Is it advisable to put entire source of my thesis up on GitHub?

The answer is in two parts:

• Yes, it's a very good idea to use an online repository with a versioning system to write your Masters thesis. It offers a nice automatic backup, you can easily sync from different locations (office, home), and (this is mostly true for papers rather than a thesis) you can easily collaborate with people outside of your university (i.e. who wouldn't have an account on your university server.

• No, it's not a good idea at to make it public. Plagiarism is real, online versioning systems do not offer any real protection, and you don't want to make it too easy to copy, especially when you're not finished yet. I'm all for the open-access of finished documents, that you can put on arXiv, but in this case, there is a real timestamp, and your work can be indexed (for instance, in Computer Science, arXiv is indexed on DBLP).

For these reasons, I've been personally using for my papers BitBucket, that offers academics a free unlimited plan (unlimited public/private repositories, unlimited collaborators). In this way, I create a private repository for each of my papers, give access rights to my co-author(s). It seems that GitHub also provides a way to have private repositories for academics: https://github.com/edu, so you can keep using it for sharing your open-source code (for instance) and use it with a private repository for your thesis.

I'm told for your field that the answer might be yes, because you're slightly less threatened in terms of being scooped than most, with physics (apparently) going largely by who submits first.

I would be extremely cautious publishing the source of my thesis in its entirety on a public repository. I'm all for repeatable science and open access, but the public should only have access to your code when this condition is met:

You have no further use of the exclusive access to your code. All the questions you've programmed have been answered, the papers and presentations that emerge from them are in press, and at this point, it is a question of reproducible research.

Once that's true, sure. Until that point? You're running the profound risk of your research being stolen.

Talk to your adviser about this. Do not make anything that is unpublished publicly available without their knowledge. Any other people who might be co-authors on your papers might also have a say.

Having said that, a private github repository is a great idea (I used one myself for my PhD dissertation & papers).