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inconsistency in FBA flavour invocations #1248

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lptolik opened this issue Jul 13, 2022 · 0 comments
Open

inconsistency in FBA flavour invocations #1248

lptolik opened this issue Jul 13, 2022 · 0 comments
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enhancement good first issue This should be a good issue to start contributing to COBRApy. help-wanted An issue that should be easy to implement for anyone in the community.

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@lptolik
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lptolik commented Jul 13, 2022

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Is your feature related to a problem? Please describe it.

There are three flavours of FBA in cobra: FBA, pFBA, and geometric FBA. The plain FBA (model.optimise) has the argument raise_error to specify whether you want an exception to be raised. Neither pFBA nor geometric FBA has this argument. I think it would be nice if the invocation of all flavours of FBA would be consistent.

Describe the solution you would like.

Within all three functions pattern

m.slim_optimize(error_value=None)
solution = get_solution(m, reactions=reactions)

is used, but only in the plain FBA (model.optimise) raise_error is propagated into get_solution.

@cdiener cdiener added enhancement help-wanted An issue that should be easy to implement for anyone in the community. good first issue This should be a good issue to start contributing to COBRApy. labels Jul 20, 2022
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Labels
enhancement good first issue This should be a good issue to start contributing to COBRApy. help-wanted An issue that should be easy to implement for anyone in the community.
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