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yeast8.4.1 #241

Merged
merged 25 commits into from
Jul 20, 2020
Merged

yeast8.4.1 #241

merged 25 commits into from
Jul 20, 2020

Commits on Jun 4, 2020

  1. fix-bug: mixed ID for MNXID and Notes 

    Which has existed in the function changerxn.m
    @feiranl
    feiranl committed Jun 4, 2020
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  2. fix: update with optimizeCbModel new output

    @feiranl
    feiranl committed Jun 4, 2020
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Commits on Jun 18, 2020

  1. fix: remove authorships in scripts 

    redundant with git blame
    @BenjaSanchez
    BenjaSanchez committed Jun 18, 2020
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Commits on Jun 19, 2020

  1. fix: update the missing BIGG IDs here in the notes part and also remo… 

    …ve the useless notes
    @feiranl
    feiranl committed Jun 19, 2020
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Commits on Jun 20, 2020

  1. Merge pull request #230 from SysBioChalmers/fix/remove-authorships 

    fix: remove authorships from scripts
    @edkerk
    edkerk authored Jun 20, 2020
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Commits on Jun 22, 2020

  1. Merge branch 'devel' into fix-MNXbug

    @BenjaSanchez
    BenjaSanchez authored Jun 22, 2020
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Commits on Jun 23, 2020

  1. Merge pull request #226 from SysBioChalmers/fix-MNXbug 

    Fix the bug for MNX rxn ID in notes field
    @BenjaSanchez
    BenjaSanchez authored Jun 23, 2020
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Commits on Jun 25, 2020

  1. doc: clarify Zenodo authorships

    @BenjaSanchez
    BenjaSanchez committed Jun 25, 2020
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  2. doc: misc releasing guidelines 

    * clarify better some sections
* use appropiate wording
* fix typo
    @BenjaSanchez
    BenjaSanchez committed Jun 25, 2020
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Commits on Jun 26, 2020

  1. Merge pull request #233 from SysBioChalmers/fix/releasing-guidelines 

    Fix/releasing guidelines
    @BenjaSanchez
    BenjaSanchez authored Jun 26, 2020
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Commits on Jul 2, 2020

  1. feat: create requirements via pip-tools 

    to easily keep track of the original requirements. Also build requirements.txt from requirements.in and adapt README accordingly.
    @BenjaSanchez
    BenjaSanchez committed Jul 2, 2020
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  2. feat: dev-requirements 

    same as user requirements but also with pip-tools
    @BenjaSanchez
    BenjaSanchez committed Jul 2, 2020
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Commits on Jul 3, 2020

  1. feat: switch to touch for creating .env 

    simplified setup
    @BenjaSanchez
    BenjaSanchez committed Jul 3, 2020
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  2. refactor: simplify dev-requirements.in 

    * don't re-list stuff
* enforce same dependencies
    @BenjaSanchez
    BenjaSanchez committed Jul 3, 2020
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  3. doc: managing python dependencies

    @BenjaSanchez
    BenjaSanchez committed Jul 3, 2020
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Commits on Jul 6, 2020

  1. Merge pull request #235 from SysBioChalmers/feat/pip-tools 

    Feat/pip tools
    @BenjaSanchez
    BenjaSanchez authored Jul 6, 2020
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Commits on Jul 15, 2020

  1. fix-rxn: change dubious metabolite name 

    - solves #201
    @edkerk
    edkerk committed Jul 15, 2020
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  2. fix-rxn: r_0241 correct cofactor 

    - as mentioned in #205
    @edkerk
    edkerk committed Jul 15, 2020
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  3. fix-rxn: r_0774 and r_0775 involve ATP hydrolysis 

    - as mentioned in #205
    @edkerk
    edkerk committed Jul 15, 2020
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  4. fix-rxn: remove incorrect gene and EC number 

    - as mentioned in #215
    @edkerk
    edkerk committed Jul 15, 2020
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Commits on Jul 16, 2020

  1. Merge pull request #237 from SysBioChalmers/fix/misc 

    fix: multiple small curations
    @edkerk
    edkerk authored Jul 16, 2020
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Commits on Jul 17, 2020

  1. doc: visualization instructions 

    caffeine & metabolic atlas
    @BenjaSanchez
    BenjaSanchez committed Jul 17, 2020
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  2. doc: correct metabolic atlas links 

    + some styling options
    @BenjaSanchez
    BenjaSanchez committed Jul 17, 2020
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  3. Merge pull request #240 from SysBioChalmers/doc/yeast-gem-viz 

    doc: visualization instructions
    @BenjaSanchez
    BenjaSanchez authored Jul 17, 2020
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  4. chore: update dependencies 

    for new release
    @BenjaSanchez
    BenjaSanchez committed Jul 17, 2020
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