Automatic file loading about cobrexa.jl HOT 7 CLOSED

The thing I'd do is to have the types that depend on each other in a single file (together with the accessors), and put the rest of the stuff (prettyprinting etc.) to another directory so that the file isn't huge.

I've got this on the list of things to make nicer; aReaction seems just wrong. 😁

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I don't mind ... the idea was to keep maintenance low (not have to maintain the list of file names), but if it introduces other inconveniences, I am fine with changing.

The only question I have is why does the order matter so much when including the files?

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@exaexa's solution would solve my issue, but I still prefer the super obvious: file-name == everything-to-do-with-that-struct "convention" I have currently. Otherwise a person new to the repo might have to go hunting for where a function is defined (I think?). However, this can quickly become murky because some functions use more than one struct, so it is debatable where they should go... At the moment each CobraTools originating file in the folder "types" only contains the really basic functions one would need for that type.

@laurentheirendt so in my case the order matters because I use Reaction in CobraModel but the file containing the definition of Reaction is alphabetically after the file containing the definition for CobraModel. This causes Julia to error when loading the package. I'm not sure if the way I am doing it is wrong though (from a style pov)?

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the main technical problem is that "you need to have all types in when you start to use them", which is partially solved by including types/ first, but doesn't really help with types that depend on other types. perhaps separate abstract_types/ type_parts/ and model_types/ ?

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No longer a huge issue due to changing CobraModel to StandardModel in #53.

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so will we keep the automatic file loading mechanism?

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Yes, I think so, maybe being creative isn't such a bad thing :)

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