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 2.10.3. 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.

[edkerk]

@feiranl Can you review this PR? If you approve, then a lot of conflicts in other PRs can be resolved.

[feiranl]

@edkerk, I noticed this PR includes significant changes to the YAML file. I'm concerned that merging it into the develop branch might cause conflicts and complications with other open PRs. If that is not the case, I can review this PR later today.

[edkerk]

Almost all YML changes are the removal of empty lines:

      - rxnNotes: ""
      - eccodes: ""
      - references: ""

This should pose very limited if any complications with any open PRs.

[feiranl]

Ok, will review this later today.

[feiranl]

Ed, Could you help check this? I am trying to run an import and output cycle, but failed with several error. I am using the RAVEN main branch.

[feiranl]

@edkerk Could you check this PR, so that we can merge this. There are around 20 PRs waiting to be approved and 20 PRs needs to be done...

[feiranl]

@edkerk Thank you so much for all the hard work yesterday! Please let me know when this PR is ready for review. I can then do a quick check.😊

[edkerk]

Ready for review!

[feiranl]

@edkerk I am not able to run the full import/ export cycle, could you fix this?

[github-actions]

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

     cellLine     TP     TN     FP    FN     accuracy    sensitivity    specificity       F1         MCC   
    __________    __    ____    __    ___    ________    ___________    ___________    ________    ________

    {'DLD1'  }    37    2165    62    277    0.86659       0.11783        0.97216       0.17918     0.15306
    {'GBM'   }    34    2147    65    294    0.85866       0.10366        0.97061       0.15925     0.12869
    {'HCT116'}    46    2189    57    305    0.86061       0.13105        0.97462       0.20264     0.18513
    {'HELA'  }    31    2246    72    249    0.87644       0.11071        0.96894       0.16188     0.12659
    {'RPE1'  }    15    2186    84    255    0.86654      0.055556          0.963      0.081301    0.029544
    {'all'   }     7    2386    96    109    0.92109      0.060345        0.96132      0.063927    0.022933

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