fix: compatibility with cobrapy

[BenjaSanchez]

Description of the issue:

We should include compatibility for cobrapy, so ideally the model can be fully used by python users. In the following what needs to be done:

• To be able to use the full model:
  • Solve issue fix: metabolite id compliance with cobrapy #101
  • Make sure no field is lost when the model is opened with cobrapy:
    • Metabolites:
      • id
      • name
      • formula
      • charge
      • annotation
        • chebi
        • kegg.compound
    • Reactions:
      • id
      • name
      • metabolites (with stoich coeffs)
      • lower_bound
      • upper_bound
      • gene_reaction_rule
      • subsystem
      • annotation
        • ec-code
        • kegg.reaction
        • pmid
      • confidence_score
    • Genes:
      • id
      • name
    • Compartments
• To be able to also contribute: Make sure the model can go through a full IO cycle without losing any of the fields, and keeping the same order (at least in the .yml and .txt)

I have crossed out all the fields I could find in the model loaded with cobrapy, but maybe I missed something @Midnighter @phantomas1234? The final of the to-do's is probably the most challenging one, so if it's too hard we can create a separate issue once we address the other points. Suggestions/things I might have forgotten are welcome @edkerk @ChristianLieven @demilappa @simas232 @hongzhonglu

I hereby confirm that I have:

• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue

[Midnighter]

As referenced in #101, a lot of the open problems in your list will be addressed by opencobra/cobrapy#685. Being able to round-trip SBML files without loss of information is certainly one of my major goals with the refactor of the SBML parser.

[BenjaSanchez]

After the merge of opencobra/cobrapy#685 and most recently #216, now every single field is readable in cobrapy. I have moved the contribution part of this issue to #218, as it requires several changes to the writing logics of both cobrapy and cobratoolbox. This issue will be closed on the next release.