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SysBioChalmers / RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
http://sysbiochalmers.github.io/RAVEN/
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fix: Made the int tolerance less sensitive in ftINIT - there was a pr… #463

Closed johan-gson closed 1 year ago

johan-gson commented 1 year ago

Main improvements in this PR:

Fixed a problem with ftINIT if the user is using Gurobi v. 10. This version of Gurobi is more sensitive to having low int tolerances, so it was increased slightly. The test cases did not pass otherwise. I have been in contact with Gurobi about this.

github-actions[bot] commented 1 year ago

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

 Running blastPlusTests . Done blastPlusTests %0A Running cdhitTests . Done cdhitTests %0A 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 %0A Running diamondTests . Done diamondTests %0A Running fillGapsLargeTests . %0A Error occurred in fillGapsLargeTests/testLargeCobra and it did not run to completion. %0A Error ID: %0A '' %0A Error Details: %0A Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsLargeTests>testLargeCobra (line 91) setRavenSolver('cobra'); %0A . Done fillGapsLargeTests %0A Running fillGapsSmallTests .. %0A Error occurred in fillGapsSmallTests/testSmallCobra and it did not run to completion. %0A Error ID: %0A '' %0A Error Details: %0A Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsSmallTests>testSmallCobra (line 91) setRavenSolver('cobra'); %0A . Done fillGapsSmallTests %0A Running hmmerTests . Done hmmerTests %0A Running importExportTests .... Done importExportTests %0A Running mafftTests . Done mafftTests %0A Running miriamTests . Done miriamTests %0A Running modelAbilitiesTests ......Getting minimal and maximal fluxes... 0%25 complete 10%25 completeCOMPLETE .. Done modelAbilitiesTests %0A Running modelConversionTests . Done modelConversionTests %0A Running modelCurationTests .......... ........ Done modelCurationTests %0A Running modelSortingTests .. Done modelSortingTests %0A Running solverTests .. %0A Verification failed in solverTests/testCobra. %0A Framework Diagnostic: %0A verifyEqual failed. --> Path to failure: <Value>.rCost --> The numeric values are not equal using "isequaln". --> The error was not within absolute tolerance. --> Failure table: Index Actual Expected Error RelativeError AbsoluteTolerance %0A %0A %0A %0A %0A %0A 22 0.0611098309167365 -0.0611098309167366 0.122219661833473 -2 0.1 26 0.0916647463751048 -0.0916647463751048 0.18332949275021 -2 0.1 28 0.0916647463751048 -0.0916647463751048 0.18332949275021 -2 0.1 29 0.0700216812587606 -0.0700216812587606 0.140043362517521 -2 0.1 30 0.0687485597813286 -0.0687485597813286 0.137497119562657 -2 0.1 39 0.0521979805747125 -0.0521979805747125 0.104395961149425 -2 0.1 Actual double: 95x1 double Expected double: 95x1 double Actual Value: struct with fields: x: [95x1 double] f: -0.873921506968430 stat: 1 msg: 'Optimal solution found' sPrice: [72x1 double] rCost: [95x1 double] Expected Value: struct with fields: x: [95x1 double] f: -0.873921506968430 stat: 1 msg: 'Optimal solution found' sPrice: [72x1 double] rCost: [95x1 double] %0A Stack Information: %0A In /home/m/actions-runner/_work/RAVEN/RAVEN/testing/unit_tests/solverTests.m (testCobra) at 113 %0A . Done solverTests %0A 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%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. 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%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. .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%25 complete 25%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. [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" ...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%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. 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%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. 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%25 complete 11%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. 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%25 complete 11%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. .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%25 complete 20%25 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%25 complete 3%25 complete100%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. . Done tinitTests %0A Failure Summary: Name Failed Incomplete Reason(s) %0A fillGapsLargeTests/testLargeCobra X X Errored. %0A fillGapsSmallTests/testSmallCobra X X Errored. %0A solverTests/testCobra X Failed by verification.

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