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1I think energynumbers answer is correct in terms of what is "correct" in academic literature. However, if the immediate issue is "I need to let a reader of the thesis/dissertation that I'm working on right now see the software", then (low-tech as it seems) you could consider including the source code in an appendix. How practical this is may depend on its length... Or ask your supervisor whether they're happy for you to provide a github link and what the format should be. Also, welcome to Stackexchange :-)– FlytoCommented Nov 11, 2013 at 15:54
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1@SimonWaldman: 7K lines of code spread over multiple modules is definitively not something I can include in an appendix. My colleague did include his MATLAB code in his thesis but I found it to be a terrible way to share code as you cannot reuse it easily (copying it in matlab would ignore the tabbing, etc.).– charlespwdCommented Nov 11, 2013 at 16:25
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@charlespwd ha, fair enough. And I agree that it's a terrible way to share code. But if this is for an examinable thesis rather than a published paper, I think the correct answer is "whatever your supervisor is happy with" ;-)– FlytoCommented Nov 11, 2013 at 17:01
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1See also this discussion: lists.software-carpentry.org/pipermail/…– Piotr MigdalCommented Nov 11, 2013 at 22:13
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3Take a look at this: [github.com/blog/1840-improving-github-for-science]. This might answer at least a part of your question.– Dohn JoeCommented May 15, 2014 at 18:18
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