doc: PR and Issues templates + contributing guidelines

[edkerk]

Main improvements in this PR:

• doc: update PR and Issues templates with new branch names and reduce number of requested input to the most meaningful
• doc: update CONTRIBUTING.md to reflect recent changes

I hereby confirm that I have:

• [ ] Tested my code with all requirements for running GECKO
• [X] Selected devel as a target branch (top left drop-down menu)

[github-actions[bot]]

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

 
Running geckoCoreFunctionTests
================================================================================
Verification failed in geckoCoreFunctionTests/testsaveECModel_tc0009.
    ---------------------
    Framework Diagnostic:
    ---------------------
    verifyEqual failed.
    --> Path to failure: .rev
        --> The numeric values are not equal using "isequaln".
        --> Failure table:
                Index    Actual    Expected    Error    RelativeError
                _____    ______    ________    _____    _____________
            
                 12        1          0          1           Inf     
                 13        1          0          1           Inf     
                 14        1          0          1           Inf     
                 15        1          0          1           Inf     
                 16        1          0          1           Inf     
                 17        1          0          1           Inf     
        
        Actual double:
            17x1 double
        Expected double:
            17x1 double
    
    Actual Value:
      struct with fields:
    
               name: 'testModel'
                 id: 'testModel'
         annotation: [1x1 struct]
               date: '2023-03-07'
        description: ''
            version: ''
               rxns: {17x1 cell}
                  S: [10x17 double]
                rev: [17x1 double]
           metNames: {10x1 cell}
              comps: {2x1 cell}
          compNames: {2x1 cell}
           metComps: [10x1 double]
               mets: {10x1 cell}
            grRules: {17x1 cell}
         rxnGeneMat: [17x5 double]
              genes: {5x1 cell}
                 ub: [17x1 double]
                 lb: [17x1 double]
                  c: [17x1 double]
           rxnNames: {17x1 cell}
                  b: [10x1 double]
            eccodes: {17x1 cell}
           metNotes: {10x1 cell}
                 ec: [1x1 struct]
    Expected Value:
      struct with fields:
    
                 id: 'testModel'
               name: 'testModel'
        description: ''
            version: ''
               date: '2023-03-07'
         annotation: [1x1 struct]
               rxns: {17x1 cell}
           rxnNames: {17x1 cell}
               mets: {10x1 cell}
           metNames: {10x1 cell}
                  S: [10x17 double]
                 lb: [17x1 double]
                 ub: [17x1 double]
                rev: [17x1 double]
                  c: [17x1 double]
                  b: [10x1 double]
              genes: {5x1 cell}
            grRules: {17x1 cell}
         rxnGeneMat: [17x5 double]
            eccodes: {17x1 cell}
           metComps: [10x1 double]
           metNotes: {10x1 cell}
              comps: {2x1 cell}
          compNames: {2x1 cell}
                 ec: [1x1 struct]
    ------------------
    Stack Information:
    ------------------
    In /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/geckoCoreFunctionTests.m (testsaveECModel_tc0009) at 232
================================================================================
Model-specific DLKcat input stored at /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/ecTestGEM/data/DLKcat_input_test.tsv
Limit has been reached. Protein P5 seems to be problematic. Consider changing the kcat 
Done geckoCoreFunctionTests
__________

Failure Summary:

     Name                                           Failed  Incomplete  Reason(s)
    ============================================================================================
     geckoCoreFunctionTests/testsaveECModel_tc0009    X                 Failed by verification.

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

[edkerk]

Very nice additions! Was there the intention to mention the GECKO 2 branch in the development guidelines? I remember suggesting it elsewhere, but now I'm not sure if it's a good idea. Also, on a personal note, the name devel has been bugging me for some time. Everywhere I look on the web develop seems to be the branch name, so maybe we could go with that? That is - if we even want that branch at all. I think Johan made a comment on this topic recently. I see the arguments on both sides. What do you think @edkerk?

• I'd be happy to change to develop.
• No intention to meantion gecko2, any changes to that code are exceptional.
• Using a development branch was not so suitable with the recent high pace of development, but this will quite down now. One thing I did include was a mention that PRs should be "as small" as possible, which addresses some of the issues that Johan mentioned.

[mihai-sysbio]

• I'd be happy to change to develop.

That would be great! For the sake of small PRs, I imagine that could also be a separate PR, although the only renaming to be done that I know of is the Contributing guidelines edited in the current PR.

[edkerk]

Changed to develop, ready for merge.