feat: function for reproducible and convenient model curation

[edkerk]

Description of the issue:

The code/ folder has various different scripts for previous model curations that are not that intuitive to reuse. Instead, it would be beneficial to have a function that can perform various model curations, plus a standardized text file format where the necessary data is kept.

Introduced in #300, code/curateMetsRxnsGenes() can do exactly that. Standardized TSV files, exemplified for a few reactions in sulfur metabolism, can be prepared for either (a) addition of new reactions, metabolites and/or genes; or (b) editing the annotation of existing reactions, metabolites and/or genes.

For future usage, one can simply take the TSV files as templates and modify for the particular curations that should be done, run curateMetsRxnsGenes() and get the updated model.

While the function does numerous checks for finding duplicate reactions etc., and the function can be used in various ways, it is not intended as covering all types of curations. However, it is at least a standardized way that should hopefully simplify future addition and editing of reactions, metabolites and genes. The function will likely move into the RAVEN toolbox, but is for now kept on the yeast-GEM repo.

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the main branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue