Human-GEM/model/ Human-GEM/code/io/

[helenaherand]

Are the files in Human-GEM/model/ generated from the xml version of the Human1 model? How can I generate the files myself? I looked in the Human-GEM/code/io/ folder but could not found the answer to the question.

[mihai-sysbio]

That is a very good question @helenaherand, and I hope you don't mind me converting it to a discussion.

To put it shortly, the xml format gets created from yml.

The develop branch uses only the yml format, and all other file formats are only created when using the main branch. The code used to do this is here:

Human-GEM/code/io/increaseHumanGEMVersion.m

Lines 53 to 61 in ff109f2

	%Load model:
	ymlFile=fullfile(modelPath,'model','Human-GEM.yml');
	ihuman = importYaml(ymlFile);
	%Include tag and save model:
	ihuman.version = newVersion;
	%Export model to multiple formats
	exportHumanGEM(ihuman,'Human-GEM',modelPath,{'mat', 'txt', 'xml', 'yml', 'xlsx'});

There are, of course, dedicated functions in exportHumanGem.m, some of which rely on the underlying functions in the RAVEN toolbox.

For more background on how branches are used, see this discussion and also the Contributing guidelines.

Is there something you were wondering about regarding the content of the different file formats?