GECKO 3.1.2

[edkerk]

Main improvements in this PR:

• Fixes:
  • makeEcModel prevent duplicated protein pseudometabolites
  • applyKcatConstraints occassionally fills S-matrix with NaN in light ecModels (solves #344)
  • calculateFfactor handle data from PAXdb if the taxonomic ID is not 4 digits long (solves #345)
  • runDLKcat correctly handles param.path if the folder name has spaces (solves #351)
  • loadDatabases throws error if duplicate protein IDs are found
  • getSubsetEcModel requires both bigEcModel and smallGEM to have derived from the same starting GEM, and will therefore check whether all reactions from smallGEM are also present in bigEcModel. (solves #353)
• Documentation:
  • Installation instructions are moved to the Wiki
  • Mention correct human-GEM version in HumanGEMAdapter.m
  • Replace Gitter with GitHub Discussions for asking support
• Refactor:
  • Have ecFSEOF follow the original implementation of FSEOF (PR #356)
• Features:
  • Navigate into new project folder after running startGECKOproject

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 3.1.1 installed
Running geckoCoreFunctionTests
Done geckoCoreFunctionTests
__________

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

[edkerk]

I'll also resolve #348 and push to develop before merging this.