bug identified in development branch

[feiranl]

import and export cycle gives an error:

model = importYaml('Human-GEM.yml');
>> exportYaml(model, 'Human-GEM.yml');
Index exceeds the number of array elements. Index must not exceed 13087.

Error in exportYaml>writeField (line 190)
            list = field{pos};  %subSystems already comes in a cell array

Error in exportYaml (line 86)
    writeField(model, fid, 'subSystems',           'txt', i, '  - subsystem')

This is due to the subsystems length is different with other rxn related field.

[mihai-sysbio]

Oh that's surprising to see. There is a GH workflow that runs the yaml conversion check. It looks like when the test fails the workflow still passes - have a look at the step Run conversion script for this workflow ron on the merged PR. Looking back through the results, the problem might have been introduced in #606.

[mihai-sysbio]

My suggestion is that the fix should also include a change in the test such that when it fails the action also fails. After this, the fix of the yaml file should be committed, and we should see the workflow pass.

[feiranl]

it errors in the check, but didnot fail in the action:

{�Index exceeds the number of array elements (13087).

Error in exportYaml>writeField (line 190)
list = field{pos}; %subSystems already comes in a cell array

Error in exportYaml (line 86)
writeField(model, fid, 'subSystems', 'txt', i, ' - subsystem')

Error in testYamlConversion (line 25)
exportYaml(model,'testYamlConversion.yml');

Error in run (line 91)
evalin('caller', strcat(script, ';'));
}�

@haowang-bioinfo maybe you can fix this?

[haowang-bioinfo]

Oh that's surprising to see. There is a GH workflow that runs the yaml conversion check. It looks like when the test fails the workflow still passes - have a look at the step Run conversion script for this workflow ron on the merged PR.

yes indeed, I observed similar cases before, i.e. testYamlConversion failed locally but the action still passed on GitHub

@haowang-bioinfo maybe you can fix this?

yes, working on this

[haowang-bioinfo]

Looking back through the results, the problem might have been introduced in #606.

the error appears to be introduced in #619, instead of #606. Because testYamlConversion would pass by using importYaml before 619

this error is neither from #606 nor #619, really not sure where was it introduced. A plausible reason might be various external dependencies that have been changing all the time

[haowang-bioinfo]

@feiranl the error encountered during yaml import and export cycle is likely fixed by commit 182010d in #629

[mihai-sysbio]

Based on the merged pull requests I will close this issue, please re-open if needed.