feat: allow non-default GAM parameters

[edkerk]

trafficstars

Addresses #133:

• getModelParameters contains the optional parameters.maxGAM, which can be used to specify the scanned GAM range (GAM = 20:5:100) in fitGAM. If not specified, a maximum GAM of 100 is used by default, as was already the case.
• the GAM parameter used in fitGAM and scaleBioMass is only the non-polymerization part of the growth associated energy cost (GAEC), not the stoichiometric coefficient of e.g. ATP in the biomass reaction, this is clarified in getModelParameters.
• splitGAEC can extract from a model the GAMpol (= polymerization part of GAEC); GAMnonPol (= 'GAM' as used in fitGAM, scaleBioMass and getModelParameters) and GAEC (= GAMpol + GAMnonPol). This function is used to fix #106 below, but can also be used to extract parameters.maxGAM for entry in getModelParameters.
• title and legend of the figure generated by fitGAM takes the carbon source from chemostatData.tsv.

Addresses #106:

• when generate_protModels scales the biomass if the protein content has changed, it will now only recalculate the polymerization part of the GAEC (GAMpol), as it takes the GAMnonPol from the unmodified batch model. Previously the total GAEC was fitted to chemostatData.tsv, where changes in polymerization costs would be cancelled out by fitting GAMnonPol.

PR #130 should first be merged with devel, which will result in a minor conflict in this PR that I'll fix.

[codecov-io]

Codecov Report

Merging #135 (f410c91) into devel (6fbc627) will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##            devel     #135   +/-   ##
=======================================
  Coverage   97.00%   97.00%           
=======================================
  Files           3        3           
  Lines         200      200           
  Branches       22       22           
=======================================
  Hits          194      194           
  Misses          4        4           
  Partials        2        2           

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 6fbc627...f410c91. Read the comment docs.

[edkerk]

The changes intended here have been superseded by various developments as part of GECKO3