GECKO 3.2.0

[edkerk]

Main improvements in this PR:

• Fixes:
  • ⚠️ specify RAVEN 2.9.1 as dependency, and provide more detailed instructions on how to upgrade
  • loadDatabases clarifies what to do if download from UniProt fails
  • calculateFfactor sometimes failed to properly read paxDB.tsv files
  • runDLKcat should parse params.path as absolute paths to docker (solves #378
  • applyKcatConstraints can handle when all kcat are zero
  • getStandardKcat should also assign standard kcat values for reactions that do have a non-empty grRules field, but are not in model.ec due to the genes not matching any of the enzymes in the uniprot.tsv file
  • calculateFfactor can take protData input
  • enzymeUsage correct mention of output units #376
  • updateProtPool is made obsolete #375
• Features:
  • ⚠️ keep protein usage reaction draw from protein pool when proteomics is integrated #375
  • new removeStandardKcat function removes all traces of getStandardKcat having modified a model
• Chores:
  • update dependencies in GitHub Actions

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

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