fixed 2021a version checking issue

see issue #165
Data2Dynamics · May 4, 2021 · 622c970 · 622c970
1 parent 137ee65
commit 622c970
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diff --git a/arFramework3/Advanced/arMyStr2Sym.m b/arFramework3/Advanced/arMyStr2Sym.m
@@ -10,7 +10,7 @@
 
 persistent matver % keeping the value from the last call
 if isempty(matver)
-    matver = ver('MATLAB');  % calling this function every time is too time-consuming
+    matver = arVer;  % calling this function every time is too time-consuming
 end
     % The explicit cast to string is necessary for MATLAB R2017a at least,
     % otherwise double will convert the string on a char by char basis.

diff --git a/arFramework3/Development/arMiniReport.m b/arFramework3/Development/arMiniReport.m
@@ -104,7 +104,7 @@ function arMiniReport(varargin)
 pti = 1 - opts.keepfilenames;
 
 % Fetch MATLAB version
-matVer = ver('MATLAB');
+matVer = arVer;
 ar.config.matlabVersion = str2double(matVer.Version);
 
 savePath = [arSave '/Latex'];

diff --git a/arFramework3/Examples/Biomodels/DallaMan2007_GlucoseInsulinSystem/Models/BIOMD0000000379.def b/arFramework3/Examples/Biomodels/DallaMan2007_GlucoseInsulinSystem/Models/BIOMD0000000379.def
@@ -1,5 +1,5 @@
 DESCRIPTION
-"DallaMan2007_MealModel_GlucoseInsulinSystem"" (DallaMan2007_MealModel_GlucoseInsulinSystem)"
+"IMPORTANT: Do not use this file with arLoadModel. Unexpected behavior may occur because of missing observable formulas.""DallaMan2007_MealModel_GlucoseInsulinSystem"" (DallaMan2007_MealModel_GlucoseInsulinSystem)"
 "SBML level 2 version 4"
 "<notes>
   <body xmlns="http://www.w3.org/1999/xhtml">
@@ -16,15 +16,14 @@ Dalla Man C, Rizza RA, Cobelli C.<em>IEEE Trans Biomed Eng.</em>2007 Oct;54(10):
     <br/>
 A simulation model of the glucose-insulin system in the postprandial state can be useful in several circumstances, including testing of glucose sensors, insulin infusion algorithms and decision support systems for diabetes. Here, we present a new simulation model in normal humans that describes the physiological events that occur after a meal, by employing the quantitative knowledge that has become available in recent years. Model parameters were set to fit the mean data of a large normal subject database that underwent a triple tracer meal protocol which provided quasi-model-independent estimates of major glucose and insulin fluxes, e.g., meal rate of appearance, endogenous glucose production, utilization of glucose, insulin secretion. By decomposing the system into subsystems, we have developed parametric models of each subsystem by using a forcing function strategy. Model results are shown in describing both a single meal and normal daily life (breakfast, lunch, dinner) in normal. The same strategy is also applied on a smaller database for extending the model to type 2 diabetes
    </p>
-  <p>This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.<br/>
+    <p>This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.<br/>
 For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>.<br/>
-To cite BioModels Database, please use: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20587024" target="_blank">Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.</a>
-</p>
-</body>
+To cite BioModels Database, please use: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20587024" target="_blank">Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.</a></p>
+  </body>
 </notes>"
 
 PREDICTOR
-t	 T	 "n/a"	 time	 0	 100	
+t	 T	 "au"	 time	 0	 100	
 
 COMPARTMENTS
 Compartment1	 V	 "n/a"	 vol.	 1
@@ -61,21 +60,25 @@ REACTIONS
 
 DERIVED
 
+OBSERVABLES
+
+ERRORS
+
 CONDITIONS
+init_G_p	 "178"
+init_G_t	 "135"
+init_I_l	 "4.5"
+init_I_p	 "1.25"
+init_Q_sto1	 "78000"
+init_Q_gut	 "0"
+init_I_1	 "25"
+init_I_d	 "25"
+init_X_state	 "0"
+init_I_po	 "3.6"
+init_Y_state	 "0"
+init_Q_sto2	 "0"
 
 PARAMETERS
-init_G_p	 178	 1	 0	 0	 1000
-init_G_t	 135	 1	 0	 0	 1000
-init_I_l	 4.5	 1	 0	 0	 1000
-init_I_p	 1.25	 1	 0	 0	 1000
-init_Q_sto1	 78000	 1	 0	 0	 780000
-init_Q_gut	 0	 1	 0	 0	 1000
-init_I_1	 25	 1	 0	 0	 1000
-init_I_d	 25	 1	 0	 0	 1000
-init_X_state	 0	 1	 0	 0	 1000
-init_I_po	 3.6	 1	 0	 0	 1000
-init_Y_state	 0	 1	 0	 0	 1000
-init_Q_sto2	 0	 1	 0	 0	 1000
 V_G	 1.88	 0	 0	 0	 1000
 k_1	 0.065	 0	 0	 0	 1000
 k_2	 0.079	 0	 0	 0	 1000

diff --git a/arFramework3/Examples/Boehm_JProteomeRes2014/Models/model_Boehm_JProteomeRes2014.def b/arFramework3/Examples/Boehm_JProteomeRes2014/Models/model_Boehm_JProteomeRes2014.def
@@ -0,0 +1,61 @@
+DESCRIPTION
+"IMPORTANT: Do not use this file with arLoadModel. Unexpected behavior may occur because of missing observable formulas.""FullModel"
+"SBML level 2 version 4"
+
+PREDICTOR
+t	 T	 "min"	 time	 0	 100	
+
+COMPARTMENTS
+cyt	 V	 "pl"	 vol.	 1.4
+nuc	 V	 "pl"	 vol.	 0.45
+
+STATES
+STAT5A	 C	 "nM"	 conc.	 cyt	 1	 "STAT5A"
+STAT5B	 C	 "nM"	 conc.	 cyt	 1	 "STAT5B"
+pApB	 C	 "nM"	 conc.	 cyt	 1	 "pApB"
+pApA	 C	 "nM"	 conc.	 cyt	 1	 "pApA"
+pBpB	 C	 "nM"	 conc.	 cyt	 1	 "pBpB"
+nucpApA	 C	 "nM"	 conc.	 nuc	 1	 "nucpApA"
+nucpApB	 C	 "nM"	 conc.	 nuc	 1	 "nucpApB"
+nucpBpB	 C	 "nM"	 conc.	 nuc	 1	 "nucpBpB"
+
+INPUTS
+BaF3_Epo	 C	 "n/a"	 conc.	"epo_level*exp(-Epo_degradation_BaF3*t)"
+
+REACTIONS
+2 STAT5A 	-> pApA 	 CUSTOM "BaF3_Epo*STAT5A^2*k_phos" 	"v1_v_0"
+STAT5A + STAT5B 	-> pApB 	 CUSTOM "BaF3_Epo*STAT5A*STAT5B*k_phos" 	"v2_v_1"
+2 STAT5B 	-> pBpB 	 CUSTOM "BaF3_Epo*STAT5B^2*k_phos" 	"v3_v_2"
+pApA 	-> nucpApA 	 CUSTOM "k_imp_homo*pApA" 	"v4_v_3"
+pApB 	-> nucpApB 	 CUSTOM "k_imp_hetero*pApB" 	"v5_v_4"
+pBpB 	-> nucpBpB 	 CUSTOM "k_imp_homo*pBpB" 	"v6_v_5"
+nucpApA 	-> 2 STAT5A 	 CUSTOM "k_exp_homo*nucpApA" 	"v7_v_6"
+nucpApB 	-> STAT5A + STAT5B 	 CUSTOM "k_exp_hetero*nucpApB" 	"v8_v_7"
+nucpBpB 	-> 2 STAT5B 	 CUSTOM "k_exp_homo*nucpBpB" 	"v9_v_8"
+
+DERIVED
+
+OBSERVABLES
+
+ERRORS
+
+CONDITIONS
+init_STAT5A	 "207.6*ratio"
+init_STAT5B	 "207.6 - 207.6*ratio"
+init_pApB	 "0"
+init_pApA	 "0"
+init_pBpB	 "0"
+init_nucpApA	 "0"
+init_nucpApB	 "0"
+init_nucpBpB	 "0"
+
+PARAMETERS
+Epo_degradation_BaF3	 0.0269765	 0	 0	 0	 1000
+epo_level	 1	 0	 0	 0	 1000
+k_exp_hetero	 1.00097e-05	 0	 0	 0	 1000
+k_exp_homo	 0.00617238	 0	 0	 0	 1000
+k_imp_hetero	 0.0163702	 0	 0	 0	 1000
+k_imp_homo	 96807.7	 0	 0	 0	 968077
+k_phos	 15767.6	 0	 0	 0	 157676
+ratio	 1	 0	 0	 0	 1000
+BaF3_Epo	 0	 0	 0	 0	 1000
diff --git a/arFramework3/Examples/Boehm_JProteomeRes2014/Setup.m b/arFramework3/Examples/Boehm_JProteomeRes2014/Setup.m
@@ -0,0 +1,4 @@
+arInit;
+arLoadModel('model_Boehm_JProteomeRes2014');
+arLoadData('measurementData_Boehm_JProteomeRes2014.tsv');
+arCompileAll;
diff --git a/arFramework3/Examples/ToyModels/TurboSplines/monotone.mat b/arFramework3/Examples/ToyModels/TurboSplines/monotone.mat
diff --git a/arFramework3/Examples/ToyModels/TurboSplines/monotone_turbo.mat b/arFramework3/Examples/ToyModels/TurboSplines/monotone_turbo.mat
diff --git a/arFramework3/MatlabTools/arSubs.m b/arFramework3/MatlabTools/arSubs.m
@@ -20,7 +20,7 @@
 end
 
 if(nargin<4)
-    matVer = ver('MATLAB');
+    matVer = arVer;
     matlab_version = str2double(matVer.Version);   
 end
 

diff --git a/arFramework3/MatlabTools/arSubsRepeated.m b/arFramework3/MatlabTools/arSubsRepeated.m
@@ -15,7 +15,7 @@
 function out = arSubsRepeated(in, old, new, matlab_version)
 
 if(nargin<4)
-    matVer = ver('MATLAB');
+    matVer = arVer;
     matlab_version = str2double(matVer.Version);   
 end
 

diff --git a/arFramework3/MatlabTools/parseArgs.m b/arFramework3/MatlabTools/parseArgs.m
@@ -44,7 +44,7 @@
 persistent matlabver
 
 if isempty(matlabver)
-    matlabver=ver('MATLAB');
+    matlabver=arVer;
     matlabver=str2double(matlabver.Version);
 end
 

diff --git a/arFramework3/Subfunctions/arCcode.m b/arFramework3/Subfunctions/arCcode.m
@@ -2,7 +2,7 @@
 % 
 %   T                 any kind of symbolic expression
 % 
-%   matlab_version    Matlab version e.g. 9.5, use ver('MATLAB')
+%   matlab_version    Matlab version e.g. 9.5, use arVer
 % 
 %   This function generalizes matlab's ccode function and keeps the
 %   functionality indpendent of Matlab verions
@@ -16,7 +16,7 @@
 % 
 % Example:
 % T = ar.model(1).condition(1).sym.fv;
-% matVer = ver('MATLAB');
+% matVer = arVer;
 % matlab_version = str2double(matVer.Version);
 % cstr = arCcode(T, matlab_version)
 % cvar = 'fv'
@@ -109,7 +109,7 @@
     str = strrep( str, total{jm}, fNew );
 end
 % because of compatibility with MATLAB2020a and later versions
-tmp = ver('MATLAB');
+tmp = arVer;
 if ~verLessThan('matlab', '9.8')
     str = strrep(str,';',',');
 end

diff --git a/arFramework3/Subfunctions/arLink.m b/arFramework3/Subfunctions/arLink.m
@@ -25,7 +25,7 @@
 
 function arLink(silent, tExpAdd, dataAdd, ix, id, im, newData, yStd, add_sec)
 
-matVer = ver('MATLAB');
+matVer = arVer;
 
 global ar
 

diff --git a/arFramework3/Subfunctions/arPlot2.m b/arFramework3/Subfunctions/arPlot2.m
@@ -76,7 +76,7 @@
     plotOnlyData = false;
 end
 
-matVer = ver('MATLAB');
+matVer = arVer;
 
 if(evalfun)
     try

diff --git a/arFramework3/Subfunctions/arPlotV.m b/arFramework3/Subfunctions/arPlotV.m
@@ -12,7 +12,7 @@
 
 function arPlotV(saveToFile, fastPlot)
 
-matVer = ver('MATLAB');
+matVer = arVer;
 
 global ar
 

diff --git a/arFramework3/Subfunctions/arPlotX.m b/arFramework3/Subfunctions/arPlotX.m
@@ -16,7 +16,7 @@
 
 function arPlotX(saveToFile, fastPlot)
 
-matVer = ver('MATLAB');
+matVer = arVer;
 
 global ar
 

diff --git a/arFramework3/Subfunctions/arPlotY.m b/arFramework3/Subfunctions/arPlotY.m
@@ -39,7 +39,7 @@
 
 function arPlotY(saveToFile, fastPlot, doLegends, varargin)
 
-matVer = ver('MATLAB');
+matVer = arVer;
 
 global ar
 

diff --git a/arFramework3/Subfunctions/arVer.m b/arFramework3/Subfunctions/arVer.m
@@ -0,0 +1,19 @@
+function matVer = arVer
+
+% matVer = arVer
+%
+% *** AVOID USING THIS FUNCTION! verLessThan IS RECOMMENDED ***
+% *** DO NOT USE ver('matlab') AS THIS WON'T WORK WITH VERSIONS >= 9.10 ***
+%
+% Return MATLAB version with fix for 2021a (9.10) which leads to unexpected
+% behaviour when converting '9.10' to double.
+
+matVer = ver('MATLAB');
+
+versplit = strsplit(matVer.Version,'.');
+if strcmp(matVer.Version, '9.10')
+    matVer.Version = '9.91';
+elseif strcmp(matVer.Version, '9.11')
+    matVer.Version = '9.92';
+end
+end
diff --git a/arFramework3/arCompileAll.m b/arFramework3/arCompileAll.m
@@ -136,7 +136,7 @@ function arCompileAll(forcedCompile, debug_mode, source_dir, simplifyEquations)
         end
     end
 
-    matVer = ver('MATLAB');
+    matVer = arVer;
     matlab_version = str2double(matVer.Version);    
 
     % calc model

diff --git a/arFramework3/arLoadData.m b/arFramework3/arLoadData.m
@@ -550,7 +550,7 @@ function arLoadData(name, m, extension, removeEmptyObs, varargin)
 
 % SUBSTITUTIONS (beta)
 substitutions = 0;
-matVer = ver('MATLAB');
+matVer = arVer;
 if ( strcmp(C{1},'SUBSTITUTIONS') )
     arFprintf( 3, '[ OK ]\nReading substitutions' );
     if(str2double(matVer.Version)>=8.4)
@@ -984,7 +984,7 @@ function checkReserved(m, d)
 
 function [ar,d, fail] = setConditions(fid, ar, m, d, jplot, header, times, data, dataCell, pcond, removeEmptyObs, dpPerShoot, opts)
 
-% matVer = ver('MATLAB');
+% matVer = arVer;
 
 % normalization of columns
 fail = 0;

diff --git a/arFramework3/arLoadModel.m b/arFramework3/arLoadModel.m
@@ -97,7 +97,7 @@ function arLoadModel(name, m, varargin)
     ar.model(m).extra_conditions = {};
 end
 
-matVer = ver('MATLAB');
+matVer = arVer;
 
 % DESCRIPTION
 [str, fid] = arTextScan(fid, '%s', 1, 'CommentStyle', ar.config.comment_string);

diff --git a/arFramework3/arPlotMulti.m b/arFramework3/arPlotMulti.m
@@ -13,7 +13,7 @@
 
 function arPlotMulti(ps, ps_weigths, saveToFile, filenameAddition)
 
-matVer = ver('MATLAB');
+matVer = arVer;
 
 global ar
 

diff --git a/arFramework3/arReport.m b/arFramework3/arReport.m
@@ -48,7 +48,7 @@ function arReport(project_name,fullODEs)
 
 
 % Fetch MATLAB version
-matVer = ver('MATLAB');
+matVer = arVer;
 ar.config.matlabVersion = str2double(matVer.Version);
 
 savePath = [arSave '/Latex']; % return argument of arSave is ar.config.savepath