yeast 8.5.0

[edkerk]

Main improvements in this PR:

• Fixes:
  • combine glycolysis + gluconeogenesis as single KEGG pathway (PR fix: combine glycolysis + gluconeogenesis #251)
  • rxn: corrects grRule of r_4590 (closes fix: wrong annotation for gene YGR191W for rxn r_4590 #252)
  • met: corrects name of s_1218 (closes fix: Wrong annotation for s_1218 #254)
  • saveYeastModel handles Unicode characters (PR fix-rxn/met: solves #252 and #254 #255)
  • indentation of yeastGEM.yml (contributes to feat: add yaml validation #236)
• Features:
  • memote as GitHub Action for pull requests (PR Feat/memote #162)
  • old subSystems changed to reaction annotation (in rxnMiriams or rxnKEGGpathways) (PR Chore: update COBRA+RAVEN toolboxes #253)
• Chore:
  • update dependencies in *requirements.txt (PR chore: update *requirements.txt #256)
  • minor changes in model file formatting due to updates in COBRA+RAVEN toolboxes (PR Chore: update COBRA+RAVEN toolboxes #253)
• Refactor:
  • follow standard-GEM specifications (PR refactor: standard-GEM #257)
  • rename master and devel branches to main and develop (PR chore: change branch names #261)

Also rename your local branches to main and develop:

git branch -m master main
git branch -m devel develop
git fetch origin
git branch -u origin/main main
git branch -u origin/develop develop
git remote set-head origin -a

PR #261 should first be merged

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected main as a target branch (top left drop-down menu)
• If needed, asked first in the Gitter chat room about this PR

[mihai-sysbio]

It should be possible to just change the target branch in this PR without opening a new one?

[mihai-sysbio]

Also, is the intention to resolve #11 as part of this release, or would it be better to postpone it?

[edkerk]

I didn't close it manually, but I did just change the name of devel to develop, in accordance with #258. It might be that GitHub is at the moment still processing the name change, and will reopen it soon again to the newly named branch.

Re #11, this would take longer to resolve, so probably good to postpone to distribute as 2.5.1?

[mihai-sysbio]

Oh, interesting side-effect of branch renaming.
Sure, it's okay reserve #11 for a subsequent release.

[edkerk]

Here is mentioned:

After the rename is complete, GitHub provides instructions on the repository's home page directing contributors to update their local Git environments.

Considering this is not showing on the home page yet, I assume they haven't finished the procedure yet. If this is not resolved by tomorrow I'll manually fix this PR.

This seems to be referring to changing name of the default branch, not other branches. Because the "from" branch is renamed, the source is missing and seems like I'll have to remake the PR. Now done as #262.