GECKO 3.2.2

[edkerk]

• Features:
  • If sensitivityTuning modifies a kcat value, it will now be indicated in model.ec.source as 'sensitivityTuning', and the previous kcat value and source will be kept in the model.ec.notes field as preTuneKcat=*value* | source:*original source*. If the kcat value had been subjected to senstivityTuning before, then the notes field will remain unchanged, so repeated runs of sensitivityTuning will not overwrite the notes.
  • runDLKcat support alternative paths and names of the DLKcat.tsv file (solves #392) .
• Fix:
  • By default, the obj.params.uniprot.reviewed parameter in the adapterTemplate is set to false, to increase the number of matching proteins.
  • The model.ec.source entry after running setKcatForReactions has been corrected to 'setKcatForReactions'.
• Documentation:
  • Update references and add MATLAB badge in README.md.
  • Clarifies the meaning of obj.params.enzyme_comp in model adapter (solves #386).

Instructions on merging this PR:

• [ ] This PR has develop as target branch, and will be resolved with a squash-merge.
• [x] 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 version 3.2.1 installed
Running geckoCoreFunctionTests
Done geckoCoreFunctionTests
__________

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