feat: uptake/secretion rates in flexibilize_proteins

[BenjaSanchez]

closes https://github.com/DD-DeCaF/scrum/issues/1162

uptake/secretion rates are now assigned when flexibilizing proteomics to ensure feasible simulations.

[codecov-io]

Codecov Report

Merging #151 into devel will increase coverage by 0.69%. The diff coverage is 100%.

@@            Coverage Diff             @@
##            devel     #151      +/-   ##
==========================================
+ Coverage   74.83%   75.52%   +0.69%     
==========================================
  Files          20       20              
  Lines         898      907       +9     
==========================================
+ Hits          672      685      +13     
+ Misses        226      222       -4

Impacted Files	Coverage Δ
src/simulations/modeling/adapter.py	66.82% <ø> (+1.92%)	:arrow_up:
src/simulations/modeling/driven.py	87.6% <100%> (+0.99%)	:arrow_up:

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[BenjaSanchez]

Update: Tested this in the frontend as well and works nicely: For this proteomics dataset + growth rate of 0.1 1/h, the flexibilization adapts accordingly:

• No glucose uptake limitations: 22 proteins removed due to flexibilization, using 7.1 mmol/gDWh of glucose.
• Glucose uptake restricted to 5 mmol/gDWh: 26 proteins removed due to flexibilization