chore: consistent names and terminology

[edkerk]

With the intense development work over the last months, there is not always consistency on what kind of terminology is used. It is helpful to be consistent, and it is good to enforce this from the first GECKO3 release onwards.

Note that the example function names indicated below are after changing them to their new name.

Term	Meaning / use	Example
ecModel	abbreviation of enzyme-constrained model
empty ecModel	ecModel after makeEcModel, without kcat values
modelAdapter	a model-specific version of ModelAdapter.m	ecYeastGEMAdapter.m
kcatList	structure that contains kcat information, can have multiple entries per reaction / enzyme / source	output of fuzzyMatching, loadDLKcatOutput()
load...()	function that reads a datafile into MATLAB	loadEcModel()
save...()	function that writes a datafile from MATLAB	saveEcModel()
gather...()	function that downloads data or places API calls to an online resource. The output of this might be a data file, data structure in MATLAB, or directly in an ecModel	gatherMetSMILES()
fill...()	function that downloads data or places API calls to an online resource	fillKcat()
apply...()	function that modifies an ecModel with information that it already contains. For instance: applyKcatConstraints takes the information from ecModel.ec.mw and ecModel.ec.kcat to modify ecModel.S.

Not all function names will be covered by this scheme. For instance fuzzyKcatMatching does not fit any of the categories. Or should we have dofuzzyKcatMatching? Or specify get...() to indicate a function that applies some analysis on the model and gives an output that is outside the model (in this case a kcatList)? Edit: Or should we just accept that for instance fuzzyKcatMatching is not covered by the scheme and keep it unchanged?

This list is not complete yet, feel free to add suggestions below.

[ae-tafur]

I thing get...() fits better . Then, following your example.

Term	Meaning / use	Example
get...()	gives an output that is outside the model	fuzzyKcatMatching()
update...()	function that update a value calculate previously inside the model	updatePoolSize()