Closed edkerk closed 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 Error occurred in solverTests/testSoplex and it did not run to completion. %0A Error ID: %0A '' %0A Error Details: %0A Error using solverTests>testSoplex (line 79) SoPlex not installed or cannot be found, test skipped %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/testSoplex X X Errored.
Note: In the case of multiple test runs, this post will be edited.
Main improvements in this PR:
setRavenSolver
can take 'soplex' as option, which assumes a succesful SCIP installation, and thatsoplex
can be directly called in the terminal. No installation instructions yet, butcheckInstallation
tests for it.importModel
,exportModel
,exportToExcelFormat
,writeYAMLmodel
andreadYAMLmodel
) show a dialog box if no file name is specified.convertToIrrev
remove warning messagesolveLP
report the correct sign of the objective function..f
with objective value was previously inverted (maximization gives negative value). If your auxiliary code reads the.f
field coming fromsolveLP
, it should be updated!I hereby confirm that I have:
devel
as a target branch