chore: update model I/O functions and documentation

[edkerk]

Main improvements in this PR:

• Refactor:

  • Use RAVEN functions readYAMLmodel, writeYAMLmodel and exportForGit, instead of the Human-GEM specific importYaml, exportYaml and exportHumanGEM.
  • Modify increaseHumanGEMVersion, and include a check that Human-GEM.yml and model/tsv files match.
  • Prepare for Human-GEM.txt to show metNames[comps] instead of metIDs.
  • Full round of I/O with Human-GEM.yml using RAVEN 2.10.0. Changes in txt (major, see above), xml and mat (both minor) will appear with next release.
  • Remove duplicate getGenesFromGrRules function, already present in RAVEN.

• Documentation:

  • Update README.md to reflect changes in model I/O functions, more clearly explain the software requirements and the ability to contribute to development without RAVEN.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
 - Found 1514 dead-end metabolites.
 - Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1977 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
 - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
 - Found 447 reactions that were some type of duplicate:
   - 0 were completely identical to at least one other reaction.
   - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
   - 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

Note: In the case of multiple test runs, this post will be edited.