I started using GitHub Issues to track progess on my FYP development. Today I found that you can close issues via commit messages.

If you uses any of the following synonyms in your commits, GitHub will reference to the commits from the issues and mark the issues closed.

 fixes #xxx
 fixed #xxx
 fix #xxx
 closes #xxx
 close #xxx
 closed #xxx

Additionally, you can create nice tasks lists in issues, pulls and comments like this, using [ ] or [x] (incomplete or complete, respectively) markdowns. For example:

 - [x] list syntax required
 - [x] this is a complete item
 - [ ] this is an incomplete item