require python 3.8 or higher

pip install -r requirements.txt

update data.yml

update spec.py

update clinical_feature.py with functions you’ll need for the spec

use query_records_closest_before to get records closest before date;

use query_records_closest_after to get records closest after date;

use query_records_closest to get records closest to date;

query_records_interval can take a start/end time

look at extant function for examples you can reuse

if you want to run individually:

fish: env PYTHONPATH=tx-utils/src python cli.py spec.py data.yaml 3
bash: PYTHONPATH=tx-utils/src python cli.py spec.py data.yaml 3

fish: env PYTHONPATH="tx-utils/src:." pytest
bash: PYTHONPATH="tx-utils/src:." pytest