fix: addRxns reverse field

[edkerk]

Main improvements in this PR:

• fix:
  • addRxns correctly defines rev field, only reactions that can go in both directions (LB<0 and UB>0) are reversible (solves #469)

I hereby confirm that I have:

• [x] Tested my code on my own machine
• [x] Followed the development guidelines.
• [x] Selected devel as a target branch
• [ ] 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 %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.