Incorporating network distance in SHEPHERD

Steps for computing and adding network distance (namely, shortest path length) for each patient:
1) If you are using your own KG, run shortest_paths.py. Alternatively, the outputs of this script are available in the data downloaded from Harvard Dataverse.
2) Run add_spl_to_patients.py
- If you want to run an already-trained SHEPHERD model on your own patient dataset, use the flag --only_test_data. Before running this script, make sure to check that MY_TEST_DATA in project_config.py is set to your own patient dataset. After running the script, make sure that MY_SPL_DATA and MY_SPL_INDEX_DATA in project_config.py is set to the output files from this script.