Current behavior:

As long desired, RAVEN now no longer adds prefixes to metabolite, reaction, gene and compartment identifiers. It is now suitable to do some refactoring at Human-GEM of the model files and input/output functions, including some other cleanup.

Suggested changes:

• Use RAVEN functions readYAMLmodel, writeYAMLmodel and exportForGit, instead of the Human-GEM specific importYaml, exportYaml and exportHumanGEM, to reduce the number of functions to be maintained.
• Update README.md to reflect changes in model I/O functions, and more clearly explain the software requirements and the ability to contribute to development without RAVEN.
• Update Human-GEM-guide to reflect changes in model I/O functions.
• Do a full round of I/O with RAVEN 2.10.0 in develop.
• Do a full round of I/O with RAVEN 2.10.0 in main.
• Change Human-GEM.txt from showing metabolite identifiers to showing metabolite names + compartments. See example from yeast-GEM, where this change was introduced in 2022:
  

Boxes above are ticked once the changes are implemented here.

To do when preparing next release

• In main, first pass the current model version through a round of I/O with the updated functions, before merging the latest develop. This separates the changes due to different I/O routines, from all other model updates, simplifying the latter diff.
• Update Human-GEM-guide to reflect changes in model I/O functions, after making the release.