Merge pull request #1370 from opencobra/develop

Regular merge of develop
opencobra · Nov 2, 2018 · 74dc79a · 74dc79a
2 parents ad4bb21 + 7b4bdee
commit 74dc79a
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -4,7 +4,7 @@ How to contribute
 :+1::tada: First off, thanks for taking the time to contribute to [The COBRA Toolbox](https://github.com/opencobra/cobratoolbox)! :tada::+1:
 
 <p align="center">
-<img src="https://cdn.rawgit.com/opencobra/MATLAB.devTools/develop/docs/source/_static/img/logo_devTools.png" height="120px"/>
+<img src="https://cdn.jsdelivr.net/gh/opencobra/MATLAB.devTools@e735bd91310e8ef10fab4d3c21833a85bf4b8159/docs/source/_static/img/logo_devTools.png" height="120px"/>
 </p>
 
 :bulb: **Check out the [MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools) - and contribute the smart way!**

diff --git a/README.rst b/README.rst
@@ -93,7 +93,7 @@ Toolbox <https://github.com/opencobra/cobratoolbox>`__! |tada| |thumbsup|
 .. raw:: html
 
    <p align="center">
-   <img src="https://cdn.rawgit.com/opencobra/MATLAB.devTools/develop/docs/source/_static/img/logo_devTools.png" height="120px" alt="devTools"/>
+   <img src="https://cdn.jsdelivr.net/gh/opencobra/MATLAB.devTools@e735bd91310e8ef10fab4d3c21833a85bf4b8159/docs/source/_static/img/logo_devTools.png" height="120px" alt="devTools"/>
    </p>
 
 

diff --git a/docs/prepareTutorials.sh b/docs/prepareTutorials.sh
@@ -119,7 +119,7 @@ buildHTMLTutorials(){
         createLocalVariables $tutorial
         # create PDF file
         /usr/local/bin/wkhtmltopdf --page-size A8 --margin-right 2 --margin-bottom 3 --margin-top 3 --margin-left 2 $pdfPath/tutorials/$tutorialFolder/$tutorialName.html $pdfPath/tutorials/$tutorialFolder/$tutorialName.pdf
-        sed 's#<html><head>#&<script type="text/javascript" src="https://cdn.rawgit.com/opencobra/cobratoolbox/gh-pages/latest/_static/js/iframeResizer.contentWindow.min.js"></script>#g' "$pdfPath/tutorials/$tutorialFolder/$tutorialName.html" > "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
+        sed 's#<html><head>#&<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/opencobra/cobratoolbox@ffa0229fc0c01c9236bb7e961f65712443277719/latest/_static/js/iframeResizer.contentWindow.min.js"></script>#g' "$pdfPath/tutorials/$tutorialFolder/$tutorialName.html" > "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
         sed -i.bak 's/white-space:\ pre-wrap/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
         sed -i.bak 's/white-space:\ pre/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
         rm "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html.bak"
@@ -132,7 +132,7 @@ buildHTMLSpecificTutorial(){
     createLocalVariables $specificTutorial
     # create PDF file
     /usr/local/bin/wkhtmltopdf --page-size A8 --margin-right 2 --margin-bottom 3 --margin-top 3 --margin-left 2 $pdfPath/tutorials/$tutorialFolder/$tutorialName.html $pdfPath/tutorials/$tutorialFolder/$tutorialName.pdf
-    sed 's#<html><head>#&<script type="text/javascript" src="https://cdn.rawgit.com/opencobra/cobratoolbox/gh-pages/latest/_static/js/iframeResizer.contentWindow.min.js"></script>#g' "$pdfPath/tutorials/$tutorialFolder/$tutorialName.html" > "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
+    sed 's#<html><head>#&<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/opencobra/cobratoolbox@ffa0229fc0c01c9236bb7e961f65712443277719/latest/_static/js/iframeResizer.contentWindow.min.js"></script>#g' "$pdfPath/tutorials/$tutorialFolder/$tutorialName.html" > "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
     sed -i.bak 's/white-space:\ pre-wrap/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
     sed -i.bak 's/white-space:\ pre/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
     rm "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html.bak"

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -47,7 +47,7 @@
     'sphinx.ext.linkcode',
     'sphinxcontrib.fulltoc']
 
-mathjax_path = 'https://cdn.rawgit.com/mathjax/MathJax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+mathjax_path = 'https://cdn.jsdelivr.net/gh/mathjax/MathJax@2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 def linkcode_resolve(domain, info):
     return github_linkcode_resolve(

diff --git a/docs/source/installation/compatMatrix.rst b/docs/source/installation/compatMatrix.rst
diff --git a/src/analysis/FVA/fastFVA/fastFVA.m b/src/analysis/FVA/fastFVA/fastFVA.m
@@ -234,20 +234,20 @@
     valuesCPLEXparams(i) = getfield(cpxControl, namesCPLEXparams{i});
 end
 
-% retrieve the b vector of the model file
-b = model.b;
+% create an LP problem
+LPproblem = buildLPproblemFromModel(model);
 
 % define the stoichiometric matrix to be solved
-if isfield(model, 'A') && (matrixAS == 'A')
-    A = model.A;
-    csense = model.csense(:);
+if matrixAS == 'A'
+    [A,b,csense,lb,ub,c] = deal(LPproblem.A,LPproblem.b,LPproblem.csense,LPproblem.lb,LPproblem.ub,LPproblem.c);
     if printLevel > 0
         fprintf(' >> Solving Model.A. (coupled) - Generalized\n');
     end
 else
-    A = model.S;
-    csense = char('E' * ones(size(A, 1), 1));
-    b = b(1:size(A, 1));
+    if ~isfield(model,'csense')
+        model.csense = repmat('E',size(model.S,1),1);
+    end
+    [A,b,csense,lb,ub,c] = deal(model.S,model.b,model.csense,model.lb,model.ub,model.c);
     if printLevel > 0
         fprintf(' >> Solving Model.S. (uncoupled) \n');
     end
@@ -352,15 +352,15 @@
         fprintf(' \n WARNING: The Sequential Version might take a long time.\n\n');
     end
     if bExtraOutputs1
-        [minFlux, maxFlux, optsol, ret, fbasol, fvamin, fvamax, statussolmin, statussolmax] = FVAc(model.c, A, b, csense, model.lb, model.ub, ...
+        [minFlux, maxFlux, optsol, ret, fbasol, fvamin, fvamax, statussolmin, statussolmax] = FVAc(c, A, b, csense, lb, ub, ...
                                                                                                    optPercentage, obj, rxnsKey, ...
                                                                                                    1, cpxControl, valuesCPLEXparams, rxnsOptMode, logFileDir, printLevel);
     elseif bExtraOutputs
-        [minFlux, maxFlux, optsol, ret, fbasol, fvamin, fvamax] = FVAc(model.c, A, b, csense, model.lb, model.ub, ...
+        [minFlux, maxFlux, optsol, ret, fbasol, fvamin, fvamax] = FVAc(c, A, b, csense, lb, ub, ...
                                                                        optPercentage, obj, rxnsKey, ...
                                                                        1, cpxControl, valuesCPLEXparams, rxnsOptMode, logFileDir, printLevel);
     else
-        [minFlux, maxFlux, optsol, ret] = FVAc(model.c, A, b, csense, model.lb, model.ub, ...
+        [minFlux, maxFlux, optsol, ret] = FVAc(c, A, b, csense, lb, ub, ...
                                                optPercentage, obj, rxnsKey, ...
                                                1, cpxControl, valuesCPLEXparams, rxnsOptMode, logFileDir, printLevel);
     end

diff --git a/src/analysis/thermo/thermoFBA/cycleFreeFlux.m b/src/analysis/thermo/thermoFBA/cycleFreeFlux.m
@@ -165,7 +165,7 @@
 if solution.stat == 1
     v1 = solution.full(1:n);
 else
-    v1 = zeros(size(v0));
+    error('No solution found for a problem that by definition has a solution.\nTry using a different solver');
 end
 
 end

diff --git a/src/base/install/prepareTest.m b/src/base/install/prepareTest.m
@@ -14,6 +14,7 @@
 %                   - `useSolversIfAvailable`: Names of solvers that should be used if available. If not empty, the resulting solvers struct will contain cell arrays (will not throw an error if not). (default: {})
 %                   - `requireOneSolverOf`: Names of solvers, at least one of which has to be available
 %                   - `excludeSolvers`: Names of solvers which should never be used for the test (because they fail)
+%                   - `useMinimalNumberOfSolvers`: Always use only one solver. This option allows tests which only use FBA to generate input, but where no expicit linear programming code is present, to only validate on one solver (default: false).
 %                   - `needsLP`: Whether a LP solver is required (default: false)
 %                   - `needsMILP`: Whether a MILP solver is required (default: false)
 %                   - `needsQP`: Whether a QP solver is required (default: false)
@@ -88,7 +89,8 @@
 parser.addParamValue('requiredSolvers', {}, @iscell);
 parser.addParamValue('useSolversIfAvailable', {}, @iscell);
 parser.addParamValue('requireOneSolverOf', {}, @iscell);
-parser.addParamValue('excludeSolvers', {}, @iscell);
+parser.addParamValue('excludeSolvers', {}, @(x) iscell(x) || ischar(x) );
+parser.addParamValue('useMinimalNumberOfSolvers', false, @(x) islogical(x) || x == 1 || x == 0);
 parser.addParamValue('needsLP', false, @(x) islogical(x) || x == 1 || x == 0);
 parser.addParamValue('needsMILP', false, @(x) islogical(x) || x == 1 || x == 0);
 parser.addParamValue('needsNLP', false, @(x) islogical(x) || x == 1 || x == 0);
@@ -118,11 +120,14 @@
 requiredSolvers = parser.Results.requiredSolvers;
 possibleSolvers = parser.Results.requireOneSolverOf;
 excludedSolvers = parser.Results.excludeSolvers;
+if ischar(excludedSolvers)
+    excludedSolvers = {excludedSolvers};
+end
 preferredSolvers = parser.Results.useSolversIfAvailable;
 
 needsWebAddress = parser.Results.needsWebAddress;
 needsWebRead = parser.Results.needsWebRead;
-
+useMinimalNumberOfSolvers = parser.Results.useMinimalNumberOfSolvers;
 runtype = getenv('CI_RUNTYPE');
 
 errorMessage = {};
@@ -154,8 +159,8 @@
 if ~isempty(needsWebAddress)
     [status_curl, result_curl] = system(['curl -s -k ' needsWebAddress]);
     if status_curl ~= 0 || isempty(result_curl)
-        errorMessage{end + 1} = sprintf('This function needs to connect to %s and was unable to do so.',needsWebAddress);    	
-    end    
+        errorMessage{end + 1} = sprintf('This function needs to connect to %s and was unable to do so.',needsWebAddress);
+    end
     if needsWebRead
         if verLessThan('MATLAB','9.3') && isunix && strncmp(needsWebAddress,'https',5)
             errorString = sprintf(['This function needs to connect to a ''https'' address using webread.\n', ...
@@ -169,9 +174,9 @@
                                    'Please note that this test will not be able to run on your system,\n',...
                                    'regardless on whether you fixed the library or not. If you want to run it,',...
                                    'you will have to remove the ''needsWebRead'' flag from the ''prepareTest''',...
-                                   'statement in the test and run it again.'],...                                   
-                                   matlabroot,matlabroot,matlabroot);                                   
-            errorMessage{end + 1} = errorString;    	
+                                   'statement in the test and run it again.'],...
+                                   matlabroot,matlabroot,matlabroot);
+            errorMessage{end + 1} = errorString;
         end
     end
 end
@@ -337,7 +342,9 @@
 % collect the Used Solvers.
 solversToUse = struct();
 problemTypes = OPT_PROB_TYPES;
-if strcmpi(runtype,'fullRun')
+% if this is the extensive test suite, and the solver use not just about
+% testing whether the actual work succeeded.
+if strcmpi(runtype, 'extensive') && ~useMinimalNumberOfSolvers
     solversToUse = solversForTest;
     %exclude pdco if not explicitly requested and available, as it does
     %have issues at the moment.

diff --git a/src/base/io/utilities/createEmptyFields.m b/src/base/io/utilities/createEmptyFields.m
@@ -80,7 +80,7 @@
         case 'cell'
             model.(fieldNames{field}) =cell(xdim,ydim);
             % need to both check, whether the eval is a char AND if it is empty.
-            if ischar(eval(defaultValue)) && strcmp(eval(defaultValue),'') 
+            if xdim > 0 && ischar(eval(defaultValue)) && strcmp(eval(defaultValue),'') 
                 model.(fieldNames{field})(:) = {''};
             else
                 for i = 1:xdim

diff --git a/src/base/io/utilities/writeSBML.m b/src/base/io/utilities/writeSBML.m
@@ -160,17 +160,39 @@
     else
         tmp_metName=emptyChar;
     end
+    % create annotations and notes
+    tmp_species.metaid=tmp_species.id;  % set the metaid for each species
+    [tmp_annot,met_notes] = makeSBMLAnnotationString(model,tmp_species.metaid,'met',i);
+
 
     if isfield(model, 'metFormulas')
-        tmp_metFormulas = model.metFormulas{i};
+        % check the chemical formula
+        tmp_metFormulas = model.metFormulas{i};        
+        if ~isempty(model.metFormulas{i})
+            coefs = regexp(model.metFormulas{i},'(?<nums>[\.0-9]+)','names');
+            intVals = cellfun(@(x) mod(str2double(x),1) == 0,{coefs.nums});
+            if any(~intVals)
+                warning('Metabolite %s has formula %s. FBC 2.1 only allows integer values for coefficients.\nDiscarding the formula.',model.mets{i},model.metFormulas{i});
+                met_notes(end+1,1:2) = {'FORMULA',tmp_metFormulas};
+                tmp_metFormulas = emptyChar;                
+            end
+        end
+
     else
         tmp_metFormulas=emptyChar; %cell(0,1)% {''};%0;%emptyChar;
     end
 
     if isfield(model, 'metCharges')
         if ~isnan(model.metCharges(i))
-            tmp_metCharge=model.metCharges(i);
-            tmp_isSetfbc_charge=1;
+            if mod(model.metCharges(i),1) ~= 0
+                warning('Metabolite %s has a charge of %f. FBC 2.1 only allows integer values for charges.\nDiscarding the value.',model.mets{i},model.metCharges(i));
+                met_notes(end+1,1:2) = {'CHARGE',num2str(model.metCharges(i))};
+                tmp_metCharge=0;
+                tmp_isSetfbc_charge=0;
+            else
+                tmp_metCharge=model.metCharges(i);
+                tmp_isSetfbc_charge=1;
+            end
         else
             tmp_metCharge=0;
             tmp_isSetfbc_charge=0;
@@ -203,13 +225,11 @@
     tmp_species.fbc_chemicalFormula=tmp_metFormulas;
     tmp_species.isSetfbc_charge=tmp_isSetfbc_charge;
     %% Add annotations for metaoblites to the reconstruction
-    tmp_species.metaid=tmp_species.id;  % set the metaid for each species
-    [tmp_annot,met_notes] = makeSBMLAnnotationString(model,tmp_species.metaid,'met',i);
 
     tmp_note = emptyChar;
     if ~isempty(met_notes)
         for noteid = 1:size(met_notes,1)
-            tmp_note = [ tmp_note ' <p>' regexprep(met_notes{noteid,1},'^rxn','') ':' met_notes{noteid,2} '</p>'];
+            tmp_note = [ tmp_note ' <p>' regexprep(met_notes{noteid,1},'^met','') ':' met_notes{noteid,2} '</p>'];
         end
     end
     if isfield(model,'metNotes')

diff --git a/src/base/io/writeCbModel.m b/src/base/io/writeCbModel.m
@@ -59,8 +59,13 @@
     if ischar(varargin{1})        
         if any(ismember(varargin{1}, newKeyWords))
             legacySignature = false;            
-        else
-            legacySignature = true;            
+        else 
+            if ~isempty(regexp(varargin{1},'\.','ONCE')) % this is a file name.
+                varargin = {'fileName', varargin{1}, varargin{2:end}};
+                legacySignature = false;            
+            else
+               legacySignature = true;            
+            end
         end
     else
         %If its not a char, its not the old signature, as that signature