fix: various minor fixes #530

edkerk · 2024-02-26T15:47:57Z

Main improvements in this PR:

fix:
- simplifyModel with irreversible backwards-only reactions (solves bug: simplifyModel with irreversible backwards-only reactions #529)
- writeYAMLmodel do not write lines with empty entries (e.g. reactions without subsystems)
- getModelFromKEGG includes model.annotation.defaultLB and model.annotation.defaultUB fields
- getGenesFromGrRules can handle genes with '|'
- getModelFromHomology remove geneFrom field (solves Error in getModelFromHomology function #533)
- getMinNrFluxes reduce default verbosity
- writeYAMLmodel allow empty id and name fields, in line with https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure
- ravenCobraWrapper prefers to use grRules in COBRA models if present (solves GECKO issue #367)
- optimizeProb will throw error when trying to solve MILP with glpk (also if glpk is set via cobra)
- writeYAMLmodel will throw an informative error if it cannot write the file to the intended directory
- mapCompartments correct horizontal concatenation of cell array
feat:
- randomSampling can run in parallel with MATLAB Parallel Computing Toolbox installed
- setParam has an additional option, 'unc' if a reaction's lower and upper bound should be set as unconstrained. If available, this will use the default bounds in model.annotation (otherwise [-1000, 1000]), and considers reversibility (in which case lower bound = 0)
- auxiliary parallelPoolRAVEN function to check if function should be running in parallel
- use alternative ProgressBar, particularly in functions containing parfor calls
- give execution rights in Terminal for new RAVEN functions

Instructions on merging this PR:

This PR has develop as target branch, and will be resolved with a squash-merge.
This PR has main as target branch, and will be resolved with a merge commit.

github-actions · 2024-02-26T15:51:23Z

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

 > Installing from location             /home/m/actions-runner/_work/RAVEN/RAVEN
 > Checking RAVEN release               DEVELOPMENT
 > Checking MATLAB release              2020b
 > Checking system architecture         glnxa64
 > Set RAVEN in MATLAB path             Pass
 > Save MATLAB path                     Pass
   > Make binaries executable           Pass

 > Add Java paths for Excel format      Pass
 > Checking libSBML version             5.19.0
 > Checking model import and export
   > Import Excel format                Pass
   > Export Excel format                Pass
   > Import SBML format                 Pass
   > Export SBML format                 Pass

 > Checking for LP solvers
   > glpk                               Pass
   > gurobi                             Fail
   > scip                               Fail
   > cobra                              Pass
 > Set RAVEN solver                     glpk

 > Checking BLAST+                      Pass
 > Checking DIAMOND                     Pass
 > Checking HMMER                       Pass

 > Checking function uniqueness         Pass

*** checkInstallation complete ***

Running blastPlusTests
.
Done blastPlusTests

Running cdhitTests
.
Done cdhitTests

Running checkTasksTests
.
Done checkTasksTests

Running diamondTests
.
Done diamondTests

Running fillGapsLargeTests

Error occurred in fillGapsLargeTests/testLargeGurobi and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using fillGapsLargeTests>testLargeGurobi (line 32)
    Solver not working
.
Error occurred in fillGapsLargeTests/testLargeSCIP and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using setRavenSolver (line 35)
    SCIP not found. RAVEN only provides the precompiled SCIP MEX binary for Windows. Instructions on how to compile the SCIP MEX file are found at
    https://github.com/scipopt/MatlabSCIPInterface
    
    Error in fillGapsLargeTests>testLargeSCIP (line 56)
    setRavenSolver('scip');
.
Done fillGapsLargeTests

Running fillGapsSmallTests

Error occurred in fillGapsSmallTests/testSmallSCIP and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using setRavenSolver (line 35)
    SCIP not found. RAVEN only provides the precompiled SCIP MEX binary for Windows. Instructions on how to compile the SCIP MEX file are found at
    https://github.com/scipopt/MatlabSCIPInterface
    
    Error in fillGapsSmallTests>testSmallSCIP (line 16)
    setRavenSolver('scip');
.
Error occurred in fillGapsSmallTests/testSmallGurobi and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using fillGapsSmallTests>testSmallGurobi (line 67)
    Solver not working
.
Done fillGapsSmallTests

Running hmmerTests
.
Done hmmerTests

Running importExportTests
....
Done importExportTests

Running mafftTests
.
Done mafftTests

Running miriamTests
.
Done miriamTests

Running modelAbilitiesTests
........
Done modelAbilitiesTests

Running modelConversionTests
.
Done modelConversionTests

Running modelCurationTests
.......... ........
Done modelCurationTests

Running modelSortingTests
..
Done modelSortingTests

Running solverTests
.
Error occurred in solverTests/testGurobi and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using solverTests>testGurobi (line 60)
    Solver not working
.
Error occurred in solverTests/testSCIP and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using solverTests>testSCIP (line 77)
    SCIP MEX binary not installed or not functional, test skipped
..
Done solverTests

Running tinitTests
.
Error occurred in tinitTests/testftINIT_T0001 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0001 (line 237)
        [~,tst1ResModel1] = evalc('ftINIT(prepDataTest1,arrayData1.tissues{1},[],[],arrayData1,[],getINITSteps(),true,true,testParams,false);');
.
Error occurred in tinitTests/testftINIT_T0002 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0002 (line 277)
        [~,tst1ResModel1] = evalc('ftINIT(prepDataTest1,arrayData1.tissues{1},[],[],arrayData1,[],getINITSteps(),true,true,testParams,false);');
.....
Error occurred in tinitTests/testftINIT_T0008 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0008 (line 377)
        [~,tst1ResModel1] = evalc('ftINIT(prepDataTest1,arrayData1.tissues{1},[],[],arrayData1,[],getINITSteps(),true,true,testParams,false);');
..
Error occurred in tinitTests/testftINIT_T0050 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0050 (line 543)
        [~,mres] = evalc('ftINIT(prepDataL,arrayDataL.tissues{1},[],[],arrayDataL,[],getINITSteps(),true,true,testParams,false);');
.
Done tinitTests

Failure Summary:

     Name                                Failed  Incomplete  Reason(s)
    ===================================================================
     fillGapsLargeTests/testLargeGurobi    X         X       Errored.
    -------------------------------------------------------------------
     fillGapsLargeTests/testLargeSCIP      X         X       Errored.
    -------------------------------------------------------------------
     fillGapsSmallTests/testSmallSCIP      X         X       Errored.
    -------------------------------------------------------------------
     fillGapsSmallTests/testSmallGurobi    X         X       Errored.
    -------------------------------------------------------------------
     solverTests/testGurobi                X         X       Errored.
    -------------------------------------------------------------------
     solverTests/testSCIP                  X         X       Errored.
    -------------------------------------------------------------------
     tinitTests/testftINIT_T0001           X         X       Errored.
    -------------------------------------------------------------------
     tinitTests/testftINIT_T0002           X         X       Errored.
    -------------------------------------------------------------------
     tinitTests/testftINIT_T0008           X         X       Errored.
    -------------------------------------------------------------------
     tinitTests/testftINIT_T0050           X         X       Errored.

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

and new progressbar2

for unconstrained reactions

works both when parfor is run in parallel or in serial, without any further changes to the code

also updated documentation

edkerk · 2024-04-26T11:43:33Z

Failing tests is likely due to invalid gurobi license on the CI server.

fix: simplifyModel w/ backwards-only irrev rxns fix: writeYAMLmodel do not write empty lines fix: getModelFromKEGG essential fields feat: printFluxes better error with empty fluxes fix: getGenesFromGrRules if '|' in gene fix: getGenesFromGrRules correct earlier fix fix: getModelFromHomology remove geneFrom field refactor: reduce default verbosity fix: writeYAMLmodel allow empty id and name fields doc: updateDocumentation fix: ravenCobraWrapper prefers to use grRules feat: optimizeProb error solving milp with glpk fix: adjust tests to separate solvers fix: writeYAMLmodel error if dir does not exist feat: parallel randomSampling and new progressbar2 feat: setParam has 'unc' as option for unconstrained reactions feat: parallelPoolRAVEN handles parallelization feat: use alternative ProgressBar function works both when parfor is run in parallel or in serial, without any further changes to the code refactor: predictLocalization builtin randsample fix: mapCompartments correct horizontal concatenation also updated documentation feat: give execution rights in Terminal for new RAVEN functions doc: update GLPK readme file feat: add GLPK compatibility with Apple Silicon

fix: simplifyModel w/ backwards-only irrev rxns

acd91f1

edkerk added 4 commits March 9, 2024 00:36

fix: writeYAMLmodel do not write empty lines

ee42300

fix: getModelFromKEGG essential fields

acd3cd0

feat: printFluxes better error with empty fluxes

42c809d

fix: getGenesFromGrRules if '|' in gene

3c078ab

edkerk changed the title ~~fix: simplifyModel w/ backwards-only irrev rxns~~ fix: various minor fixes Mar 8, 2024

edkerk added 7 commits March 12, 2024 00:05

fix: getGenesFromGrRules correct earlier fix

4d7853d

fix: getModelFromHomology remove geneFrom field

48ff147

refactor: reduce default verbosity

ff086b4

fix: writeYAMLmodel allow empty id and name fields

4f4354a

doc: updateDocumentation

2966725

fix: ravenCobraWrapper prefers to use grRules

f8b0c44

feat: optimizeProb error solving milp with glpk

10d0055

edkerk marked this pull request as draft March 27, 2024 16:06

fix: adjust tests to separate solvers

9421480

edkerk marked this pull request as ready for review March 27, 2024 17:41

edkerk added 3 commits March 28, 2024 09:53

fix: writeYAMLmodel error if dir does not exist

3ce4fd8

feat: parallel randomSampling

027b433

and new progressbar2

feat: setParam has 'unc' as option

70fe6d6

for unconstrained reactions

edkerk force-pushed the fix/simplifyModel branch from a41925b to 6d30204 Compare April 11, 2024 18:09

feat: parallelPoolRAVEN handles parallelization

f2b4a23

edkerk force-pushed the fix/simplifyModel branch from 6d30204 to 62c47f6 Compare April 11, 2024 20:06

feat: use alternative ProgressBar function

8918962

works both when parfor is run in parallel or in serial, without any further changes to the code

edkerk force-pushed the fix/simplifyModel branch from 62c47f6 to 8918962 Compare April 11, 2024 20:14

edkerk requested a review from simas232 April 12, 2024 08:42

edkerk and others added 4 commits April 25, 2024 16:52

refactor: predictLocalization builtin randsample

f2c8278

fix: mapCompartments correct horizontal concatenation

5af66b4

also updated documentation

feat: give execution rights in Terminal for new RAVEN functions

b2ded2e

doc: update GLPK readme file

5f723c7

feat: add GLPK compatibility with Apple Silicon

9bc343f

simas232 approved these changes Apr 26, 2024

View reviewed changes

edkerk merged commit 321a6f5 into develop Apr 26, 2024
1 check passed

edkerk deleted the fix/simplifyModel branch April 26, 2024 11:44

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fix: various minor fixes #530

fix: various minor fixes #530

edkerk commented Feb 26, 2024 •

edited by simas232

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github-actions bot commented Feb 26, 2024 •

edited

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edkerk commented Apr 26, 2024

fix: various minor fixes #530

fix: various minor fixes #530

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edkerk commented Feb 26, 2024 • edited by simas232 Loading

Main improvements in this PR:

Instructions on merging this PR:

github-actions bot commented Feb 26, 2024 • edited Loading

edkerk commented Apr 26, 2024

edkerk commented Feb 26, 2024 •

edited by simas232

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github-actions bot commented Feb 26, 2024 •

edited

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