fix: constructEquations

[haowang-bioinfo]

Main improvements in this PR:

• fix: get the reversibility information by querying both lb and ub fields, instead of the obsolete rev field that could be inaccurate or unavailable
• doc: refine function description with Input and Output sub-headings
• feat: additional option is added for allowing the generation of equations with met formulas

NOTE: None of these changes affect backward-compatibility of any of the modified functions. All reactions in a model should be organized in their forward direction, typically by setting ub = 1000 and lb = -1000 (or 0), so that their equations can be correctly constructed by the constructEquations function.

I hereby confirm that I have:

• Tested my code on my own machine
• Followed the development guidelines.
• Selected devel as a target branch

[edkerk]

It makes a lot of sense to stop using the rev field, but it needs to be mentioned explicitely in the documentation that the lb fields is queried for determining reversibility. There can be cases where ub = 0 and lb = -1000, is this strictly reversible? True, the reaction should then have been defined in the other direction, but it can be good to mention this.

Something like:

All reactions are defined in their forward direction, while the lb field is queried to determine whether reactions can also support a flux in reverse direction.

[edkerk]

Also, in the process of abandoning the use of the rev field, the functionality of convertToIrrev should be changed, as this currently uses the rev field to identify what reactions are reversible.

[BenjaSanchez]

@edkerk based on a previous discussion in #184 (comment), will the rev vector still be able to be read by convertToIrrev with some readRevVector=TRUE flag? As GECKO uses convertToIrrev as one of the first steps, would be nice to know so I can handle the change later.

[haowang-bioinfo]

How about having an option of constructing reactions using metFormulas, this appears to be quite useful when balancing reaction.

[edkerk]

How about having an option of constructing reactions using metFormulas, this appears to be quite useful when balancing reaction.

Sure! I'm not sure when this is useful, but if you find a use for it that's great. You've implemented it correctly, not breaking previous functionality, so I have no problem with this part.