Fix for links and instructions for testing warnings

Fix for gurobi - QP

Fix for gurobi variables

Fix for OS compatibility in retrieveModels

Fix for global variables

.github/guides/TESTGUIDE.md

@@ -1,6 +1,6 @@
 # Guide for writing a test
 
-Before starting to write a test on your own, it might be instructive to follow common test practices in `/test/verifiedTests`. A style guide on how to write tests is given [here](STYLEGUIDE.md).
+Before starting to write a test on your own, it might be instructive to follow common test practices in `/test/verifiedTests`. A style guide on how to write tests is given [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/STYLEGUIDE.md).
 
 ## Test if an output is correct
 
@@ -34,7 +34,7 @@ The test succeeds if the argument of `assert()` yields a `true` logical conditio
 
 ## Test if a function throws an error or warning message
 
-If you want to test whether your `function1` correctly throws an error/warning message, you can test as follows:
+If you want to test whether your `function1` correctly throws an **error** message, you can test as follows:
 ````Matlab
 % Case 5: test with 2 input and 1 output arguments (2nd input argument is of wrong dimension)
 try
@@ -43,11 +43,19 @@ catch ME
     assert(length(ME.message) > 0)
 end
 ````
+
+If you want to test whether your `function1` correctly throws a **warning** message, you can test as follows:
+````Matlab
+warning('off', 'all')
+    output1 = function1(input1, input2');
+    assert(length(lastwarn()) > 0)
+warning('on', 'all')
+````
 Note that this allows the error message to be thrown without failing the test.
 
 ## Test template
 
-A test template is readily available [here](testTemplate.m). The following sections shall be included in a test file:
+A test template is readily available [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/testTemplate.m). The following sections shall be included in a test file:
 
 #### 1. Header
 ````Matlab

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="https://raw.githubusercontent.com/laurentheirendt/cobratoolbox/simplified-doc/docs/source/_static/logo.png" height="160px"/>
+  <img src="https://raw.githubusercontent.com/opencobra/cobratoolbox/master/docs/source/_static/logo.png" height="160px"/>
 </p>
 
 The COBRA Toolbox <br> COnstraint-Based Reconstruction and Analysis Toolbox

initCobraToolbox.m

@@ -28,6 +28,11 @@ function initCobraToolbox()
     global CBTDIR;
     global SOLVERS;
     global OPT_PROB_TYPES;
+    global CBT_LP_SOLVER;
+    global CBT_MILP_SOLVER;
+    global CBT_QP_SOLVER;
+    global CBT_MIQP_SOLVER;
+    global CBT_NLP_SOLVER;
     global GUROBI_PATH;
     global ILOG_CPLEX_PATH;
     global TOMLAB_PATH;
@@ -328,11 +333,15 @@ function initCobraToolbox()
         end
     end
 
-    % set the default solver
+    % set the default solver and print out the default variables
     if ENV_VARS.printLevel
-        fprintf(' > Setting default LP solver to GLPK ... ');
+        fprintf(' > Setting default solvers ...\n');
         changeCobraSolver('glpk', 'LP');
-        fprintf('Done.\n');
+        for k = 1:length(OPT_PROB_TYPES)
+            varName = horzcat(['CBT_', OPT_PROB_TYPES{k}, '_SOLVER']);
+            fprintf(['   - ', varName, ' = \''', eval(varName), '\'';\n'])
+        end
+        fprintf('   Done.\n');
     end
 
     % print out a summary table
@@ -400,9 +409,8 @@ function initCobraToolbox()
             end
         end
     end
-
     if ENV_VARS.printLevel
-        fprintf('\n')
+        fprintf('\n');
     end
 
     % change back to the current directory

src/solvers/changeCobraSolver.m

@@ -167,7 +167,7 @@
 end
 
 % legacy support for other versions of gurobi
-if strcmp(solverName, 'gurobi') || strcmp(solverName, 'gurobi6') ||  strcmp(solverName, 'gurobi7')
+if strcmpi(solverName, 'gurobi') || strcmpi(solverName, 'gurobi6') ||  strcmpi(solverName, 'gurobi7')
     solverName = 'gurobi';
 end
 
@@ -182,7 +182,7 @@
 end
 
 % Attempt to set the user provided solver for all optimization problem types
-if (strcmp(solverType, 'ALL'))
+if strcmpi(solverType, 'all')
     for i = 1:length(OPT_PROB_TYPES)
         changeCobraSolver(solverName, OPT_PROB_TYPES{i}, 0);
     end
@@ -267,7 +267,8 @@
     case 'gurobi_mex'
         solverOK = checkSolverInstallationFile(solverName, 'gurobi_mex', printLevel);
     case 'gurobi'
-        if isunix, tmpGurobi = 'gurobi.sh', else, 'gurobi.bat', end;
+        tmpGurobi = 'gurobi.sh';
+        if ispc, tmpGurobi = 'gurobi.bat'; end
         solverOK = checkGurobiInstallation(solverName, tmpGurobi, printLevel);
     case 'mps'
         solverOK = checkSolverInstallationFile(solverName, 'BuildMPS', printLevel);
@@ -295,6 +296,9 @@
 if solverOK
     varName = horzcat(['CBT_', solverType, '_SOLVER']);
     eval([varName ' =  solverName;']);
+    if strcmpi(solverType, 'all')
+        fprintf([' > ', varName, ' has been set to ', solverName, '.\n']);
+    end
 end
 
 end

src/solvers/solveCobraMILP.m

@@ -295,7 +295,7 @@
             solStat = 3; % Other problem, but integer solution exists
         end
 
-   case 'gurobi'
+   case 'gurobi_mex'
         % Free academic licenses for the Gurobi solver can be obtained from
         % http://www.gurobi.com/html/academic.html
         %
@@ -419,7 +419,7 @@
             delete('clone1.log')
         end
 
- case {'gurobi5','gurobi6'}
+ case 'gurobi'
         %% gurobi 5
         % Free academic licenses for the Gurobi solver can be obtained from
         % http://www.gurobi.com/html/academic.html

src/solvers/solveCobraMIQP.m

@@ -3,7 +3,7 @@
 %
 % solution = solveCobraQP(MIQPproblem,solver,verbFlag,solverParams)
 %
-% % Solves problems of the type 
+% % Solves problems of the type
 %
 %      min   osense * 0.5 x' * F * x + osense * c' * x
 %      s/t   lb <= x <= ub
@@ -20,8 +20,8 @@
 %  lb               Lower bound vector
 %  ub               Upper bound vector
 %  osense           Objective sense (-1 max, +1 min)
-%  csense           Constraint senses, a string containting the constraint 
-%                   sense for each row in A ('E', equality, 'G' greater 
+%  csense           Constraint senses, a string containting the constraint
+%                   sense for each row in A ('E', equality, 'G' greater
 %                   than, 'L' less than).
 %
 %OPTIONAL INPUTS
@@ -30,7 +30,7 @@
 %
 % parameters    Structure containing optional parameters as fields.
 %  printLevel   Print level for solver
-%  saveInput    Saves LPproblem to filename specified in field. 
+%  saveInput    Saves LPproblem to filename specified in field.
 %               Setting parameters = 'default' uses default setting set in
 %               getCobraSolverParameters.
 %
@@ -49,7 +49,7 @@
 %                       0   Infeasible QP
 %                      -1   No optimal solution found (time limit etc)
 %                       3   Solution exists but with problems
-%  origStat         Original status returned by the specific solver 
+%  origStat         Original status returned by the specific solver
 %  time             Solve time in seconds
 %
 %
@@ -107,10 +107,10 @@
         tomlabProblem  = miqpAssign(osense*F, osense*c, A, b_L, b_U, lb, ub,[], ...
                              intVars, [],[],[],'CobraMIQP');
         tomlabProblem.CPLEX.LogFile = 'MIQPproblem.log';
-        
+
         %optional parameters
         PriLvl = printLevel;
-        
+
         %Save Input if selected
         if ~isempty(saveInput)
             fileName = parameters.saveInput;
@@ -123,7 +123,7 @@
         tomlabProblem.MIP.cpxControl.TILIM = timeLimit; % time limit
         tomlabProblem.MIP.cpxControl.THREADS = 1; % by default use only one thread
         Result = tomRun('cplex', tomlabProblem, PriLvl);
-        
+
         x = Result.x_k;
         f = osense*Result.f_k;
         stat = Result.Inform;
@@ -143,7 +143,7 @@
             solStat = 3; % Solution exists, but either scaling problems or not proven to be optimal
         end
             %%
-    case 'gurobi'
+    case 'gurobi_mex'
         % Free academic licenses for the Gurobi solver can be obtained from
         % http://www.gurobi.com/html/academic.html
         %
@@ -153,15 +153,15 @@
         clear opts            % Use the default parameter settings
         if printLevel == 0
            % Version v1.10 of Gurobi Mex has a minor bug. For complete silence
-           % Remove Line 736 of gurobi_mex.c: mexPrintf("\n"); 
+           % Remove Line 736 of gurobi_mex.c: mexPrintf("\n");
            opts.Display = 0;
            opts.DisplayInterval = 0;
         else
            opts.Display = 1;
         end
 
-        
-        
+
+
         if (isempty(csense))
             clear csense
             csense(1:length(b),1) = '=';
@@ -171,26 +171,26 @@
             csense(csense == 'E') = '=';
             csense = csense(:);
         end
-        
-        % Gurobi passes individual terms instead of an F matrix. qrow and 
+
+        % Gurobi passes individual terms instead of an F matrix. qrow and
         % qcol specify which variables are multipled to get each term,
         % while qval specifies the coefficients of each term.
 
         [qrow,qcol,qval]=find(F);
         qrow=qrow'-1;   % -1 because gurobi numbers indices from zero, not one.
         qcol=qcol'-1;
         qval=0.5*qval';
-        
-        opts.QP.qrow = int32(qrow); 
-        opts.QP.qcol = int32(qcol); 
+
+        opts.QP.qrow = int32(qrow);
+        opts.QP.qcol = int32(qcol);
         opts.QP.qval = qval;
         opts.Method = 0;    % 0 - primal, 1 - dual
         opts.Presolve = -1; % -1 - auto, 0 - no, 1 - conserv, 2 - aggressive
         opts.FeasibilityTol = 1e-6;
         opts.IntFeasTol = 1e-5;
         opts.OptimalityTol = 1e-6;
         %opt.Quad=1;
-        
+
         %gurobi_mex doesn't cast logicals to doubles automatically
     	c = double(c);
         [x,f,origStat,output,y] = gurobi_mex(c,osense,sparse(A),b, ...
@@ -207,13 +207,13 @@
            stat = -1; % Solution not optimal or solver problem
         end
         solStat = stat;
-    case 'gurobi5'
+    case 'gurobi'
      %% gurobi5
      % Free academic licenses for the Gurobi solver can be obtained from
         % http://www.gurobi.com/html/academic.html
         resultgurobi = struct('x',[],'objval',[],'pi',[]);
         clear params            % Use the default parameter settings
-        if printLevel == 0 
+        if printLevel == 0
             params.OutputFlag = 0;
             params.DisplayInterval = 1;
         else
@@ -226,7 +226,7 @@
         params.IntFeasTol = 1e-5;
         params.FeasibilityTol = 1e-6;
         params.OptimalityTol = 1e-6;
-        
+
         if (isempty(MIQPproblem.csense))
             clear MIQPproblem.csense
             MIQPproblem.csense(1:length(b),1) = '=';
@@ -236,13 +236,13 @@
             MIQPproblem.csense(MIQPproblem.csense == 'E') = '=';
             MIQPproblem.csense = MIQPproblem.csense(:);
         end
-	
+
         if MIQPproblem.osense == -1
             MIQPproblem.osense = 'max';
         else
             MIQPproblem.osense = 'min';
         end
-        
+
         MIQPproblem.vtype = vartype;
         MIQPproblem.Q = 0.5*sparse(MIQPproblem.F);
         MIQPproblem.modelsense = MIQPproblem.osense;
@@ -251,7 +251,7 @@
         solStat = resultgurobi.status;
         if strcmp(resultgurobi.status,'OPTIMAL')
            stat = 1; % Optimal solution found
-           
+
            if exist('resultgurobi.pi')
                [x,f,y] = deal(resultgurobi.x,resultgurobi.objval,resultgurobi.pi);
            else
@@ -276,6 +276,6 @@
 solution.obj = f;
 solution.solver = solver;
 solution.stat = solStat;
-solution.origStat = stat; 
+solution.origStat = stat;
 solution.time = t;
-solution.full = x;
+solution.full = x;