[PyHealth2.0 Bounty] OMOP Readmission Prediction

[EricSchrock]

Overview

This PR updates the readmission_prediction_omop_fn for PyHealth 2.0. It is a follow on to #751.

In addition to supporting PyHealth 2.0, the new ReadmissionPredictionOMOP task has the following improvements. First, it takes a datetime.timedelta instead of an int for the readmission window, making the input parameter clearer and more flexible. Second, it can optionally exclude visits where the patient was under 18 years old (a previously unimplemented #todo).

Besides the items listed above, ReadmissionPredictionOMOP should be logically equivalent to readmission_prediction_omop_fn.

Other Changes

I ported the best practices from #777 to examples/readmission_mimic3_rnn.py (main guard and resource cleanup). To avoid creating a merge conflict with #773, I also moved this updated example file to examples/readmission/.

Additionally, I updated tests/core/test_omop.py to fail if it cannot find test-resources/omop instead of skipping.

Testing

• Added tests/core/test_omop_readmission_prediction.py
• Added a few canned entries to test-resources/omop to facilitate unit testing
• Added and ran examples/readmission/readmission_omop_rnn.py
• Ran the updated examples/readmission/readmission_mimic3_rnn.py

[jhnwu3]

Lgtm! Thanks! Actually, OMOP is often a pretty big request for us!