refactored parameters gurobi and mosek

Author: rmtfleming

initCobraToolbox.m

@@ -16,11 +16,8 @@ function initCobraToolbox(updateToolbox)
 %
 %     initCobraToolbox
 %           -or-
-%     changeCobraSolver('gurobi');
-%     changeCobraSolver('gurobi', 'MILP');
-%     changeCobraSolver('tomlab_cplex', 'QP');
-%     changeCobraSolver('tomlab_cplex', 'MIQP');
-%     changeCbMapOutput('svg');
+%     changeCobraSolver('gurobi','all');
+%     changeCobraSolver('mosek', 'CLP');
 %
 %     Maintained by Ronan M.T. Fleming
 
@@ -362,18 +359,7 @@ function initCobraToolbox(updateToolbox)
 % requires the solver compatibility to be re-read at each initialisation
 clear isCompatible
 
-%These default tolerances are based on the default values for the Gurobi LP
-%solver. Do not change them without first consulting with other developers.
-%https://www.gurobi.com/documentation/9.0/refman/parameters.html
-% (primal) feasibility tolerance
-changeCobraSolverParams('LP', 'feasTol', 1e-6);
-% (dual) optimality tolerance
-changeCobraSolverParams('LP', 'optTol', 1e-6);
 
-% (primal) feasibility tolerance
-changeCobraSolverParams('EP', 'feasTol', 1e-8);
-% (dual) optimality tolerance
-changeCobraSolverParams('EP', 'optTol', 1e-12);
 
 % Check that SBML toolbox is installed and accessible
 if ~exist('TranslateSBML', 'file')
@@ -409,10 +395,8 @@ function initCobraToolbox(updateToolbox)
 %Define a set of "use first" solvers, other supported solvers will also be added to the struct.
 %This allows to assign them in any order but keep the most commonly used ones on top of the struct.
 SOLVERS = struct('gurobi',struct(),...
-    'ibm_cplex',struct(),...
-    'tomlab_cplex',struct(),...
-    'glpk',struct(),...
     'mosek',struct(),...
+    'glpk',struct(),...
     'matlab',struct());
 
 % active support - supported solvers
@@ -423,25 +407,24 @@ function initCobraToolbox(updateToolbox)
 SOLVERS.quadMinos.type = {'LP'};
 SOLVERS.dqqMinos.type = {'LP','QP'};
 SOLVERS.matlab.type = {'LP', 'NLP'};
-% active support of cplex interfaces - supported solvers
-SOLVERS.cplex_direct.type = {'LP', 'MILP', 'QP'};
-SOLVERS.ibm_cplex.type = {'LP', 'MILP', 'QP', 'MIQP'};
-SOLVERS.cplexlp.type = {'LP'};
-SOLVERS.tomlab_cplex.type = {'LP', 'MILP', 'QP', 'MIQP'};
+
 
 % passive support - solver interfaces
 SOLVERS.qpng.type = {'QP'};
 SOLVERS.tomlab_snopt.type = {'NLP'};
 
 % legacy solvers
+SOLVERS.cplex_direct.type = {'LP', 'MILP', 'QP'};
+SOLVERS.ibm_cplex.type = {'LP', 'MILP', 'QP', 'MIQP'};
+SOLVERS.cplexlp.type = {'LP'};
+SOLVERS.tomlab_cplex.type = {'LP', 'MILP', 'QP', 'MIQP'};
 %SOLVERS.gurobi_mex.type = {'LP', 'MILP', 'QP', 'MIQP'};
 %SOLVERS.lindo_old.type = {'LP'};
 %SOLVERS.lindo_legacy.type = {'LP'};
 SOLVERS.lp_solve.type = {'LP'};
 %SOLVERS.opti.type = {'LP', 'MILP', 'QP', 'MIQP', 'NLP'};
 
 % definition of category of solvers with active support
-
 SOLVERS.dqqMinos.categ = 'active';
 SOLVERS.glpk.categ = 'active';
 SOLVERS.gurobi.categ = 'active';
@@ -450,11 +433,6 @@ function initCobraToolbox(updateToolbox)
 SOLVERS.pdco.categ = 'active';
 SOLVERS.quadMinos.categ = 'active';
 
-SOLVERS.cplex_direct.categ = 'active';
-SOLVERS.ibm_cplex.categ = 'active';
-SOLVERS.cplexlp.categ = 'active';
-SOLVERS.tomlab_cplex.categ = 'active';
-
 % definition of category of solvers with passive support
 SOLVERS.qpng.categ = 'passive';
 SOLVERS.tomlab_snopt.categ = 'passive';
@@ -464,6 +442,10 @@ function initCobraToolbox(updateToolbox)
 %SOLVERS.lindo_old.categ = 'legacy';
 %SOLVERS.lindo_legacy.categ = 'legacy';
 SOLVERS.lp_solve.categ = 'legacy';
+SOLVERS.cplex_direct.categ = 'legacy';
+SOLVERS.ibm_cplex.categ = 'legacy';
+SOLVERS.cplexlp.categ = 'legacy';
+SOLVERS.tomlab_cplex.categ = 'legacy';
 %SOLVERS.opti.categ = 'legacy';
 
 % definition of categories of solvers
@@ -484,17 +466,19 @@ function initCobraToolbox(updateToolbox)
     end
 end
 
-% check the installation of the solver
+supportedSolversNames = setdiff(supportedSolversNames,{'cplex_direct','ibm_cplex','cplexlp','tomlab_cplex'});
+
+% check the installation of the solver - except cplex
 for i = 1:length(supportedSolversNames)
     if 0 %set to 1 to debug a new solver
         disp(supportedSolversNames{i})
-        if strcmp(supportedSolversNames{i},'quadMinos')
-            pause(0.1)
+        if strcmp(supportedSolversNames{i},'quadMinos') 
+            disp(supportedSolversNames{i})
         end
     end
     %We will validate all solvers in init. After this, all solvers are
     %checked, whether they actually work and the SOLVERS field is set.
-    [solverOK,solverInstalled] = changeCobraSolver(supportedSolversNames{i},SOLVERS.(supportedSolversNames{i}).type{1},0, 2);
+    [solverOK,solverInstalled] = changeCobraSolver(supportedSolversNames{i},SOLVERS.(supportedSolversNames{i}).type{1},0, 1);
     if strcmp(supportedSolversNames{i},'gurobi') && 0%use fordebugging
         disp(supportedSolversNames{i});
     end
@@ -667,7 +651,6 @@ function initCobraToolbox(updateToolbox)
 
 % use Gurobi (if installed) as the default solver for LP, QP and MILP problems
 changeCobraSolver('gurobi', 'ALL', 0);
-%changeCobraSolver('ibm_cplex', 'QP', 0); %until problem with gurobi QP sorted
 
 % check if a new update exists
 if installedGit && ENV_VARS.printLevel && status_curl == 0 && contains(result_curl, ' 200') && updateToolbox