feat: support for metSmiles field

[edkerk]

Main improvements in this PR:

• feat:
  • support in various functions for a model.metSmiles, which contains SMILES for each metabolite.

Note: SBML currently does not have a dedicated way to store this information, and it is not worth the effort to redefine the Excel format to add a new column. However, readYAMLmodel and writeYAMLmodel support I/O of this model field.

Requires #444 to be merged first (this PR now also includes commits from #444).

I hereby confirm that I have:

• [ ] Tested my code on my own machine
• [x] Followed the development guidelines.
• [x] Selected devel as a target branch
• [x] If needed, asked first in the Gitter chat room about this PR

[github-actions[bot]]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 Running blastPlusTests . Done blastPlusTests 
 Running cdhitTests . Done cdhitTests 
 Running checkTasksTests PASS: [Gen e[s] from a[s]] Gen e[s] from a[s] FAIL: [Gen e[s] from a[s]] Gen e[s] from a[s] . Done checkTasksTests 
 Running diamondTests . Done diamondTests 
 Running fillGapsLargeTests . 
 Error occurred in fillGapsLargeTests/testLargeCobra and it did not run to completion. 
 Error ID: 
 '' 
 Error Details: 
 Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsLargeTests>testLargeCobra (line 91) setRavenSolver('cobra'); 
 . Done fillGapsLargeTests 
 Running fillGapsSmallTests .. 
 Error occurred in fillGapsSmallTests/testSmallCobra and it did not run to completion. 
 Error ID: 
 '' 
 Error Details: 
 Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsSmallTests>testSmallCobra (line 91) setRavenSolver('cobra'); 
 . Done fillGapsSmallTests 
 Running hmmerTests . Done hmmerTests 
 Running importExportTests .... Done importExportTests 
 Running mafftTests . Done mafftTests 
 Running miriamTests . Done miriamTests 
 Running modelAbilitiesTests ......Getting minimal and maximal fluxes... 0% complete 10% completeCOMPLETE .. Done modelAbilitiesTests 
 Running modelConversionTests . Done modelConversionTests 
 Running modelCurationTests .......... ........ Done modelCurationTests 
 Running modelSortingTests .. Done modelSortingTests 
 Running solverTests ... Done solverTests 
 Running tinitTests .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 20% completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 9 rows, 18 columns and 30 nonzeros Model fingerprint: 0x3e3066cf Variable types: 15 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 7 rows and 13 columns Presolve time: 0.00s Presolved: 2 rows, 5 columns, 7 nonzeros Variable types: 3 continuous, 2 integer (2 binary) Found heuristic solution: objective -8.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: -8 No other solutions better than -8 Optimal solution found (tolerance 4.00e-04) Best objective -8.000000000000e+00, best bound -8.000000000000e+00, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 5 rows, 11 columns and 17 nonzeros Model fingerprint: 0x55fd1892 Variable types: 8 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 2e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Found heuristic solution: objective 0.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 0 Optimal solution found (tolerance 4.00e-04) Best objective 0.000000000000e+00, best bound 0.000000000000e+00, gap 0.0000% Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 20% completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 6 rows, 13 columns and 21 nonzeros Model fingerprint: 0x1e693252 Variable types: 11 continuous, 2 integer (2 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 2 rows and 5 columns Presolve time: 0.00s Presolved: 4 rows, 8 columns, 12 nonzeros Variable types: 6 continuous, 2 integer (2 binary) Found heuristic solution: objective -7.5000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: -7.5 No other solutions better than -7.5 Optimal solution found (tolerance 4.00e-04) Best objective -7.500000000000e+00, best bound -7.500000000000e+00, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 6 rows, 13 columns and 21 nonzeros Model fingerprint: 0x6f39bd61 Variable types: 10 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 3e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 6 rows and 13 columns Presolve time: 0.00s Presolve: All rows and columns removed Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 2 Optimal solution found (tolerance 4.00e-04) Best objective 2.000000000000e+00, best bound 2.000000000000e+00, gap 0.0000% .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) PASS: [Gen e[s] from a[s]] Gen e[s] from a[s] Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 25% completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 8 rows, 16 columns and 27 nonzeros Model fingerprint: 0xde347ee0 Variable types: 14 continuous, 2 integer (2 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 2 rows and 7 columns Presolve time: 0.00s Presolved: 6 rows, 9 columns, 16 nonzeros Variable types: 7 continuous, 2 integer (2 binary) Found heuristic solution: objective -8.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: -8 No other solutions better than -8 Optimal solution found (tolerance 4.00e-04) Best objective -8.000000000000e+00, best bound -8.000000000000e+00, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 3 rows, 7 columns and 11 nonzeros Model fingerprint: 0x77320562 Variable types: 6 continuous, 1 integer (1 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 5e-01] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 3 rows and 7 columns Presolve time: 0.00s Presolve: All rows and columns removed Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 0 Optimal solution found (tolerance 4.00e-04) Best objective 0.000000000000e+00, best bound 0.000000000000e+00, gap 0.0000% [Gen e[s] from a[s]] Gen e[s] from a[s]: Added 0 reaction(s), 0 reactions added in total .WARNING: "[Gen e[s] from a[s]] Gen e[s] from a[s]" could not be performed for any set of reactions . New genes added to the model: G10 G11 G5 G6 G7 G8 G9 No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001" . expRes = 2x1 cell array {'a[s] => ' } {'b[c] + c[c] <=> a[c]'} . miniModel = struct with fields: S: [2x2 double] rxns: {2x1 cell} miniModel = struct with fields: S: [2x2 double] rxns: {2x1 cell} mets: {2x1 cell} .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 20% completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 9 rows, 18 columns and 30 nonzeros Model fingerprint: 0x3e3066cf Variable types: 15 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 7 rows and 13 columns Presolve time: 0.00s Presolved: 2 rows, 5 columns, 7 nonzeros Variable types: 3 continuous, 2 integer (2 binary) Found heuristic solution: objective -8.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: -8 No other solutions better than -8 Optimal solution found (tolerance 4.00e-04) Best objective -8.000000000000e+00, best bound -8.000000000000e+00, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 5 rows, 11 columns and 17 nonzeros Model fingerprint: 0x55fd1892 Variable types: 8 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 2e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Found heuristic solution: objective 0.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 0 Optimal solution found (tolerance 4.00e-04) Best objective 0.000000000000e+00, best bound 0.000000000000e+00, gap 0.0000% Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 20% completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 6 rows, 13 columns and 21 nonzeros Model fingerprint: 0x1e693252 Variable types: 11 continuous, 2 integer (2 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 2 rows and 5 columns Presolve time: 0.00s Presolved: 4 rows, 8 columns, 12 nonzeros Variable types: 6 continuous, 2 integer (2 binary) Found heuristic solution: objective -7.5000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: -7.5 No other solutions better than -7.5 Optimal solution found (tolerance 4.00e-04) Best objective -7.500000000000e+00, best bound -7.500000000000e+00, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 6 rows, 13 columns and 21 nonzeros Model fingerprint: 0x6f39bd61 Variable types: 10 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 3e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 6 rows and 13 columns Presolve time: 0.00s Presolve: All rows and columns removed Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 2 Optimal solution found (tolerance 4.00e-04) Best objective 2.000000000000e+00, best bound 2.000000000000e+00, gap 0.0000% ans = 1 1 2 3 2 3 4 4 5 5 ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 10 rows, 19 columns and 34 nonzeros Model fingerprint: 0x060e283c Variable types: 16 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 3 rows and 10 columns Presolve time: 0.00s Presolved: 7 rows, 9 columns, 19 nonzeros Variable types: 6 continuous, 3 integer (3 binary) Found heuristic solution: objective -9.0000000 Root relaxation presolve removed 4 rows and 3 columns Root relaxation presolved: 3 rows, 7 columns, 10 nonzeros Root relaxation: objective -9.500000e+00, 3 iterations, 0.00 seconds (0.00 work units) Nodes | Current Node | Objective Bounds | Work Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time 0 0 -9.50000 0 1 -9.00000 -9.50000 5.56% - 0s H 0 0 -9.5000000 -9.50000 0.00% - 0s 0 0 -9.50000 0 1 -9.50000 -9.50000 0.00% - 0s Explored 1 nodes (3 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 2: -9.5 -9 No other solutions better than -9.5 Optimal solution found (tolerance 4.00e-04) Best objective -9.500000000000e+00, best bound -9.500000000000e+00, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 4 rows, 9 columns and 14 nonzeros Model fingerprint: 0xe9c167f1 Variable types: 7 continuous, 2 integer (2 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 2e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 4 rows and 9 columns Presolve time: 0.00s Presolve: All rows and columns removed Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 0 Optimal solution found (tolerance 4.00e-04) Best objective 0.000000000000e+00, best bound 0.000000000000e+00, gap 0.0000% ans = 1 1 2 3 2 3 4 4 5 5 ans = 1 1 2 3 2 3 4 4 5 5 ans = 1 1 2 3 2 3 4 4 5 5 ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 15 rows, 28 columns and 55 nonzeros Model fingerprint: 0xd1e5c799 Variable types: 25 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 5 rows and 17 columns Presolve time: 0.00s Presolved: 10 rows, 11 columns, 28 nonzeros Variable types: 8 continuous, 3 integer (3 binary) Found heuristic solution: objective -19.0000000 Found heuristic solution: objective -19.5000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 2: -19.5 -19 No other solutions better than -19.5 Optimal solution found (tolerance 4.00e-04) Best objective -1.950000000000e+01, best bound -1.950000000000e+01, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 4 rows, 9 columns and 14 nonzeros Model fingerprint: 0x45127102 Variable types: 7 continuous, 2 integer (2 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 2e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Found heuristic solution: objective 0.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 0 Optimal solution found (tolerance 4.00e-04) Best objective 0.000000000000e+00, best bound 0.000000000000e+00, gap 0.0000% ans = 1 1 2 3 2 3 4 4 5 5 ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 8 rows, 16 columns and 27 nonzeros Model fingerprint: 0x8219e69f Variable types: 14 continuous, 2 integer (2 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 3 rows and 8 columns Presolve time: 0.00s Presolved: 5 rows, 8 columns, 14 nonzeros Variable types: 6 continuous, 2 integer (2 binary) Found heuristic solution: objective -9.0000000 Root relaxation presolve removed 5 rows and 8 columns Root relaxation presolve: All rows and columns removed Root relaxation: objective -1.200000e+01, 0 iterations, 0.00 seconds (0.00 work units) Nodes | Current Node | Objective Bounds | Work Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time core doc external hpa INIT installation io legacy LICENSE.md pathway plotting RAVEN2.png readme README.md software solver struct_conversion testing tutorial 0 0 0 -12.0000000 -12.00000 0.00% - 0s Explored 1 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 2: -12 -9 No other solutions better than -12 Optimal solution found (tolerance 4.00e-04) Best objective -1.200000000000e+01, best bound -1.200000000000e+01, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 5 rows, 11 columns and 18 nonzeros Model fingerprint: 0x0ecc0192 Variable types: 9 continuous, 2 integer (2 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [2e+00, 3e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 5 rows and 11 columns Presolve time: 0.00s Presolve: All rows and columns removed Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 1 (of 4 available processors) Solution count 1: 2 Optimal solution found (tolerance 4.00e-04) Best objective 2.000000000000e+00, best bound 2.000000000000e+00, gap 0.0000% New genes added to the model: G11 G12 G13 G14 No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001" Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 11% completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 15 rows, 33 columns and 57 nonzeros Model fingerprint: 0xa51f415c Variable types: 27 continuous, 6 integer (6 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 5 rows and 12 columns Presolve time: 0.00s Presolved: 10 rows, 21 columns, 45 nonzeros Variable types: 15 continuous, 6 integer (6 binary) Found heuristic solution: objective -7.5000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: -7.5 No other solutions better than -7.5 Optimal solution found (tolerance 4.00e-04) Best objective -7.500000000000e+00, best bound -7.500000000000e+00, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 15 rows, 33 columns and 57 nonzeros Model fingerprint: 0x013c2686 Variable types: 26 continuous, 7 integer (7 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 3e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 6 rows and 16 columns Presolve time: 0.00s Presolved: 9 rows, 17 columns, 37 nonzeros Variable types: 11 continuous, 6 integer (6 binary) Found heuristic solution: objective 5.0000000 Root relaxation presolve removed 2 rows and 2 columns Root relaxation presolved: 7 rows, 15 columns, 33 nonzeros Root relaxation: objective 1.980000e-03, 6 iterations, 0.00 seconds (0.00 work units) Nodes | Current Node | Objective Bounds | Work Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time 0 0 0.00198 0 1 5.00000 0.00198 100% - 0s H 0 0 2.0000000 0.00198 100% - 0s 0 0 infeasible 0 2.00000 2.00000 0.00% - 0s Cutting planes: Network: 1 Explored 1 nodes (8 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 2: 2 5 Optimal solution found (tolerance 4.00e-04) Best objective 2.000000000000e+00, best bound 2.000000000000e+00, gap 0.0000% Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 11% completeCOMPLETE Step 5: Final work ans = 1 1 2 3 2 3 4 4 5 5 0 0 0 0 ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 29 rows, 53 columns and 106 nonzeros Model fingerprint: 0x05408d0e Variable types: 42 continuous, 11 integer (11 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [5e-01, 8e+00] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Found heuristic solution: objective -0.0000000 Presolve removed 6 rows and 30 columns Presolve time: 0.00s Presolved: 23 rows, 23 columns, 72 nonzeros Variable types: 12 continuous, 11 integer (11 binary) Found heuristic solution: objective -3.0000000 Root relaxation presolve removed 10 rows and 6 columns Root relaxation presolved: 13 rows, 17 columns, 52 nonzeros Root relaxation: objective -1.150000e+01, 4 iterations, 0.00 seconds (0.00 work units) Nodes | Current Node | Objective Bounds | Work Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time 0 0 -11.50000 0 2 -3.00000 -11.50000 283% - 0s H 0 0 -10.5000000 -11.50000 9.52% - 0s 0 0 -11.49890 0 1 -10.50000 -11.49890 9.51% - 0s Cutting planes: Flow cover: 2 Relax-and-lift: 1 Explored 1 nodes (7 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 3: -10.5 -3 -4.44089e-16 No other solutions better than -10.5 Optimal solution found (tolerance 4.00e-04) Best objective -1.050000000000e+01, best bound -1.050000000000e+01, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 12 rows, 27 columns and 46 nonzeros Model fingerprint: 0xde909beb Variable types: 21 continuous, 6 integer (6 binary) Coefficient statistics: Matrix range [1e+00, 1e+02] Objective range [5e-01, 3e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 3 rows and 9 columns Presolve time: 0.00s Presolved: 9 rows, 18 columns, 37 nonzeros Variable types: 12 continuous, 6 integer (6 binary) Found heuristic solution: objective 0.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: 0 Optimal solution found (tolerance 4.00e-04) Best objective 0.000000000000e+00, best bound 0.000000000000e+00, gap 0.0000% .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 20% completeCOMPLETE Step 5: Final work .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0% complete 3% complete100% completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 120 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 34 rows, 60 columns and 111 nonzeros Model fingerprint: 0x123f24e2 Variable types: 54 continuous, 6 integer (6 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [1e+00, 2e+01] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 15 rows and 36 columns Presolve time: 0.00s Presolved: 19 rows, 24 columns, 56 nonzeros Variable types: 21 continuous, 3 integer (3 binary) Found heuristic solution: objective -49.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: -49 No other solutions better than -49 Optimal solution found (tolerance 4.00e-04) Best objective -4.900000000000e+01, best bound -4.900000000000e+01, gap 0.0000% ftINIT: Running step 2 MILP detected. Set parameter Username Set parameter TimeLimit to value 5 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 14 rows, 24 columns and 48 nonzeros Model fingerprint: 0x840ee39d Variable types: 21 continuous, 3 integer (3 binary) Coefficient statistics: Matrix range [7e-01, 1e+02] Objective range [1e+00, 7e+00] Bounds range [1e-01, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 6 rows and 9 columns Presolve time: 0.00s Presolved: 8 rows, 15 columns, 31 nonzeros Variable types: 12 continuous, 3 integer (3 binary) Found heuristic solution: objective 1.0000000 Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 1: 1 Optimal solution found (tolerance 4.00e-04) Best objective 1.000000000000e+00, best bound 1.000000000000e+00, gap 0.0000% ftINIT: Running step 1 MILP detected. Set parameter Username Set parameter TimeLimit to value 10000 Set parameter FeasibilityTol to value 1e-09 Set parameter IntFeasTol to value 1e-08 Set parameter MIPGap to value 0.0004 Set parameter OptimalityTol to value 1e-09 Set parameter DisplayInterval to value 1 Set parameter Presolve to value 2 Set parameter Seed to value 1 Academic license - for non-commercial use only - expires 2023-04-20 Gurobi Optimizer version 9.5.1 build v9.5.1rc2 (linux64) Thread count: 4 physical cores, 4 logical processors, using up to 4 threads Optimize a model with 36 rows, 65 columns and 119 nonzeros Model fingerprint: 0x8706bb55 Variable types: 56 continuous, 9 integer (9 binary) Coefficient statistics: Matrix range [1e-01, 1e+02] Objective range [1e+00, 1e+01] Bounds range [1e+00, 1e+03] RHS range [0e+00, 0e+00] Presolve removed 13 rows and 34 columns Presolve time: 0.00s Presolved: 23 rows, 31 columns, 71 nonzeros Variable types: 23 continuous, 8 integer (8 binary) Found heuristic solution: objective 0.0000000 Root relaxation presolve removed 5 rows and 5 columns Root relaxation presolved: 18 rows, 26 columns, 61 nonzeros Root relaxation: objective -3.196950e+01, 9 iterations, 0.00 seconds (0.00 work units) Nodes | Current Node | Objective Bounds | Work Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time 0 0 -31.96950 0 4 0.00000 -31.96950 - - 0s H 0 0 -26.0000000 -31.96950 23.0% - 0s Cutting planes: MIR: 1 Flow cover: 2 Relax-and-lift: 1 Explored 1 nodes (9 simplex iterations) in 0.00 seconds (0.00 work units) Thread count was 4 (of 4 available processors) Solution count 2: -26 0 No other solutions better than -26 Optimal solution found (tolerance 4.00e-04) Best objective -2.600000000000e+01, best bound -2.600000000000e+01, gap 0.0000% . Done tinitTests 
 Failure Summary: Name Failed Incomplete Reason(s) 
 fillGapsLargeTests/testLargeCobra X X Errored. 
 fillGapsSmallTests/testSmallCobra X X Errored.

Note: In the case of multiple test runs, this post will be edited.