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Regular merge of develop#1456

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artenobot merged 139 commits intomasteropencobra/cobratoolbox:masterfrom developopencobra/cobratoolbox:developCopy head branch name to clipboardApr 2, 2019

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Commits on Jan 14, 2019

• added visualization for epistasis

  

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• moved testVisualizeEpistasis to verfiedTests from additionalTests

  

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• the input model is read using readCbModel rather than load function

  

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Commits on Jan 15, 2019

• Bug fixes in MMT functions, new tutorial

  

  almut-heinken

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Commits on Jan 16, 2019

• fixed the function headers of visualizeEpistasis

  

  cjos238

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• changing file permissions from 755 to 644

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• linting calculateReactionAbundance

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• linting correlateFluxWithTaxonAbundance

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• linting of createPanModels

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• linting of createMultipleSpeciesModel

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• Adding index files for doc. of visualizeEpistasis

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• minor changes for documentation generation

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• linting convertGene2PathwayInteractions

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• linting findSubsystemOfGenes

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• linting visualizePathwayInEpistasis

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• renaming test files

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• changes to test to fit overall structure

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• changes to testConvertGene2PathwayInteractions and testFindSubsystemOfGenes for loading ref data

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• Merge pull request #1417 from almut-heinken/MMTupdate

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• Merge pull request #1415 from cjos238/add-epivis

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• [documentation] adding instructions how to install gfortran

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• Merge pull request #1418 from laurentheirendt/add-gfortran

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Commits on Jan 30, 2019

• Fix broken iMAT algorithm by renaming modelCom

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Commits on Jan 31, 2019

• Merge pull request #1420 from pablormier/patch-1

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Commits on Feb 4, 2019

• added rxns as input for printFluxBounds

  

  cjos238

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Commits on Feb 13, 2019

• correction of little bugs

  lvalcarcel

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• possible old score

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• selection of KO list

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Commits on Feb 17, 2019

• Also fixing modelCom in iMAT

  

  Thomas Pfau

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Commits on Feb 21, 2019

• [documentation] update of citation

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• Merge pull request #1428 from laurentheirendt/update-cit

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• Merge pull request #1426 from tpfau/imatPatch

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• [documentation] update papers submodule

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Commits on Feb 27, 2019

• Merge pull request #1429 from laurentheirendt/update-submodules-2

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Commits on Feb 28, 2019

• repository of cobra models migration

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• updating the cobra.models repository

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• Revert "updating the cobra.models repository"

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• updating models repo

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• Rebuild commit

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Commits on Mar 4, 2019

• deploy tutorials bash script

  laurentheirendt

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• draft script of deploy tutorials

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• remove scp at end of preparetutorials

  laurentheirendt

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• change of env vars

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• script to deploy tuts

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Commits on Mar 5, 2019

• Rebuild commit v2

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Commits on Mar 6, 2019

• modifications in yml script to deploy tutorials

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• add volume and pages to citation

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• minor whitespace changes

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• update of tutorials submodule

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• change of linux path to path with env var

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• fix errors in artenolis.yml

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• change of HEAD to currentBranch after merge ff

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• fix in postMINERVArequest for unsecure connections

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Commits on Mar 7, 2019

• [artenolis] fix for codegrade badge

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• debugging env var

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• Revert "debugging env var"

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• temporary fix for testIsCompatible

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Commits on Mar 8, 2019

• Revert "fix in postMINERVArequest for unsecure connections"

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Commits on Mar 9, 2019

• change of paths to env vars for windows

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• change of env variable name for node label

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• debugging for matlab r2017b

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Commits on Mar 10, 2019

• fix for string comparison in testPrintLabeledData

  laurentheirendt

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• bug in testWriteCytoscapeEdgeAttributeTable

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• Merge pull request #1441 from laurentheirendt/artenolis

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Commits on Mar 11, 2019

• Merge pull request #1424 from lvalcarcel/rMTA_201902

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• first ROOM implementation

  lvalcarcel

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• change from optional to paramenter

  lvalcarcel

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• eliminate startsWith

  lvalcarcel

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• [documentation] update for build badges

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• update links for macos

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Commits on Mar 12, 2019

• Merge pull request #1421 from cjos238/print-rxn-fluxes

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• [documentation] change url of overall badges

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• [documentation] change of urls

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• update of codegrade location

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• fix of path for tutorials

  laurentheirendt

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• Ensure FBA is minimized where needed

  almut-heinken

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• change url of apple.png

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• change of url for art.png

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• fix of url for bug.png

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• fix of url for bulb.png

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• Merge pull request #1442 from almut-heinken/fixMinFBA

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• remove broken link

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• update url of rdir module

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• change of urls of docs dependencies

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Commits on Mar 15, 2019

• essential changes for special characters

  laurentheirendt

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• adding index files for ROOM

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• Merge pull request #1425 from lvalcarcel/ROOM_20190213

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Commits on Mar 18, 2019

• Adding ibm_cplex as MIQP solver

  

  tpfau

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  Thomas Pfau

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• Removing cplex_direct from MIQP list

  

  tpfau

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• Updates

  

  tpfau

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  Thomas Pfau

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• Fixing problems

  

  tpfau

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  Thomas Pfau

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• Fixed dimensions

  

  tpfau

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  Thomas Pfau

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• Minimal changes

  

  tpfau

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• Updates

  

  tpfau

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  Thomas Pfau

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• Fixing parenthesis

  

  tpfau

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  Thomas Pfau

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• Correcting comparison

  

  tpfau

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  Thomas Pfau

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• Adding fallback to simplex when method is auto

  

  tpfau

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  Thomas Pfau

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• Corrected solver Setting

  

  tpfau

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  Thomas Pfau

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• Also manually checking tolerance when running automatic solver selection

  

  tpfau

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• Also setting correct solver in non parallel test

  

  tpfau

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• Only test, when there is a solution

  

  tpfau

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• Switched to simplex as default method if no other method is enforced

  

  tpfau

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• Removed retries (included in setCplexParametersForProblem)

  

  tpfau

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• [documentation] Added Docu on what setCplexParam and setCplexParametersForProblem do

  

  tpfau

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• Also setting BArrier feasibility tolerances

  

  tpfau

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• Removing persistence, as it leads to non solver specific information

  

  Thomas Pfau

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• Fixing logging target for logFile =n0

  

  Thomas Pfau

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Commits on Mar 19, 2019

• Merge pull request #1408 from tpfau/cplexMIQP

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• fix for logfile output argument in setCplexParametersForProblem

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Commits on Mar 20, 2019

• [documentation] fix for urls of docs deps

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• fix url of matlabdomain dep

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• [documentation] temporarily deactivate deployment of tutorials for debugging

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• [documentation] remove temporarily tut gen

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Commits on Mar 25, 2019

• [documentation] change of location of stats

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• Revert "[documentation] remove temporarily tut gen"

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• [documentation] enable generation of tuts

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• [documentation] update url of computer

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• [documentation] update url of fire

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• [documentation] update url of greenheart

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Commits on Mar 26, 2019

• debugging only

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• change of local tmp directory for generation of doc

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Commits on Mar 27, 2019

• [documentation] fix for documentation

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• Revert "debugging only"

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Commits on Mar 29, 2019

• change of urls for certain images

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• fix urls of remaining images

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• Merge branch 'update-badges' into develop

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• fix for test

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• Merge pull request #1454 from laurentheirendt/fix-testAnalyzeGCdesign

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Commits on Apr 1, 2019

• [documentation] fix for local path of generated tutorials

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• change location of deploy tutorials script

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• Update submodule

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• Revert "Update submodule"

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• Fix columnVector to handle empty vectors properly

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• debugging

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• fix for path of tutorial pdfs

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Commits on Apr 2, 2019

• update url of zip release

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• update tutorials submodule

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• update url of submodule

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• Merge pull request #1455 from shjchan/fix_columnVector

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