Quick Start

1. Create the environment

   conda create -f ua_oncophenotype_env.yml
   conda activate ua_oncophenotype_env
   # the environment contains all of the dependencies, but we'll install the package in 
   # editable mode
   pip install -e ua_oncophenotype
   # install the test requirements
   pip install -r test_requirements.txt

2. Run the unit tests

   ./run_checks.py -t

3. Run the sample scripts
   1. Copy the sample config and edit to point to your AOAI instance

      cd ua_oncophenotype/tests/sample_configs/config/openai_config
      cp sample_openai_config.yaml local_openai_config.yaml

   2. Edit the local_openai_config.yaml to point to your AOAI resource and add the appropriate key Note: Alternatively copy and modify sample_openai_identity_auth_config.yaml
   3. Run the sample script

      # go to ua_oncophenotype/tests
      cd ../../..
      ./run_test_experiment.sh

Usage and License Notices

The software described in this repository is provided for research use only. The software is not intended for use in clinical decision-making or for any other clinical use, and the performance of model for clinical use has not been established. You bear sole responsibility for any use of this software, including incorporation into any product intended for clinical use.