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RAVEN 2.7.0 #417

Merged
merged 60 commits into from
May 13, 2022
Merged

RAVEN 2.7.0 #417

merged 60 commits into from
May 13, 2022

Commits on Apr 11, 2022

  1. refactor: parsing of linear problem to solver

    @edkerk
    edkerk committed Apr 11, 2022
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  2. feat: prepare for glpk as alternative solver

    @edkerk
    edkerk committed Apr 11, 2022
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  3. refactor: use findRAVENroot as aux. function

    @edkerk
    edkerk committed Apr 11, 2022
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  4. feat: add GLPK binary

    @edkerk
    edkerk committed Apr 11, 2022
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  5. feat: tests for solvers and model I/O

    @edkerk
    edkerk committed Apr 11, 2022
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  6. feat: checkInstallation uses unit_tests

    @edkerk
    edkerk committed Apr 11, 2022
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  7. chore: updateDocumentation

    @edkerk
    edkerk committed Apr 11, 2022
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Commits on Apr 12, 2022

  1. fix: set solver tolerances to previous values 

    - set to values used by RAVEN before recent refactoring
    @edkerk
    edkerk committed Apr 12, 2022
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  2. feat: add fillGaps / MILP tests checkInstallation

    @edkerk
    edkerk committed Apr 12, 2022
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  3. refactor: cosmetic changes checkInstallation

    @edkerk
    edkerk committed Apr 12, 2022
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  4. refactor: distribute libSBML and force its use

    @edkerk
    edkerk committed Apr 12, 2022
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  5. fix: properly fail test if solver fails

    @edkerk
    edkerk committed Apr 12, 2022
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Commits on Apr 13, 2022

  1. fix: glpk readme

    @edkerk
    edkerk committed Apr 13, 2022
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Commits on Apr 21, 2022

  1. chore: updateDocumentation

    @edkerk
    edkerk committed Apr 21, 2022
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  2. Merge pull request #408 from SysBioChalmers/feat/glpk 

    feat: distribute glpk as free solver alternative
    @edkerk
    edkerk authored Apr 21, 2022
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  3. fix: force use of mex file in w64

    @edkerk
    edkerk committed Apr 21, 2022
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  4. Merge remote-tracking branch 'origin/devel' into feat/libSBML

    @edkerk
    edkerk committed Apr 21, 2022
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  5. chore: updateDocumentation

    @edkerk
    edkerk committed Apr 21, 2022
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Commits on Apr 22, 2022

  1. fix: test result parsing

    @mihai-sysbio
    mihai-sysbio committed Apr 22, 2022
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  2. fix: test result substring

    @mihai-sysbio
    mihai-sysbio authored Apr 22, 2022
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  3. fix: bash var in quotes 

    Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
    @mihai-sysbio @edkerk
    mihai-sysbio and edkerk authored Apr 22, 2022
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  4. fix: typo

    @mihai-sysbio
    mihai-sysbio committed Apr 22, 2022
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  5. fix: gh actions char escaping

    @mihai-sysbio
    mihai-sysbio committed Apr 22, 2022
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  6. fix: remove quotes

    @mihai-sysbio
    mihai-sysbio committed Apr 22, 2022
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  7. Merge pull request #411 from SysBioChalmers/fix/actions-comment-length 

    fix: posting results from tests via Actions
    @mihai-sysbio
    mihai-sysbio authored Apr 22, 2022
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  8. Merge remote-tracking branch 'origin/devel' into feat/libSBML

    @edkerk
    edkerk committed Apr 22, 2022
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Commits on Apr 26, 2022

  1. Merge pull request #409 from SysBioChalmers/feat/libSBML 

    feat: distribute libSBML
    @edkerk
    edkerk authored Apr 26, 2022
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Commits on Apr 29, 2022

  1. fix: ravenCobraWrapper and define test

    @edkerk
    edkerk committed Apr 29, 2022
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Commits on Apr 30, 2022

  1. chore: updateDocumentation

    @edkerk
    edkerk committed Apr 30, 2022
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  2. feat: remove unnecessary output wrap test

    @edkerk
    edkerk committed Apr 30, 2022
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  3. Merge pull request #412 from SysBioChalmers/fix/ravenCobraWrapper 

    fix: ravenCobraWrapper
    @edkerk
    edkerk authored Apr 30, 2022
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  4. fix: minor bugs

    @edkerk
    edkerk committed Apr 30, 2022
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  5. refactor: error handling and error messages

    @edkerk
    edkerk committed Apr 30, 2022
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  6. chore: updateDocumentation

    @edkerk
    edkerk committed Apr 30, 2022
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  7. Merge pull request #413 from SysBioChalmers/fix/minorBugs 

    fix: minor bugs
    @edkerk
    edkerk authored Apr 30, 2022
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  8. refactor: convert string input to char

    @edkerk
    edkerk committed Apr 30, 2022
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Commits on May 1, 2022

  1. feat: convertCharArray function 

    - all functions in this commit are tested by a unit_test
    @edkerk
    edkerk committed May 1, 2022
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  2. feat: convertCharArray without tests

    @edkerk
    edkerk committed May 1, 2022
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Commits on May 2, 2022

  1. chore: updateDocumentation

    @edkerk
    edkerk committed May 2, 2022
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Commits on May 4, 2022

  1. fix: remove dependency on stats toolbox 

    for removeBadRxns function
    @edkerk
    edkerk committed May 4, 2022
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  2. fix: setExchangeBounds not dependent on stats tlbx

    @edkerk
    edkerk committed May 4, 2022
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  3. fix: allow tolerance in modelAbilitiesTests

    @edkerk
    edkerk committed May 4, 2022
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  4. chore: updateDocumentation

    @edkerk
    edkerk committed May 4, 2022
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Commits on May 6, 2022

  1. fix: extractMiriam consistent output as cell array

    @edkerk
    edkerk committed May 6, 2022
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Commits on May 9, 2022

  1. refactor: more appropriate folder

    @edkerk
    edkerk committed May 9, 2022
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  2. doc: informative error compareMultipleModels

    @edkerk
    edkerk committed May 9, 2022
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  3. feat: exportForGit has optional cobra output

    @edkerk
    edkerk committed May 9, 2022
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  4. chore: updateDocumentation

    @edkerk
    edkerk committed May 9, 2022
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  5. fix: exportForGit text format write grRules

    @edkerk
    edkerk committed May 9, 2022
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Commits on May 12, 2022

  1. doc: informative error with txt analytics toolbox

    @edkerk
    edkerk committed May 12, 2022
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  2. refactor: correct permissions

    @edkerk
    edkerk committed May 12, 2022
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  3. Merge pull request #416 from SysBioChalmers/fix/small-fixes 

    doc: more informative warnings/errors
    @edkerk
    edkerk authored May 12, 2022
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  4. Merge branch 'fix/small-fixes' into refactor/charAndStringInput 

    # Conflicts:
#	doc/core/compareMultipleModels.html
#	doc/core/index.html
#	doc/index.html
#	doc/io/exportForGit.html
    @edkerk
    edkerk committed May 12, 2022
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  5. chore: updateDocumentation

    @edkerk
    edkerk committed May 12, 2022
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  6. doc: more informative error solver tests

    @edkerk
    edkerk committed May 12, 2022
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  7. fix: cdhitTests on mac

    @edkerk
    edkerk committed May 12, 2022
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Commits on May 13, 2022

  1. fix: prevent unnecessary output modelAbilitiesTest

    @edkerk
    edkerk committed May 13, 2022
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  2. feat: remove dependency for COBRA

    @edkerk
    edkerk committed May 13, 2022
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  3. fix: add missing end

    @edkerk
    edkerk committed May 13, 2022
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  4. Merge pull request #415 from SysBioChalmers/refactor/charAndStringInput 

    refactor: char, string and cell array input
    @edkerk
    edkerk authored May 13, 2022
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