fix: minor patches

[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 runDLKcat() cannot find path to data #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.
• Features:
  • 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.
• This PR has main as target branch, and will be resolved with a merge commit.

[github-actions]

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

 
[�Warning: Cannot find RAVEN Toolbox in the MATLAB path, or the version is too old for this GECKO version (RAVEN 2.9.1 is required). Make sure you have installed RAVEN following the
instructions available here, including running 'checkInstallation()'.]� 
[�> In GECKOInstaller.checkRAVENversion (line 80)
In GECKOInstaller.install (line 13)]� 
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.