % CM_Drive;
+    % Arate = TargetFunVal;
+    % names = ["Light intensity", "CO2AR"];
+    % values = [TestLi; Arate];
+elseif (driver == 4)
+    Arate = EPS_Drive(TestLi, TestCa, WeatherTemp);
+    names = [];
+    values = [Arate];
+end
+WriteTable(OutputFile, names, values);
+end

tests/data/InputATPCost.txt

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+ATPCost	0

tests/data/InputEnzyme.txt

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+V1	120	   
+V2	1241.24	   
+V3	166.35	   
+V5	50.2	   
+V6	29.91	   
+V7	128.58	   
+V8	50.2	   
+V9	13.35	   
+V10	128.57	   
+V13	446.19	   
+V23	8.01	   
+V16	150	   
+V112	1572.6	   
+V113	171.47	   
+V121	43.68	   
+V122	99.19	   
+V123	300.29	   
+V124	82.37	   
+V131	74.84	   
+V51	3.22	   
+V52	1.92	   
+V55	3.46	   
+V56	1.67	   
+V57	16.65	   
+V58	0.5	   
+V59	3.03	   
+Jmax	180	   
+K1	1000000	   
+K2	500	   
+K3	50000000	   
+K4	50000000	   
+K5	50000000	   
+K6	50000000	   
+K7	10000	   
+K8	1000	   
+K9	8300000	   
+K10	800000000	   
+Vmax11	6	   
+Kau	10000000000	   
+Kua	10000000000	   
+Kf	6300000	   
+Kd 	200000000	   
+K15	10000000000	   
+K16	100000	   
+V2M 	27.8	   
+kA_d	200000000	   
+kA_f	1260000	   
+kA_U	10000000000	   
+kU_A	10000000000	   
+kU_d	200000000	   
+kU_f	1260000	   
+k1	2.5E+11	   
+k_r1	300000000	   
+kz	5000000	   
+k12	30000	   
+k23	10000	   
+k30	3000	   
+k01	500	   
+k2	2000000000	   
+kAB1	2500	   
+kBA1	200	   
+kAB2	3300	   
+kBA2	250	   
+k3	800	   
+k_r3	80	   
+k_pq_oxy	500	 

tests/data/InputEvn.txt

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+CO2                     400.0
+PAR                     470.0  # umol s**-1 m**-2
+PAR_in_Wpm2             0
+SucPath	                0
+WeatherTemperature	25.0
+ProteinTotalRatio	0.973
+GRNC                    1.0