Implement knockouts in an efficient way about cobrexa.jl HOT 7 CLOSED

I've implemented two variants for this, one working on the model itself, and one as a callback only acting on the optimization model. So far I think both might have their merits, depending on their use context.

This version here acts on the model and will delete reactions in-place:
function knockout!(model::StandardModel, gene_id::String)
function knockout!(model::StandardModel, gene_ids::Array{String})

The other one uses the callback scheme and just sets the upper and lower bound of the corresponding reactions to 0.
function knockout_callback(gene_id::String)
function knockout_callback(gene_ids::Array{String,1})

You can check them both out in d58ef65

from cobrexa.jl.

I'm in no way clingy to the name knockout_callback by the way. It could also just be knockout for example, but I get too easily confused when working with similar-sounding functions, so for development I named them like this

from cobrexa.jl.

I'm in no way clingy to the name knockout_callback by the way. It could also just be knockout for example, but I get too easily confused when working with similar-sounding functions, so for development I named them like this

No problem, but in the merge iteration they should be called knockout! since dispatch will take care of the thinking for you :)

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But it's not an inplace operation. It returns a function, just like the other callbacks. In all of these cases (change_sense, change_objective, ..), we also (correctly) did not use the !, so I think this would lead to confusion at best.

from cobrexa.jl.

But it's not an inplace operation. It returns a function, just like the other callbacks. In all of these cases (change_sense, change_objective, ..), we also (correctly) did not use the !, so I think this would lead to confusion at best.

yeah without the ! is better :)

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@marvinvanaalst I guess this is now done by merging the knockouts?

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@marvinvanaalst I guess this is now done by merging the knockouts?

yes, I think so. Closing!

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