Feat/growth check

[BenjaSanchez]

Main improvements in this PR:

After discussion in #242, saveYeastModel now checks if the model can grow under aerobic/anaerobic conditions, and returns warnings if not (based on a low threshold) or if the simulation turns unfeasible. If the allowNoGrowth flag is set to false, then instead it will error; this latter option is now used by increaseVersion when making new releases.

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected devel as a target branch (top left drop-down menu)

[feiranl]

Great! Work perfectly!

[feiranl]

@BenjaSanchez @edkerk However, I noticed that our saving function is very heavy, which takes over 4mins. I am not sure which function took so long, is that possible to improve this?

[edkerk]

@Feiran You can run profile on; saveYeastModel(model); profile viewer to see how which parts of a function (and it's subfunctions) take the longest.

[BenjaSanchez]

@edkerk thanks for the suggestion, @feiranl see below that from the ~5 mins it takes in my computer, more than 4 mins are taken by writeSBML, which is the COBRA function for saving the .xml file. On our side saveYeastModel itself only takes 11 seconds, and RAVEN's exportForGit takes 30 seconds (most of it by writeYaml for saving the .yml file).