Awesome project, really exciting and innovative work! In the current master version the project cannot correctly parse new input files and will also fail on the default new york dataset due to indexing issues.
Went ahead and wrote (what I'm pretty sure are) the needed fixes in a fork, happy to raise a pull request if needed. Diffs from current master are here: https://github.com/j4freeman/DeepGravity/pull/1/files