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fix: remove dash from model ID while exporting to SMBL format #167

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merged 5 commits into from
Apr 22, 2020

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JonathanRob
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@JonathanRob JonathanRob commented Apr 20, 2020

The dash in the model ID Human-GEM causes problems with SBML I/O, so this fix removes the dash (HumanGEM) in only the SBML file. The model ID will remain as Human-GEM everywhere else.

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  • Selected devel as a target branch

dash causes problems when exporting to SBML
@JonathanRob JonathanRob changed the base branch from master to devel April 20, 2020 13:11
@JonathanRob JonathanRob reopened this Apr 21, 2020
@mihai-sysbio
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Nice fix! Would it make sense to also rename the .yml file to Human-GEM.yml?

@JonathanRob
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@mihai-sysbio Yes, it would probably be a good idea to change the model filenames as well to be consistent. We just need to make sure that the names of all other model versions (.xml, .mat, etc.) and all functions reading/writing these files are also updated.

@haowang-bioinfo
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yes, we could add a project "Aligning model filenames with ID of repo and model" to coordinate efforts toward this goal, probably through multiple commits/PRs.

@haowang-bioinfo haowang-bioinfo changed the title fix: remove dash from Human-GEM in short_name field fix: remove dash from model ID while exporting to SMBL format Apr 22, 2020
@haowang-bioinfo haowang-bioinfo merged commit 9752326 into devel Apr 22, 2020
@JonathanRob
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@Hao-Chalmers I think creating an issue is sufficient, it's not a big enough change to be considered a "project."

@haowang-bioinfo haowang-bioinfo deleted the fix/model_id branch April 22, 2020 09:18
@haowang-bioinfo haowang-bioinfo mentioned this pull request Apr 24, 2020
migp11 added a commit to bsc-life/Human-GEM that referenced this pull request May 10, 2024
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3 participants