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fix: various minor fixes #530

Merged
merged 23 commits into from
Apr 26, 2024
Merged

fix: various minor fixes #530

merged 23 commits into from
Apr 26, 2024

Commits on Feb 26, 2024

  1. fix: simplifyModel w/ backwards-only irrev rxns

    @edkerk
    edkerk committed Feb 26, 2024
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Commits on Mar 8, 2024

  1. fix: writeYAMLmodel do not write empty lines

    @edkerk
    edkerk committed Mar 8, 2024
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  2. fix: getModelFromKEGG essential fields

    @edkerk
    edkerk committed Mar 8, 2024
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  3. feat: printFluxes better error with empty fluxes

    @edkerk
    edkerk committed Mar 8, 2024
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  4. fix: getGenesFromGrRules if '|' in gene

    @edkerk
    edkerk committed Mar 8, 2024
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Commits on Mar 11, 2024

  1. fix: getGenesFromGrRules correct earlier fix

    @edkerk
    edkerk committed Mar 11, 2024
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Commits on Mar 14, 2024

  1. fix: getModelFromHomology remove geneFrom field

    @edkerk
    edkerk committed Mar 14, 2024
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  2. refactor: reduce default verbosity

    @edkerk
    edkerk committed Mar 14, 2024
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  3. fix: writeYAMLmodel allow empty id and name fields

    @edkerk
    edkerk committed Mar 14, 2024
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  4. doc: updateDocumentation

    @edkerk
    edkerk committed Mar 14, 2024
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  5. fix: ravenCobraWrapper prefers to use grRules

    @edkerk
    edkerk committed Mar 14, 2024
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Commits on Mar 27, 2024

  1. feat: optimizeProb error solving milp with glpk

    @edkerk
    edkerk committed Mar 27, 2024
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  2. fix: adjust tests to separate solvers

    @edkerk
    edkerk committed Mar 27, 2024
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Commits on Mar 28, 2024

  1. fix: writeYAMLmodel error if dir does not exist

    @edkerk
    edkerk committed Mar 28, 2024
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Commits on Apr 11, 2024

  1. feat: parallel randomSampling 

    and new progressbar2
    @edkerk
    edkerk committed Apr 11, 2024
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  2. feat: setParam has 'unc' as option 

    for unconstrained reactions
    @edkerk
    edkerk committed Apr 11, 2024
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  3. feat: parallelPoolRAVEN handles parallelization

    @edkerk
    edkerk committed Apr 11, 2024
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  4. feat: use alternative ProgressBar function 

    works both when parfor is run in parallel or in serial, without any further changes to the code
    @edkerk
    edkerk committed Apr 11, 2024
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Commits on Apr 25, 2024

  1. refactor: predictLocalization builtin randsample

    @edkerk
    edkerk committed Apr 25, 2024
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Commits on Apr 26, 2024

  1. fix: mapCompartments correct horizontal concatenation 

    also updated documentation
    @simas232
    simas232 committed Apr 26, 2024
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  2. feat: give execution rights in Terminal for new RAVEN functions

    @simas232
    simas232 committed Apr 26, 2024
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  3. doc: update GLPK readme file

    @simas232
    simas232 committed Apr 26, 2024
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  4. feat: add GLPK compatibility with Apple Silicon

    @simas232
    simas232 committed Apr 26, 2024
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