fix/feat: various, including ecFVA, enzymeUsage, constrainEnzConcs, constrainFluxData

[edkerk]

Main improvements in this PR:

• Fixes:
  • getStandardKcat.m removed enzymes when it was run on a model already containing standard kcat values
  • ecFVA will swap min and max values the reaction directionality was swapped when mapping from ec- to conventional model
  • plotEcFVA will use its own cdfplot function, to avoid dependency on MATLAB Statistics and Machine Learning Toolbox. Blocked reactions are excluded from the graph. ⚠️ The plot in full_ecModel shows minor differences, also due to code changes introduced by GECKO 3.2.0
• Features:
  • ´calculateFfactorcan handleprotData` with multiple conditions (in which case, averages over all conditions are taken)
  • setKcatForReactions allows multiple kcat values as input, allowing to set kcat of multiple reactions at the same time
  • reportEnzymeUsage will report both the summed usage of isoenzymes, as well as the individual usage of the separate reactions. topUsage and highCapUsage outputs columns are harmonized
  • constrainFluxData if a provided constraint is either -1000 or 1000, lower and upper bound will be constraint to either uptake or excretion only, irrespective of what option is given as the looseStrictFlux parameter
  • constrainEnzConcs can also remove enzyme concentration constraints
• Refactor:
  • fuzzyKcatMatching to avoid warnings "Colon operands must be real scalars" in recent MATLAB versions
• Documentation:
  • various function documentations, warnings and error messages have been improved

Instructions on merging this PR:

• [x] This PR has develop as target branch, and will be resolved with a squash-merge.
• [ ] This PR has main as target branch, and will be resolved with a merge commit.

[github-actions[bot]]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
GECKO installed, unknown version (cannot find version.txt).
Running geckoCoreFunctionTests
Done geckoCoreFunctionTests
__________

Note: In the case of multiple test runs, this post will be edited.