From 0fd7b53d903d9f5f7df208f73380051af7b98522 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Mon, 5 Nov 2018 08:03:48 +0100
Subject: [PATCH 01/29] Adapt QP solver list

---
 test/verifiedTests/base/testSolvers/testSolveCobraQP.m | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/test/verifiedTests/base/testSolvers/testSolveCobraQP.m b/test/verifiedTests/base/testSolvers/testSolveCobraQP.m
index f643b60f14..e413efd804 100644
--- a/test/verifiedTests/base/testSolvers/testSolveCobraQP.m
+++ b/test/verifiedTests/base/testSolvers/testSolveCobraQP.m
@@ -23,7 +23,9 @@
 
 % test solver packages
 useIfAvailable = {'tomlab_cplex','ibm_cplex', 'gurobi','qpng','ibm_cplex','mosek'};
-solverPkgs = prepareTest('needsQP',true,'useSolversIfAvailable', useIfAvailable);
+% pdco is a normalizing solver not a general purpose QP solver, so it will
+% fail the test
+solverPkgs = prepareTest('needsQP',true,'useSolversIfAvailable', useIfAvailable,'excludeSolvers',{'pdco'});
 
 %QP Solver test: http://tomopt.com/docs/quickguide/quickguide005.php
 

From 6f72a68e99bc81e8d399727d59ad0e5efd0a78fc Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Mon, 5 Nov 2018 11:05:00 +0100
Subject: [PATCH 02/29] Adjust tolerance

---
 .../analysis/testFBA/testMinimizeModelFlux.m         | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/test/verifiedTests/analysis/testFBA/testMinimizeModelFlux.m b/test/verifiedTests/analysis/testFBA/testMinimizeModelFlux.m
index c8cb2f7c0e..e798e6d12d 100644
--- a/test/verifiedTests/analysis/testFBA/testMinimizeModelFlux.m
+++ b/test/verifiedTests/analysis/testFBA/testMinimizeModelFlux.m
@@ -29,21 +29,21 @@
     % qpng does not support this model size, so we don't use quadratic
     % minimzation.
     sol = minimizeModelFlux(currentmodel,'min','one');
-    assert(sol.x(end) == 0);
+    assert(abs(sol.x(end)) < tol);
     sol = minimizeModelFlux(currentmodel);
-    assert(sol.x(end) == 12000); %Since its reversible, exchangers cycle and all rev reactions cycle.
+    assert(abs(sol.x(end) - 12000) <= tol); %Since its reversible, exchangers cycle and all rev reactions cycle.
     sol = minimizeModelFlux(currentmodel,'max','one'); %same as before.
-    assert(sol.x(end) == 12000); %Since its reversible, exchangers cycle and all rev reactions cycle.
+    assert(abs(sol.x(end) - 12000 ) <= tol); %Since its reversible, exchangers cycle and all rev reactions cycle.
     currentmodel.osenseStr = 'min';
     modelChanged = changeRxnBounds(currentmodel,'R3',5,'l');
     sol = minimizeModelFlux(modelChanged);
-    assert(sol.x(end) == 20); %Can only come from the cycle
+    assert(abs(sol.x(end) - 20)  <= tol); %Can only come from the cycle
     sol = minimizeModelFlux(modelChanged,'max');
-    assert(sol.x(end) == 11000); %MAx flux through C-> E and Exchangers, + 3 reactions from the cycle.
+    assert(abs(sol.x(end) - 11000)  <= tol); %MAx flux through C-> E and Exchangers, + 3 reactions from the cycle.
     modelChanged = changeRxnBounds(currentmodel,'EX_E',5,'l'); %Force production of E
     sol = minimizeModelFlux(modelChanged);
     modelChanged = rmfield(modelChanged,'osenseStr');
-    assert(sol.x(end) == 25); %Flux -> A -> B -> C -> E -> 
+    assert(abs(sol.x(end) - 25)  <= tol); %Flux -> A -> B -> C -> E -> 
 end
 
 % change the directory

From 12f691ddd39be5689a67a09442cbb5474b9ae994 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Mon, 5 Nov 2018 11:48:21 +0100
Subject: [PATCH 03/29] Further adjustments for Tests

---
 src/base/install/prepareTest.m                | 19 ++++++++++++++++++-
 test/verifiedTests/analysis/testFVA/testFVA.m |  7 +++++--
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/src/base/install/prepareTest.m b/src/base/install/prepareTest.m
index 521f5f05b0..feb89b2112 100644
--- a/src/base/install/prepareTest.m
+++ b/src/base/install/prepareTest.m
@@ -9,7 +9,8 @@
 % OPTIONAL INPUTS:
 %    varagin:      `ParameterName` value pairs with the following options:
 %
-%                   - `toolboxes` or `requiredToolboxes`: Names of required toolboxes (the license feature name) (default: {})
+%                   - `toolboxes` or `requiredToolboxes`: Names of required toolboxes (the license feature name).(default: {})
+%                   - `minimalMatlabSolverVersion`: Minimal version of the optimization toolbox required to use the matlab solver.(default: 0)
 %                   - `requiredSolvers`: Names of all solvers that MUST be available. If not empty, the resulting solvers struct will contain cell arrays (default: {})
 %                   - `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
@@ -86,6 +87,8 @@
 parser = inputParser();
 parser.addParamValue('toolboxes', {}, @iscell);
 parser.addParamValue('requiredToolboxes', {}, @iscell);
+parser.addParamValue('minimalMatlabSolverVersion',0,@isnumeric);
+
 parser.addParamValue('requiredSolvers', {}, @iscell);
 parser.addParamValue('useSolversIfAvailable', {}, @iscell);
 parser.addParamValue('requireOneSolverOf', {}, @iscell);
@@ -103,6 +106,7 @@
 parser.addParamValue('needsWebAddress', '', @ischar);
 parser.addParamValue('needsWebRead', false, @(x) islogical(x) || x == 1 || x == 0);
 
+
 parser.parse(varargin{:});
 
 useQP = parser.Results.needsQP;
@@ -130,6 +134,8 @@
 useMinimalNumberOfSolvers = parser.Results.useMinimalNumberOfSolvers;
 runtype = getenv('CI_RUNTYPE');
 
+minimalMatlabSolverVersion = parser.Results.minimalMatlabSolverVersion;
+
 errorMessage = {};
 infoMessage = {};
 
@@ -191,6 +197,17 @@
 % restrict the solvers available for this test
 solversForTest = availableSolvers;
 
+if any(ismember(solversForTest.LP,'matlab'))
+    boxes = ver();
+    optBox = find(ismember({boxes.Name},'Optimization Toolbox'));
+    if ~isempty(optBox)
+        optVer = boxes(optBox).Version;
+        if str2double(optVer) < minimalMatlabSolverVersion                
+            excludedSolvers = [columnVector(excludedSolvers);'matlab'];
+        end
+    end
+end
+
 if ~isempty(excludedSolvers)
     solverTypes = fieldnames(availableSolvers);
     for i = 1:numel(solverTypes)
diff --git a/test/verifiedTests/analysis/testFVA/testFVA.m b/test/verifiedTests/analysis/testFVA/testFVA.m
index 6732136626..165b5c107f 100644
--- a/test/verifiedTests/analysis/testFVA/testFVA.m
+++ b/test/verifiedTests/analysis/testFVA/testFVA.m
@@ -22,7 +22,10 @@
 
 % define the solver packages to be used to run this test, can't use
 % dqq/Minos for the parallel part.
-solverPkgs = prepareTest('needsLP',true,'needsMILP',true,'needsQP',true,'useSolversIfAvailable',{'ibm_cplex'},'excludeSolvers',{'dqqMinos','quadMinos'});
+solverPkgs = prepareTest('needsLP',true,'needsMILP',true,'needsQP',true,...
+                         'useSolversIfAvailable',{'ibm_cplex'},...
+                         'excludeSolvers',{'dqqMinos','quadMinos'},...
+                         'minimalMatlabSolverVersion',8.0);
 
 
 
@@ -143,7 +146,7 @@
 %there
 pttoolboxPath = which('parpool');
 % here, we can use dqq and quadMinos again, because this is not parallel.
-solverPkgs = prepareTest('needsLP',true,'needsMILP',true,'needsQP',true,'useSolversIfAvailable',{'ibm_cplex'});
+solverPkgs = prepareTest('needsLP',true,'needsMILP',true,'needsQP',true,'useSolversIfAvailable',{'ibm_cplex'},'minimalMatlabSolverVersion',8.0);
 if ~isempty(pttoolboxPath)
     %We also have to shut down the parallel pool, as otherwise problems
     %occur with the pool.

From 4c8bbf4c331211fdd4268e62a7cd7da9b4de695e Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Tue, 6 Nov 2018 09:42:50 +0100
Subject: [PATCH 04/29] Allow empty Objective - no objective in the SBML

---
 src/base/io/utilities/writeSBML.m | 80 ++++++++++++++++---------------
 1 file changed, 42 insertions(+), 38 deletions(-)

diff --git a/src/base/io/utilities/writeSBML.m b/src/base/io/utilities/writeSBML.m
index 241fda05dd..ee5023818f 100644
--- a/src/base/io/utilities/writeSBML.m
+++ b/src/base/io/utilities/writeSBML.m
@@ -552,54 +552,58 @@
 
 %% Set the objective sense of the FBC objective according to the osenseStr in
 %the model.
-objectiveSense = 'maximize';
-
-if isfield(model,'osenseStr') && strcmpi(model.osenseStr,'min')
-    objectiveSense = 'minimize';
-end
-
-tmp_fbc_objective=getSBMLDefaultStruct('SBML_FBC_OBJECTIVE',sbmlLevel, sbmlVersion,sbmlPackages, sbmlPackageVersions);
-tmp_fbc_objective.fbc_id = 'obj';
-tmp_fbc_objective.fbc_type = objectiveSense;
-sbmlModel.fbc_activeObjective = 'obj';
-
-tmp_fbc_objective.fbc_fluxObjective=getSBMLDefaultStruct('SBML_FBC_FLUXOBJECTIVE',sbmlLevel, sbmlVersion,sbmlPackages, sbmlPackageVersions);
-
 %%%%% multiple objectives
 if ~isnumeric(model.c)
     model.c=double(cell2mat(model.c)); % convert the variable type to double
 end
-% check=~isempty(model.c(model.c~=0)) the following block is necessry for
-% libSBML library 5.11
-% % % % % % % if isempty(model.c(model.c~=0)) % if no objective function is defined, the first reaction is set as the objective function.
-% % % % % % %     model.c(1)=1;
-% % % % % % % end
-%if ~isempty(model.c(model.c~=0))
-% Construct a default structure of objective reactions and set intial values.
-%     fbc_objective.fbc_fluxObjective=fbc_fluxObjective;
-ind=find(model.c); % Find the index numbers for the objective reactions
-% The fields of a COBRA model are converted into respective fields of a FBCv2 structure.
-if isempty(ind)
-    tmp_fbc_objective.fbc_fluxObjective.fbc_coefficient=0; % no objective function is set
-    sbmlModel.fbc_objective=tmp_fbc_objective;
-else
-    for i=1:length(ind)
-        %     model.c(ind(i));
-        values=model.c(model.c~=0);
-        tmp_fbc_objective.fbc_fluxObjective.fbc_reaction=sbmlModel.reaction(ind(i)).id; % the reaction.id contains the  % model.rxns{ind(i)};
-        tmp_fbc_objective.fbc_fluxObjective.fbc_coefficient=values(i);
-        tmp_fbc_objective.fbc_fluxObjective.isSetfbc_coefficient=1;
-        if i==1
-            sbmlModel.fbc_objective=tmp_fbc_objective;
-        else
-            sbmlModel.fbc_objective.fbc_fluxObjective=[sbmlModel.fbc_objective.fbc_fluxObjective,tmp_fbc_objective.fbc_fluxObjective];
+if ~all(model.c == 0)
+    
+    
+    objectiveSense = 'maximize';
+    
+    if isfield(model,'osenseStr') && strcmpi(model.osenseStr,'min')
+        objectiveSense = 'minimize';
+    end
+    
+    tmp_fbc_objective=getSBMLDefaultStruct('SBML_FBC_OBJECTIVE',sbmlLevel, sbmlVersion,sbmlPackages, sbmlPackageVersions);
+    tmp_fbc_objective.fbc_id = 'obj';
+    tmp_fbc_objective.fbc_type = objectiveSense;
+    sbmlModel.fbc_activeObjective = 'obj';
+    
+    tmp_fbc_objective.fbc_fluxObjective=getSBMLDefaultStruct('SBML_FBC_FLUXOBJECTIVE',sbmlLevel, sbmlVersion,sbmlPackages, sbmlPackageVersions);
+    
+    
+    % check=~isempty(model.c(model.c~=0)) the following block is necessry for
+    % libSBML library 5.11
+    % % % % % % % if isempty(model.c(model.c~=0)) % if no objective function is defined, the first reaction is set as the objective function.
+    % % % % % % %     model.c(1)=1;
+    % % % % % % % end
+    %if ~isempty(model.c(model.c~=0))
+    % Construct a default structure of objective reactions and set intial values.
+    %     fbc_objective.fbc_fluxObjective=fbc_fluxObjective;
+    ind=find(model.c); % Find the index numbers for the objective reactions
+    % The fields of a COBRA model are converted into respective fields of a FBCv2 structure.
+    if isempty(ind)
+        tmp_fbc_objective.fbc_fluxObjective.fbc_coefficient=0; % no objective function is set
+        sbmlModel.fbc_objective=tmp_fbc_objective;
+    else
+        for i=1:length(ind)
+            %     model.c(ind(i));
+            values=model.c(model.c~=0);
+            tmp_fbc_objective.fbc_fluxObjective.fbc_reaction=sbmlModel.reaction(ind(i)).id; % the reaction.id contains the  % model.rxns{ind(i)};
+            tmp_fbc_objective.fbc_fluxObjective.fbc_coefficient=values(i);
+            tmp_fbc_objective.fbc_fluxObjective.isSetfbc_coefficient=1;
+            if i==1
+                sbmlModel.fbc_objective=tmp_fbc_objective;
+            else
+                sbmlModel.fbc_objective.fbc_fluxObjective=[sbmlModel.fbc_objective.fbc_fluxObjective,tmp_fbc_objective.fbc_fluxObjective];
+            end
         end
     end
 end
 
 
 
-
 %end
 
 sbmlModel.namespaces=struct('prefix',{'','fbc','groups'},...

From 8f2d0524193423ff89f725b9906ac648aa77758c Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Tue, 6 Nov 2018 14:59:28 +0100
Subject: [PATCH 05/29] Adjust function Name

---
 .../transcriptomics/eFlux/verifyEFluxExpressionStruct.m       | 2 +-
 .../refinement/{removeGenes.m => removeGenesFromModel.m}      | 4 ++--
 test/verifiedTests/dataIntegration/testEFlux/testEFlux.m      | 2 +-
 .../testModelManipulation/testModelManipulation.m             | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)
 rename src/reconstruction/refinement/{removeGenes.m => removeGenesFromModel.m} (95%)

diff --git a/src/dataIntegration/transcriptomics/eFlux/verifyEFluxExpressionStruct.m b/src/dataIntegration/transcriptomics/eFlux/verifyEFluxExpressionStruct.m
index c3b824f5e4..d22df3ff73 100644
--- a/src/dataIntegration/transcriptomics/eFlux/verifyEFluxExpressionStruct.m
+++ b/src/dataIntegration/transcriptomics/eFlux/verifyEFluxExpressionStruct.m
@@ -17,7 +17,7 @@
     % checkoptional field preprocessed
     % This leads to -1 for unassociated genes
     if ~isempty(setdiff(model.genes,expression.target))
-        error('The following genes are lacking assignments:\n%s\nAll genes need to be assigned in order to use eFlux. You can remove genes by using the removeGenes function',strjoin(setdiff(model.genes,expression.target),'\n')); 
+        error('The following genes are lacking assignments:\n%s\nAll genes need to be assigned in order to use eFlux. You can remove genes by using the removeGenesFromModel function',strjoin(setdiff(model.genes,expression.target),'\n')); 
     end                
 end
 % check sizes of the value/target fields. They must be of equal size.
diff --git a/src/reconstruction/refinement/removeGenes.m b/src/reconstruction/refinement/removeGenesFromModel.m
similarity index 95%
rename from src/reconstruction/refinement/removeGenes.m
rename to src/reconstruction/refinement/removeGenesFromModel.m
index 3fc2bcc78a..98b87d7cd5 100644
--- a/src/reconstruction/refinement/removeGenes.m
+++ b/src/reconstruction/refinement/removeGenesFromModel.m
@@ -1,4 +1,4 @@
-function [model, affectedRxns, originalGPRs, deletedReaction] = removeGenes(model, geneList, varargin)
+function [model, affectedRxns, originalGPRs, deletedReaction] = removeGenesFromModel(model, geneList, varargin)
 % Removes the given genes from the model. GPR rules will be adjusted to reflect the removal.
 % By default, the rules are converted to DNF and all clauses containing any of the given
 % genes are removed. Note, that this function is not supposed to be used to model
@@ -6,7 +6,7 @@
 %
 % USAGE:
 %
-%    [model, affectedRxns, originalGPRs, deletedReactions] = deleteModelGenes(model, geneList)
+%    [model, affectedRxns, originalGPRs, deletedReactions] = removeGenesFromModel(model, geneList)
 %
 % INPUT:
 %    model:               COBRA model with the appropriate constrains for a
diff --git a/test/verifiedTests/dataIntegration/testEFlux/testEFlux.m b/test/verifiedTests/dataIntegration/testEFlux/testEFlux.m
index edad6321ac..c443e72845 100644
--- a/test/verifiedTests/dataIntegration/testEFlux/testEFlux.m
+++ b/test/verifiedTests/dataIntegration/testEFlux/testEFlux.m
@@ -16,7 +16,7 @@
 solverPkgs = prepareTest('needsLP',true,'toolboxes',{'bioinformatics_toolbox'},'needsWebAddress','https://www.ncbi.nlm.nih.gov/geo/query/','excludeSolvers',{'matlab'});
 
 model = getDistributedModel('ecoli_core_model.mat');
-model = removeGenes(model,'s0001','keepReactions',true);
+model = removeGenesFromModel(model,'s0001','keepReactions',true);
 geoaddress = 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?form=text&acc=%s&view=full';
 anaerobic = geosoftread(urlread(sprintf(geoaddress,'GSM1010240')));
 aerobic = geosoftread(urlread(sprintf(geoaddress,'GSM1126445')));
diff --git a/test/verifiedTests/reconstruction/testModelManipulation/testModelManipulation.m b/test/verifiedTests/reconstruction/testModelManipulation/testModelManipulation.m
index a08b9c0faf..d1b8c143d4 100644
--- a/test/verifiedTests/reconstruction/testModelManipulation/testModelManipulation.m
+++ b/test/verifiedTests/reconstruction/testModelManipulation/testModelManipulation.m
@@ -455,14 +455,14 @@
 fprintf('>> Done \n\n >> Testing Gene removal...\n');
 
 %Test removal of a gene
-modelMod1 = removeGenes(modelMod,'G1');
+modelMod1 = removeGenesFromModel(modelMod,'G1');
 % now, rules{1} and rules{3} should be equal;
 fp = FormulaParser();
 rule = fp.parseFormula(modelMod1.rules{1});
 rule2 = fp.parseFormula(modelMod1.rules{3});
 assert(rule2.isequal(rule));
 % and now without keeping the clauses
-modelMod2 = removeGenes(modelMod,'G1','keepClauses',false);
+modelMod2 = removeGenesFromModel(modelMod,'G1','keepClauses',false);
 fp = FormulaParser();
 rule = fp.parseFormula(modelMod2.rules{1});
 rule2 = fp.parseFormula(modelMod2.rules{2});

From a64e07e562474d735a83d49c7a519a5782f64b51 Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Mon, 5 Nov 2018 11:27:55 +0100
Subject: [PATCH 06/29] testing calculateLODs function

---
 .../testMetaboTools/testCalculateLODs.m       | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m

diff --git a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
new file mode 100644
index 0000000000..be2d3261df
--- /dev/null
+++ b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
@@ -0,0 +1,35 @@
+% The COBRA Toolbox: testcalculateLODs
+%
+% Purpose:
+%     - tests the calculateLODs function
+%
+% Authors:
+%     Loic Marx, November 2018
+%     
+%
+   
+
+% save the current path
+currentDir = pwd;
+
+% initialize the test
+fileDir = fileparts(which('testcalculateLODs'));
+cd(fileDir);
+
+% calculate reference value
+theo_mass = (10: - 1:1);
+lod_gL = 1;
+
+v_ref = lod_gL ./theo_mass*1000;
+
+%calculate inputs 
+theo_mass = (10: - 1:1);
+lod_ngmL = 1;
+
+calculateLOD = calculateLODs(theo_mass,lod_ngmL)
+% Comparison to ref value
+ assert(isequal(calculateLOD, v_ref))
+
+
+% change the directory
+cd(currentDir)

From cbf051049e6ed93ccf766c493c3dfedb13402d38 Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Mon, 5 Nov 2018 16:59:06 +0100
Subject: [PATCH 07/29] testing  calculateLODs function

---
 .../metabotools/calculateLODs.m               | 14 ++++++++++++-
 .../testMetaboTools/testCalculateLODs.m       | 21 ++++++++++++-------
 2 files changed, 26 insertions(+), 9 deletions(-)

diff --git a/src/dataIntegration/metabotools/calculateLODs.m b/src/dataIntegration/metabotools/calculateLODs.m
index 1882e3053c..7c19a61fe6 100644
--- a/src/dataIntegration/metabotools/calculateLODs.m
+++ b/src/dataIntegration/metabotools/calculateLODs.m
@@ -14,10 +14,22 @@
 %   lod_mM:            Detection limits in mM
 %
 % .. Author: - Maike K. Aurich 27/05/15
+%  Modified by Loic Marx
+
+% input checking
+if length(lod_ngmL) == 1
+    lod_ngmL = repmat(lod_ngmL, length(theo_mass)) 
+    % throw a warning
+warning(The inputs have different size but we fixed it)
+end    
+
+if length(lod_ngmL) ~= 1
+    error ('both inputs do not have the same size')
+end
 
 lod_gL = lod_ngmL* 0.000001;
 
-lodmM =[];
+lod_mM =[];
 
 for i=1:length(lod_gL)
 
diff --git a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
index be2d3261df..d56b61a51e 100644
--- a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
+++ b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
@@ -17,19 +17,24 @@
 cd(fileDir);
 
 % calculate reference value
-theo_mass = (10: - 1:1);
-lod_gL = 1;
+theo_mass = [1, 2];
+v_ref = [1000, 500];
 
-v_ref = lod_gL ./theo_mass*1000;
-
-%calculate inputs 
-theo_mass = (10: - 1:1);
+%calculate inputs
 lod_ngmL = 1;
 
 calculateLOD = calculateLODs(theo_mass,lod_ngmL)
 % Comparison to ref value
- assert(isequal(calculateLOD, v_ref))
-
 
+assert(isequal(calculateLOD, v_ref))
+% throwing an error if the dimension are not equal
+lod_ngmL_unequal = [1, 2, 3]
+assert(verifyCobraFunctionError('calculateLODs', 'theo_mass,lod_ngmL_unequal ', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'both inputs do not have the same size'));
+% Testing the case where lod_ngmL is a vector of the same size as theo_mass
+lod_ngmL_vector = [1, 2]
+v_ref_vector = [1000, 1000]
+% Comparison to the ref value
+calculateLOD_vector = calculateLODs(theo_mass,lod_ngmL)
+assert(isequal(calculateLOD_vector, v_ref_vector))
 % change the directory
 cd(currentDir)

From 1041d2d8a306e680aa65b25dd94517585c43986a Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Tue, 6 Nov 2018 14:21:59 +0100
Subject: [PATCH 08/29] final testing function

---
 .../testMetaboTools/testCalculateLODs.m       | 20 ++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
index d56b61a51e..a9ba9a39c6 100644
--- a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
+++ b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
@@ -18,23 +18,25 @@
 
 % calculate reference value
 theo_mass = [1, 2];
-v_ref = [1000, 500];
+v_ref = 1e-3 * [1; 0.5];
 
 %calculate inputs
 lod_ngmL = 1;
 
-calculateLOD = calculateLODs(theo_mass,lod_ngmL)
+calculateLOD = calculateLODs(theo_mass,lod_ngmL);
 % Comparison to ref value
 
 assert(isequal(calculateLOD, v_ref))
-% throwing an error if the dimension are not equal
-lod_ngmL_unequal = [1, 2, 3]
-assert(verifyCobraFunctionError('calculateLODs', 'theo_mass,lod_ngmL_unequal ', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'both inputs do not have the same size'));
+% throwing an error if the dimensions are not equal
+lod_ngmL_unequal = [1, 2, 3];
+
+assert(verifyCobraFunctionError('calculateLODs', 'inputs', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'both inputs do not have the same size'));
 % Testing the case where lod_ngmL is a vector of the same size as theo_mass
-lod_ngmL_vector = [1, 2]
-v_ref_vector = [1000, 1000]
+
+lod_ngmL_vector = [1, 2];
+v_ref_vector = 1e-3 * [1; 1];
 % Comparison to the ref value
-calculateLOD_vector = calculateLODs(theo_mass,lod_ngmL)
-assert(isequal(calculateLOD_vector, v_ref_vector))
+calculateLOD_vector = calculateLODs(theo_mass,lod_ngmL_vector);
+assert(isequal(calculateLOD_vector, v_ref_vector));
 % change the directory
 cd(currentDir)

From f78f1ba3a2a4fc36375c58fe2247d063b23450bb Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Tue, 6 Nov 2018 14:23:29 +0100
Subject: [PATCH 09/29] Modification of the function calculateLOD

---
 src/dataIntegration/metabotools/calculateLODs.m | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/dataIntegration/metabotools/calculateLODs.m b/src/dataIntegration/metabotools/calculateLODs.m
index 7c19a61fe6..be39fe4188 100644
--- a/src/dataIntegration/metabotools/calculateLODs.m
+++ b/src/dataIntegration/metabotools/calculateLODs.m
@@ -18,22 +18,22 @@
 
 % input checking
 if length(lod_ngmL) == 1
-    lod_ngmL = repmat(lod_ngmL, length(theo_mass)) 
+    lod_ngmL = repmat(lod_ngmL, 1, length(theo_mass)); 
     % throw a warning
-warning(The inputs have different size but we fixed it)
+    warning('The inputs have different size');
 end    
 
-if length(lod_ngmL) ~= 1
-    error ('both inputs do not have the same size')
+if length(lod_ngmL) ~= length(theo_mass)
+    error('both inputs do not have the same size');
 end
 
 lod_gL = lod_ngmL* 0.000001;
 
-lod_mM =[];
+lod_mM = zeros(length(lod_gL), 1);
 
 for i=1:length(lod_gL)
 
-    lod_mM(i,1)= lod_gL(i,1)/theo_mass(i,1)*1000;
+    lod_mM(i)= lod_gL(i)/theo_mass(i)*1000;
 
 end
 

From 23bb009aea0373772b42778a702c925ec0827596 Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Tue, 6 Nov 2018 15:06:31 +0100
Subject: [PATCH 10/29] rewriting the code

---
 .../metabotools/calculateLODs.m               | 16 ++++++----
 .../testMetaboTools/testCalculateLODs.m       | 31 +++++++++++++------
 2 files changed, 31 insertions(+), 16 deletions(-)

diff --git a/src/dataIntegration/metabotools/calculateLODs.m b/src/dataIntegration/metabotools/calculateLODs.m
index be39fe4188..e24fbfd949 100644
--- a/src/dataIntegration/metabotools/calculateLODs.m
+++ b/src/dataIntegration/metabotools/calculateLODs.m
@@ -14,26 +14,30 @@
 %   lod_mM:            Detection limits in mM
 %
 % .. Author: - Maike K. Aurich 27/05/15
-%  Modified by Loic Marx
+%  Modified by Loic Marx, November 2018
 
 % input checking
 if length(lod_ngmL) == 1
+    
     lod_ngmL = repmat(lod_ngmL, 1, length(theo_mass)); 
+    
     % throw a warning
-    warning('The inputs have different size');
+    warning('The inputs have different size but we managed to fix this problem');
+    
 end    
 
 if length(lod_ngmL) ~= length(theo_mass)
-    error('both inputs do not have the same size');
+    
+    error('The length of the inputs are not the same');
 end
 
-lod_gL = lod_ngmL* 0.000001;
+lod_gL = lod_ngmL * 0.000001;
 
 lod_mM = zeros(length(lod_gL), 1);
 
-for i=1:length(lod_gL)
+for i=1 : length(lod_gL)
 
-    lod_mM(i)= lod_gL(i)/theo_mass(i)*1000;
+    lod_mM(i) = lod_gL(i)/theo_mass(i)*1000;
 
 end
 
diff --git a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
index a9ba9a39c6..27cac42b2c 100644
--- a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
+++ b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
@@ -9,34 +9,45 @@
 %
    
 
-% save the current path
+% Save the current path
 currentDir = pwd;
 
-% initialize the test
+% Initialize the test
 fileDir = fileparts(which('testcalculateLODs'));
+
 cd(fileDir);
 
-% calculate reference value
+% Defining the inputs
+lod_ngmL = 1;
+
 theo_mass = [1, 2];
+
+% Calculate the reference value
+
 v_ref = 1e-3 * [1; 0.5];
 
-%calculate inputs
-lod_ngmL = 1;
+% Calculate the actual value by using the function
 
 calculateLOD = calculateLODs(theo_mass,lod_ngmL);
-% Comparison to ref value
+
+% Comparison between calculate value and ref value
 
 assert(isequal(calculateLOD, v_ref))
-% throwing an error if the dimensions are not equal
+
+% Throwing an error if the dimensions of both inputs are not equal
 lod_ngmL_unequal = [1, 2, 3];
 
 assert(verifyCobraFunctionError('calculateLODs', 'inputs', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'both inputs do not have the same size'));
-% Testing the case where lod_ngmL is a vector of the same size as theo_mass
 
+% If both inputs are two vectors of the same size
 lod_ngmL_vector = [1, 2];
+
 v_ref_vector = 1e-3 * [1; 1];
-% Comparison to the ref value
+
+% Comparison between the values calculated when the inputs have the same size and the reference value
 calculateLOD_vector = calculateLODs(theo_mass,lod_ngmL_vector);
+
 assert(isequal(calculateLOD_vector, v_ref_vector));
-% change the directory
+
+% Change the directory
 cd(currentDir)

From baf5dce92e3d76b3e4d0e9178ce766b11713d47c Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Thu, 8 Nov 2018 11:17:44 +0100
Subject: [PATCH 11/29] Final modification on the function

---
 src/dataIntegration/metabotools/calculateLODs.m | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/src/dataIntegration/metabotools/calculateLODs.m b/src/dataIntegration/metabotools/calculateLODs.m
index e24fbfd949..f80c657bd6 100644
--- a/src/dataIntegration/metabotools/calculateLODs.m
+++ b/src/dataIntegration/metabotools/calculateLODs.m
@@ -21,17 +21,14 @@
     
     lod_ngmL = repmat(lod_ngmL, 1, length(theo_mass)); 
     
-    % throw a warning
-    warning('The inputs have different size but we managed to fix this problem');
-    
 end    
 
-if length(lod_ngmL) ~= length(theo_mass)
+if numel(lod_ngmL) ~= numel(theo_mass)
     
-    error('The length of the inputs are not the same');
+    error('The number of elements in the input vectors do not match. They have to be either the same size, or lod_ngmL has to be a single value which is used for all elements');
 end
 
-lod_gL = lod_ngmL * 0.000001;
+lod_gL = lod_ngmL * 1e-6; 
 
 lod_mM = zeros(length(lod_gL), 1);
 

From e11c9a0db524329f4225c64819645577a738c349 Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Thu, 8 Nov 2018 11:19:39 +0100
Subject: [PATCH 12/29] Changing error message on the code

---
 .../dataIntegration/testMetaboTools/testCalculateLODs.m         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
index 27cac42b2c..f9ba90bda0 100644
--- a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
+++ b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
@@ -37,7 +37,7 @@
 % Throwing an error if the dimensions of both inputs are not equal
 lod_ngmL_unequal = [1, 2, 3];
 
-assert(verifyCobraFunctionError('calculateLODs', 'inputs', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'both inputs do not have the same size'));
+assert(verifyCobraFunctionError('calculateLODs', 'inputs', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'The number of elements in the input vectors do not match. They have to be either the same size, or lod_ngmL has to be a single value which is used for all elements'));
 
 % If both inputs are two vectors of the same size
 lod_ngmL_vector = [1, 2];

From e8217c3a91cba5f61066516d388aae848c486aac Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Thu, 8 Nov 2018 13:53:14 +0100
Subject: [PATCH 13/29] Updating the code

---
 src/dataIntegration/metabotools/calculateLODs.m     |  2 +-
 .../testMetaboTools/testCalculateLODs.m             | 13 ++++++-------
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/dataIntegration/metabotools/calculateLODs.m b/src/dataIntegration/metabotools/calculateLODs.m
index f80c657bd6..ab62dd3f21 100644
--- a/src/dataIntegration/metabotools/calculateLODs.m
+++ b/src/dataIntegration/metabotools/calculateLODs.m
@@ -14,7 +14,7 @@
 %   lod_mM:            Detection limits in mM
 %
 % .. Author: - Maike K. Aurich 27/05/15
-%  Modified by Loic Marx, November 2018
+%    Modified by Loic Marx, November 2018
 
 % input checking
 if length(lod_ngmL) == 1
diff --git a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
index f9ba90bda0..d562f9c213 100644
--- a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
+++ b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
@@ -5,8 +5,7 @@
 %
 % Authors:
 %     Loic Marx, November 2018
-%     
-%
+%    
    
 
 % Save the current path
@@ -17,7 +16,7 @@
 
 cd(fileDir);
 
-% Defining the inputs
+% Define the inputs
 lod_ngmL = 1;
 
 theo_mass = [1, 2];
@@ -30,21 +29,21 @@
 
 calculateLOD = calculateLODs(theo_mass,lod_ngmL);
 
-% Comparison between calculate value and ref value
+% Compare between the calculated value and the reference value
 
 assert(isequal(calculateLOD, v_ref))
 
-% Throwing an error if the dimensions of both inputs are not equal
+% Throw an error if the dimensions of both inputs are not equal
 lod_ngmL_unequal = [1, 2, 3];
 
 assert(verifyCobraFunctionError('calculateLODs', 'inputs', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'The number of elements in the input vectors do not match. They have to be either the same size, or lod_ngmL has to be a single value which is used for all elements'));
 
-% If both inputs are two vectors of the same size
+% lod_ngmL and theo_mass are two vectors of the same size
 lod_ngmL_vector = [1, 2];
 
 v_ref_vector = 1e-3 * [1; 1];
 
-% Comparison between the values calculated when the inputs have the same size and the reference value
+% Compare the values calculated when the inputs have the same size and the reference value
 calculateLOD_vector = calculateLODs(theo_mass,lod_ngmL_vector);
 
 assert(isequal(calculateLOD_vector, v_ref_vector));

From 2dd1a2bb8a76241fb08e7e8e71ee278485ecf854 Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Thu, 8 Nov 2018 15:52:52 +0100
Subject: [PATCH 14/29] Reformating the style

---
 .../metabotools/calculateLODs.m               | 16 +++-------
 .../testMetaboTools/testCalculateLODs.m       | 32 +++++++------------
 2 files changed, 16 insertions(+), 32 deletions(-)

diff --git a/src/dataIntegration/metabotools/calculateLODs.m b/src/dataIntegration/metabotools/calculateLODs.m
index ab62dd3f21..a3e183c3f9 100644
--- a/src/dataIntegration/metabotools/calculateLODs.m
+++ b/src/dataIntegration/metabotools/calculateLODs.m
@@ -14,28 +14,22 @@
 %   lod_mM:            Detection limits in mM
 %
 % .. Author: - Maike K. Aurich 27/05/15
-%    Modified by Loic Marx, November 2018
+%            - Modified by Loic Marx, November 2018
 
 % input checking
-if length(lod_ngmL) == 1
-    
+if size(lod_ngmL) == 1
     lod_ngmL = repmat(lod_ngmL, 1, length(theo_mass)); 
-    
-end    
+    end    
 
-if numel(lod_ngmL) ~= numel(theo_mass)
-    
+if size(lod_ngmL) ~= size(theo_mass)
     error('The number of elements in the input vectors do not match. They have to be either the same size, or lod_ngmL has to be a single value which is used for all elements');
 end
 
 lod_gL = lod_ngmL * 1e-6; 
-
 lod_mM = zeros(length(lod_gL), 1);
 
-for i=1 : length(lod_gL)
-
+for i = 1 : length(lod_gL)
     lod_mM(i) = lod_gL(i)/theo_mass(i)*1000;
-
 end
 
 end
diff --git a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
index d562f9c213..b9c379fff2 100644
--- a/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
+++ b/test/verifiedTests/dataIntegration/testMetaboTools/testCalculateLODs.m
@@ -3,50 +3,40 @@
 % Purpose:
 %     - tests the calculateLODs function
 %
-% Authors:
-%     Loic Marx, November 2018
+% Author: - Loic Marx, November 2018
 %    
-   
-
-% Save the current path
+  
+% save the current path
 currentDir = pwd;
 
-% Initialize the test
+% initialize the test
 fileDir = fileparts(which('testcalculateLODs'));
-
 cd(fileDir);
 
-% Define the inputs
+% define the inputs
 lod_ngmL = 1;
-
 theo_mass = [1, 2];
 
-% Calculate the reference value
-
+% calculate the reference value
 v_ref = 1e-3 * [1; 0.5];
 
-% Calculate the actual value by using the function
-
+% calculate the actual value by using the function
 calculateLOD = calculateLODs(theo_mass,lod_ngmL);
 
-% Compare between the calculated value and the reference value
-
+% compare the calculated value and the reference value
 assert(isequal(calculateLOD, v_ref))
 
-% Throw an error if the dimensions of both inputs are not equal
+% throw an error if the dimensions of both inputs are not equal
 lod_ngmL_unequal = [1, 2, 3];
-
 assert(verifyCobraFunctionError('calculateLODs', 'inputs', {theo_mass,lod_ngmL_unequal'}, 'testMessage', 'The number of elements in the input vectors do not match. They have to be either the same size, or lod_ngmL has to be a single value which is used for all elements'));
 
 % lod_ngmL and theo_mass are two vectors of the same size
 lod_ngmL_vector = [1, 2];
-
 v_ref_vector = 1e-3 * [1; 1];
 
-% Compare the values calculated when the inputs have the same size and the reference value
+% compare the values calculated when the inputs have the same size and the reference value
 calculateLOD_vector = calculateLODs(theo_mass,lod_ngmL_vector);
-
 assert(isequal(calculateLOD_vector, v_ref_vector));
 
-% Change the directory
+% change the directory
 cd(currentDir)

From 6c850895d8fa21f25cd1b5b5b16f6a3d2ad4dfca Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Thu, 8 Nov 2018 08:42:28 +0100
Subject: [PATCH 15/29] Removing Matlab test from 2016b and earlier

---
 test/verifiedTests/analysis/testGeometricFBA/testGeometricFBA.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/verifiedTests/analysis/testGeometricFBA/testGeometricFBA.m b/test/verifiedTests/analysis/testGeometricFBA/testGeometricFBA.m
index 19dee473b7..4361b2795c 100644
--- a/test/verifiedTests/analysis/testGeometricFBA/testGeometricFBA.m
+++ b/test/verifiedTests/analysis/testGeometricFBA/testGeometricFBA.m
@@ -26,7 +26,7 @@
 
 %When detectDeadEnds is changed according to Ronans suggestion, we need to test
 %multiple solvers.
-solverPkgs = prepareTest('needsLP', true);
+solverPkgs = prepareTest('needsLP', true, 'minimalMatlabSolverVersion',8.0);
 tol = 1e-4;
 for k = 1:length(solverPkgs.LP)
     % set the solver

From 25f3b88ad2c3b4278a93af187a302c00256175f8 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 08:25:46 +0100
Subject: [PATCH 16/29] Increase test verbosity to deterine error

---
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index fc6ecdccc7..ef11a97b54 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -340,7 +340,8 @@
                 for j3 = 1:numel(vRef)
                     if abs(vRef(j3)) < 1e-5
                         assert(abs(vRef(j3) - v(j3)) < 1e-5)
-                    else
+                    else    
+                        fprintf('%2.8f <-> %2.8f', vRef(j3), v(j3));
                         assert(abs(vRef(j3) - v(j3)) / abs(vRef(j3)) < tolPercent)
                     end
                 end

From cf4d2b006498f60a5f287466cfe3708b8bb90675 Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Fri, 9 Nov 2018 08:33:36 +0100
Subject: [PATCH 17/29] [documentation] update to tutorials submodule

---
 tutorials | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials b/tutorials
index 100b2fe0d4..21dbe32953 160000
--- a/tutorials
+++ b/tutorials
@@ -1 +1 @@
-Subproject commit 100b2fe0d4faefff88625bbb29c1d48042716bdc
+Subproject commit 21dbe32953a018ad2bb9b7ed96f5337383de73c5

From 9a00db5623e50b481cc1400925b7f93cf6ff0358 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 09:58:26 +0100
Subject: [PATCH 18/29] Cleanup before the test

---
 src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m    | 11 ++++-------
 .../SteadyCom/subroutines/SteadyComFVAgr.m            |  9 +++------
 .../analysis/testSteadyCom/testSteadyCom.m            |  7 ++++++-
 3 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m b/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m
index 3c5fcf43b3..9c327968eb 100644
--- a/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m
+++ b/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m
@@ -286,14 +286,11 @@
             kDisp = 0;
         end
     end
-    directory = strsplit(saveFVA,filesep);
-    if numel(directory) > 1
+    [folder,filename] = fileparts(saveFVA);
+    if ~isempty(folder) && ~isfolder(folder)
         % not saving in the current directory. Create the directory.
-        directory = strjoin([{pwd}, directory(1:end-1)],filesep);
-        if ~exist(directory, 'dir')
-            mkdir(directory);
-        end
-    end
+        mkdir(folder);
+    end        
     if ibm_cplex
         LPmodel = LP.Model;  % the Cplex dynamic object is not good for saving
         LPstart = LP.Start;
diff --git a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
index e10ed64e66..756ead86fb 100644
--- a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
+++ b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
@@ -279,13 +279,10 @@
 end
 % check save directory
 if ~isempty(saveFVA)
-    directory = strsplit(saveFVA,filesep);
-    if numel(directory) > 1
+    [directory,filename] = fileparts(saveFVA);
+    if ~isempty(directory) && ~isdir(directory)
         % not saving in the current directory. Check existence
-        directory = strjoin([{pwd}, directory(1:end-1)],filesep);
-        if ~exist(directory, 'dir')
-            mkdir(directory);
-        end
+        mkdir(directory);        
     end
 end
 if verbFlag
diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index ef11a97b54..26bdf40587 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -21,6 +21,11 @@
 % initialize the test
 fileDir = fileparts(which('testSteadyCom'));
 cd(fileDir);
+% Make sure, that no old data exists!
+if exist([fileDir filesep 'testSteadyComFVAsave'])
+    rmdir([fileDir filesep 'testSteadyComFVAsave'],'s');    
+end
+
 %Test for parallel toolbox
 try
     poolobj = gcp('nocreate');% create a toy model
@@ -341,7 +346,7 @@
                     if abs(vRef(j3)) < 1e-5
                         assert(abs(vRef(j3) - v(j3)) < 1e-5)
                     else    
-                        fprintf('%2.8f <-> %2.8f', vRef(j3), v(j3));
+                        fprintf('%2.8f <-> %2.8f\n', vRef(j3), v(j3));
                         assert(abs(vRef(j3) - v(j3)) / abs(vRef(j3)) < tolPercent)
                     end
                 end

From cd1afed8c3e98ea3a8c5323065c711cb5a183ed2 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 10:30:29 +0100
Subject: [PATCH 19/29] Further printout adjustments

---
 .../multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m       | 2 ++
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m     | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
index 756ead86fb..95a5c1e621 100644
--- a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
+++ b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
@@ -308,6 +308,7 @@
         % continue from previous saved file
         if ~isempty(saveFVA)
             if exist([saveFVA '.mat'], 'file')
+                fprintf('In non parallel mode found save file at %s\n', which([saveFVA '.mat']));
                 load([saveFVA '.mat'], 'i0', 'minFlux', 'maxFlux', 'minFD', 'maxFD');
                 if i0 == nRxnFVA
                     fprintf('FVA was already finished previously and saved in %s.mat.\n', saveFVA);
@@ -373,6 +374,7 @@
     if ~isempty(saveFVA)
         %check if previous results from single-thread computation exist
         if exist([saveFVA '.mat'], 'file')
+            fprintf('In parallel mode found save file at %s\n', which([saveFVA '.mat']));
             load([saveFVA '.mat'], 'i0');
             i0P = i0;
             clear i0
diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index 26bdf40587..33d7e46b48 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -489,8 +489,8 @@
             end
             % remove all created files
 
-            rmdir([pwd filesep 'testSteadyComFVAsave'], 's')
-            rmdir([pwd filesep 'testSteadyComFVAsavePar'], 's')
+            rmdir([fileDir filesep 'testSteadyComFVAsave'], 's')
+            rmdir([fileDir filesep 'testSteadyComFVAsavePar'], 's')
         else
             disp('Skipping Parallel Test, No Parallel toolbox installed');
         end

From dfde74f3251c69d26784e70a18c9efd701df03b5 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 10:30:51 +0100
Subject: [PATCH 20/29] Temporary Restrict tests

---
 test/runTestSuite.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/runTestSuite.m b/test/runTestSuite.m
index 9777003c39..c11308fd5f 100644
--- a/test/runTestSuite.m
+++ b/test/runTestSuite.m
@@ -36,7 +36,7 @@
 currentDir = cd(testDir);
 
 % get all names of test files
-testFiles = rdir(['verifiedTests' filesep '**' filesep 'test*.m']);
+testFiles = rdir(['verifiedTests' filesep '**' filesep 'testSteadyCom*.m']);
 testFileNames = {testFiles.name};
 testFileNames = testFileNames(~cellfun(@(x) isempty(regexp(x,testNames,'ONCE')),testFileNames));
 

From 52ba56680851baf5b66270415a9c45b373a1f4a9 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 10:40:55 +0100
Subject: [PATCH 21/29] Verbose cleanup

---
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index 33d7e46b48..12cef169be 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -22,7 +22,8 @@
 fileDir = fileparts(which('testSteadyCom'));
 cd(fileDir);
 % Make sure, that no old data exists!
-if exist([fileDir filesep 'testSteadyComFVAsave'])
+if isfolder([fileDir filesep 'testSteadyComFVAsave'])
+    fprintf('The save folder exists and will be deleted at %s\n', [fileDir filesep 'testSteadyComFVAsave'] );
     rmdir([fileDir filesep 'testSteadyComFVAsave'],'s');    
 end
 

From 9288e9be78c0d883f84ae3518e602fd4ef474775 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 10:44:49 +0100
Subject: [PATCH 22/29] Even more verbosity

---
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index 12cef169be..7929dd3da1 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -21,6 +21,8 @@
 % initialize the test
 fileDir = fileparts(which('testSteadyCom'));
 cd(fileDir);
+
+fprintf('The test is running in the following folder:\n%s\n',fileDir);
 % Make sure, that no old data exists!
 if isfolder([fileDir filesep 'testSteadyComFVAsave'])
     fprintf('The save folder exists and will be deleted at %s\n', [fileDir filesep 'testSteadyComFVAsave'] );

From 48057679cd3ccc3a241e55129c01c378027daac8 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 10:57:40 +0100
Subject: [PATCH 23/29] Resetting the path on the CI

---
 test/testAll.m | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/test/testAll.m b/test/testAll.m
index 3b3d20f62e..9891653b76 100644
--- a/test/testAll.m
+++ b/test/testAll.m
@@ -25,7 +25,10 @@
     else
         launchTestSuite = false;
     end
-else
+else            
+    % on the CI, always reset the path to make absolutely sure, that we test
+    % the current version
+    restoredefaultpath()
     launchTestSuite = true;
 end
 
@@ -166,7 +169,7 @@
     if launchTestSuite
         % save the userpath
         originalUserPath = path;
-
+        
         % run the tests in the subfolder verifiedTests/ recursively
         [result, resultTable] = runTestSuite();
 

From 8c0de3e71e487b82f90cc70265cb78e51201f1dd Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 11:02:43 +0100
Subject: [PATCH 24/29] Revert "Even more verbosity"

This reverts commit 9288e9be78c0d883f84ae3518e602fd4ef474775.
---
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index 7929dd3da1..12cef169be 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -21,8 +21,6 @@
 % initialize the test
 fileDir = fileparts(which('testSteadyCom'));
 cd(fileDir);
-
-fprintf('The test is running in the following folder:\n%s\n',fileDir);
 % Make sure, that no old data exists!
 if isfolder([fileDir filesep 'testSteadyComFVAsave'])
     fprintf('The save folder exists and will be deleted at %s\n', [fileDir filesep 'testSteadyComFVAsave'] );

From 09c10a96e7f6837d179270af2b6d2e4fc8f553ab Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 11:02:57 +0100
Subject: [PATCH 25/29] Revert "Verbose cleanup"

This reverts commit 52ba56680851baf5b66270415a9c45b373a1f4a9.
---
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index 12cef169be..33d7e46b48 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -22,8 +22,7 @@
 fileDir = fileparts(which('testSteadyCom'));
 cd(fileDir);
 % Make sure, that no old data exists!
-if isfolder([fileDir filesep 'testSteadyComFVAsave'])
-    fprintf('The save folder exists and will be deleted at %s\n', [fileDir filesep 'testSteadyComFVAsave'] );
+if exist([fileDir filesep 'testSteadyComFVAsave'])
     rmdir([fileDir filesep 'testSteadyComFVAsave'],'s');    
 end
 

From 458a0be607f661cb73bc9e563bc8c902b0476d85 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 11:03:09 +0100
Subject: [PATCH 26/29] Revert "Temporary Restrict tests"

This reverts commit dfde74f3251c69d26784e70a18c9efd701df03b5.
---
 test/runTestSuite.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/runTestSuite.m b/test/runTestSuite.m
index c11308fd5f..9777003c39 100644
--- a/test/runTestSuite.m
+++ b/test/runTestSuite.m
@@ -36,7 +36,7 @@
 currentDir = cd(testDir);
 
 % get all names of test files
-testFiles = rdir(['verifiedTests' filesep '**' filesep 'testSteadyCom*.m']);
+testFiles = rdir(['verifiedTests' filesep '**' filesep 'test*.m']);
 testFileNames = {testFiles.name};
 testFileNames = testFileNames(~cellfun(@(x) isempty(regexp(x,testNames,'ONCE')),testFileNames));
 

From 85d2647201eb87a454aeabc921d0a31739042845 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 11:03:19 +0100
Subject: [PATCH 27/29] Revert "Further printout adjustments"

This reverts commit cd1afed8c3e98ea3a8c5323065c711cb5a183ed2.
---
 .../multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m       | 2 --
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m     | 4 ++--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
index 95a5c1e621..756ead86fb 100644
--- a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
+++ b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
@@ -308,7 +308,6 @@
         % continue from previous saved file
         if ~isempty(saveFVA)
             if exist([saveFVA '.mat'], 'file')
-                fprintf('In non parallel mode found save file at %s\n', which([saveFVA '.mat']));
                 load([saveFVA '.mat'], 'i0', 'minFlux', 'maxFlux', 'minFD', 'maxFD');
                 if i0 == nRxnFVA
                     fprintf('FVA was already finished previously and saved in %s.mat.\n', saveFVA);
@@ -374,7 +373,6 @@
     if ~isempty(saveFVA)
         %check if previous results from single-thread computation exist
         if exist([saveFVA '.mat'], 'file')
-            fprintf('In parallel mode found save file at %s\n', which([saveFVA '.mat']));
             load([saveFVA '.mat'], 'i0');
             i0P = i0;
             clear i0
diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index 33d7e46b48..26bdf40587 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -489,8 +489,8 @@
             end
             % remove all created files
 
-            rmdir([fileDir filesep 'testSteadyComFVAsave'], 's')
-            rmdir([fileDir filesep 'testSteadyComFVAsavePar'], 's')
+            rmdir([pwd filesep 'testSteadyComFVAsave'], 's')
+            rmdir([pwd filesep 'testSteadyComFVAsavePar'], 's')
         else
             disp('Skipping Parallel Test, No Parallel toolbox installed');
         end

From 012dd59681f8dba093ee04a4418acdd208d95476 Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 11:03:28 +0100
Subject: [PATCH 28/29] Revert "Cleanup before the test"

This reverts commit 9a00db5623e50b481cc1400925b7f93cf6ff0358.
---
 src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m    | 11 +++++++----
 .../SteadyCom/subroutines/SteadyComFVAgr.m            |  9 ++++++---
 .../analysis/testSteadyCom/testSteadyCom.m            |  7 +------
 3 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m b/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m
index 9c327968eb..3c5fcf43b3 100644
--- a/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m
+++ b/src/analysis/multiSpecies/SteadyCom/SteadyComFVA.m
@@ -286,11 +286,14 @@
             kDisp = 0;
         end
     end
-    [folder,filename] = fileparts(saveFVA);
-    if ~isempty(folder) && ~isfolder(folder)
+    directory = strsplit(saveFVA,filesep);
+    if numel(directory) > 1
         % not saving in the current directory. Create the directory.
-        mkdir(folder);
-    end        
+        directory = strjoin([{pwd}, directory(1:end-1)],filesep);
+        if ~exist(directory, 'dir')
+            mkdir(directory);
+        end
+    end
     if ibm_cplex
         LPmodel = LP.Model;  % the Cplex dynamic object is not good for saving
         LPstart = LP.Start;
diff --git a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
index 756ead86fb..e10ed64e66 100644
--- a/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
+++ b/src/analysis/multiSpecies/SteadyCom/subroutines/SteadyComFVAgr.m
@@ -279,10 +279,13 @@
 end
 % check save directory
 if ~isempty(saveFVA)
-    [directory,filename] = fileparts(saveFVA);
-    if ~isempty(directory) && ~isdir(directory)
+    directory = strsplit(saveFVA,filesep);
+    if numel(directory) > 1
         % not saving in the current directory. Check existence
-        mkdir(directory);        
+        directory = strjoin([{pwd}, directory(1:end-1)],filesep);
+        if ~exist(directory, 'dir')
+            mkdir(directory);
+        end
     end
 end
 if verbFlag
diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index 26bdf40587..ef11a97b54 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -21,11 +21,6 @@
 % initialize the test
 fileDir = fileparts(which('testSteadyCom'));
 cd(fileDir);
-% Make sure, that no old data exists!
-if exist([fileDir filesep 'testSteadyComFVAsave'])
-    rmdir([fileDir filesep 'testSteadyComFVAsave'],'s');    
-end
-
 %Test for parallel toolbox
 try
     poolobj = gcp('nocreate');% create a toy model
@@ -346,7 +341,7 @@
                     if abs(vRef(j3)) < 1e-5
                         assert(abs(vRef(j3) - v(j3)) < 1e-5)
                     else    
-                        fprintf('%2.8f <-> %2.8f\n', vRef(j3), v(j3));
+                        fprintf('%2.8f <-> %2.8f', vRef(j3), v(j3));
                         assert(abs(vRef(j3) - v(j3)) / abs(vRef(j3)) < tolPercent)
                     end
                 end

From 08b1fd2fd07cceaad53d94617c9fcc50ea2e012a Mon Sep 17 00:00:00 2001
From: Thomas Pfau <thomas.pfau@uni.lu>
Date: Fri, 9 Nov 2018 11:03:35 +0100
Subject: [PATCH 29/29] Revert "Increase test verbosity to deterine error"

This reverts commit 25f3b88ad2c3b4278a93af187a302c00256175f8.
---
 test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
index ef11a97b54..fc6ecdccc7 100644
--- a/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
+++ b/test/verifiedTests/analysis/testSteadyCom/testSteadyCom.m
@@ -340,8 +340,7 @@
                 for j3 = 1:numel(vRef)
                     if abs(vRef(j3)) < 1e-5
                         assert(abs(vRef(j3) - v(j3)) < 1e-5)
-                    else    
-                        fprintf('%2.8f <-> %2.8f', vRef(j3), v(j3));
+                    else
                         assert(abs(vRef(j3) - v(j3)) / abs(vRef(j3)) < tolPercent)
                     end
                 end