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implement get_defaults(mdl::SBML.Model) method #18

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paulflang
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I am trying to modify the kwargs in ReactionSystem and ODESystem, but it does not work. It actually feels a bit fishy to do this. Any suggestions on style/how to get this work?

@paulflang paulflang marked this pull request as draft July 20, 2021 14:59
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paulflang commented Jul 20, 2021

also, we need the commits in #16 for this to work. @anandijain can you please comment there or here why you reverted #16 ?

@anandijain anandijain mentioned this pull request Jul 20, 2021
@anandijain anandijain closed this Jul 20, 2021
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there is no need for a get_defaults(::Model) particularly in this repo. we want to keep this as much of a shim package as possible

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I disagree. Our package is to import SBML. It is very basic functionality to extract the ReactionSystem, u0map and paramap and thus dafaults separately from the file. In my opinion there is no better place to put these functions than SBMLToolkit. get_u0map, get_paramap and get_defaults are MTK specific, so they definitely don't belong in SBML.jl. They also don't belong in MTK, cause they extract from SBML.Model.

@paulflang paulflang reopened this Jul 20, 2021
@anandijain anandijain closed this Jul 20, 2021
@paulflang paulflang deleted the pl-pass_defaults_to_odesys branch June 17, 2022 12:16
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2 participants