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fix: COBRA introduced a conflicting function with RAVEN #183

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BenjaSanchez opened this issue Nov 6, 2018 · 8 comments
Closed
3 tasks done

fix: COBRA introduced a conflicting function with RAVEN #183

BenjaSanchez opened this issue Nov 6, 2018 · 8 comments
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discussion Not yet settled whether change in code is required. question This issue/PR contains a question that hasn't been answered.

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@BenjaSanchez
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Description of the issue:

On the latest release of COBRA, the function removeGenes.m was introduced, which conflicts with our own removeGenes.m.

I hereby confirm that I have:

@BenjaSanchez BenjaSanchez added question This issue/PR contains a question that hasn't been answered. discussion Not yet settled whether change in code is required. labels Nov 6, 2018
@haowang-bioinfo
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@BenjaSanchez could you give examples or descriptions to clarify the conflicts between them.

@BenjaSanchez
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@Hao-Chalmers the name is the same, so if I have both toolboxes in my Matlab path and I call let's say RAVEN's removeGenes.m, COBRA's removeGenes.m might be used instead

@simas232
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simas232 commented Nov 6, 2018

Should we ask COBRA developers to change the function name from their side? This function was introduced in RAVEN earlier than in COBRA, so I think we have a right to ask them so. The similar case was with mergeModels one year ago, @Hao-Chalmers asked them for function renaming in COBRA and they did that.

@haowang-bioinfo
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Yes, I did that before for another function mergeModels.m. And this probably need to be done again.

But it seems this issue should be addressed to COBRA, instead of RAVEN.

@tpfau
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tpfau commented Nov 6, 2018

One more reason to get #184 running :)
Sorry for that I'll have a look how I can rename this function.

@BenjaSanchez
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@Hao-Chalmers @simas232 thanks for the feedback, I was not sure where to raise the issue.

@tpfau thanks for the quick fix in opencobra/cobratoolbox#1373

@laurentheirendt
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This is now fixed on the develop branch of the COBRA Toolbox. Thanks @BenjaSanchez for reporting and @tpfau for fixing! 👍

@haowang-bioinfo
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@laurentheirendt @tpfau thanks for the swift fixing. I think this issue has been nicely resolved.

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